Laura Albrecht, Katie A. Wilson and Stacey D. Wetmore
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- Φωτινή Κανακάρης-Ρούφος
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1 S1 of S25 Supplementry Mterils: Computtionl Evlution of Nucleotide Insertion Opposite Expnded nd Widened Dy the Trnslesion Synthesis Polymerse Dpo4 Lur Albrecht, Ktie A. Wilson nd Stcey D. Wetmore Figure S1. Overly of representtive MD structures for the Dpo4 ternry complex for the repliction of () modified pyrimidines nd dt (white) or (b) modified purines nd dg (blck), highlighting the interction with Tyr12.
2 S2 of S25 Figure S2.. Overly of representtive MD structures for the Dpo4 ternry complex for the repliction of () modified purines nd dg (blck) or (b) modified pyrimidines nd dt (white), highlighting the interctions with the dntp. Only the intercting portion (side or min chin) of the mino cid residue is shown, with n * indicting tht only the bckbone is shown for tht residue. Figure S3. Snpshots tken from the simultion trjectory to show exmples of bse-pir distortions for the DNA helix contining dya:dttp in the Dpo4 ternry complex.
3 S3 of S25 Figure S4. Snpshots tken from the simultion trjectory to show exmples of bse-pir distortions for the DNA helix contining dyc:dgtp in the Dpo4 ternry complex. Figure S5. Averge nd stndrd devitions of bse-pir prmeters for the DNA, xdna or ydna helix in the Dpo4 ternry complex. See Figure S11 for numbering of the bse pirs.
4 S4 of S25 Figure S6. Averge nd stndrd devitions of bse-step prmeters for the DNA, xdna or ydna helix in the Dpo4 ternry complex. In the bse-step numbering, the first step includes the dn:dntp nd n 1 bse pirs, the second step includes the n 1 nd n 2 bse pirs, nd so on. See Figure S11 for numbering of the bse pirs.
5 S5 of S25 Figure S7. Overly of representtive MD structures for the Dpo4 ternry complex for the repliction of () modified purines nd dg (blck) or (b) modified pyrimidines nd dt (white), highlighting the structure of the dn:dntp nd n 1 bse pirs.
6 S6 of S25 Figure S8. Overly of representtive MD structures for the Dpo4 ternry complex for the repliction of () modified purines nd dg (blck) or (b) modified pyrimidines nd dt (white), highlighting the interctions with the d(x,y)n bckbone.
7 S7 of S25 Figure S9. Overly of representtive MD structures for the Dpo4 ternry complex for the repliction of () modified purines nd dg (blck) or (b) modified pyrimidines nd dt (white), highlighting the structure of the dn:dntp bse pir nd ceiling region.
8 S8 of S25 Figure S10. Overly of representtive MD structures for the Dpo4 ternry complex for the repliction of () modified purines nd dg (blck) or (b) modified pyrimidines nd dt (white), highlighting the overll structure of Dpo4. See Figure 2 for lbeling of the domins.
9 S9 of S25 Figure S11. Numbering of the bses nd bse pirs in the DNA helix used throughout the nlysis.
10 S10 of S25 Tble S1. Averge MM/GBSA binding energy (kcl mol 1 ) between individul residues nd the dntp or dn over 40 ns MD simultions of the Dpo4 ternry complex for the repliction of DNA, xdna or ydse.,b Active Site Bse Pir dntp Thr45 dntp Arg51 dntp Tyr10 dntp Lys159 dntp Mg343 dntp Mg342 dn Ser34 dn Ser40 dg:dctp 11.1 ± ± ± ± ± ± ± ± 1.4 dt:datp 11.2 ± ± ± ± ± ± ± ± 1.9 dxa:dttp 10.5 ± ± ± ± ± ± ± ± 2.6 dya:dttp 11.1 ± ± ± ± ± ± ± ± 2.8 dxg:dctp 10.2 ± ± ± ± ± ± ± ± 1.8 dyg:dctp 10.3 ± ± ± ± ± ± ± ± 1.6 dxt:datp 11.1 ± ± ± ± ± ± ± ± 1.8 dyt:datp 11.0 ± ± ± ± ± ± ± ± 2.6 dxc:dgtp 2.9 ± ± ± ± ± ± ± ± 1.6 dyc:dgtp 3.0 ± ± ± ± ± ± ± ± 1.4 All interctions listed hve contribution of >5 kcl mol 1 in one or more of the simultions. b Interction energy is for the DNA (including dntp) lignd binding to the Dpo4 receptor.
11 Tble S2. Percent occupncy, verge distnce nd verge ngle for hydrogen-bonding interctions tht stbilize the dntp during 40 ns MD simultions of the Dpo4 ternry complex for the repliction of DNA, xdna or ydse. Active Site Bse Pir Prmeter dntp(o3') Tyr12(NH) dntp(oβ) Phe11(NH) dntp(oβγ) Arg51(Nη1H) dntp(oγ) Arg51(Nη2H) dntp(oγ) Lys159(NζH) dntp(oγ) Tyr10(NH) dntp(oγ) Tyr48(OH) dntp(oβ) Thr45(OγH) dg:dctp Å dt:datp Å dxa:dttp Å dya:dttp Å dxg:dctp Å dyg:dctp Å dxc:dgtp Å dyc:dgtp Å dxt:datp Å dyt:datp Å Hydrogen-bonding occupncies re bsed on distnce cutoff of <3.4 Å nd n ngle cutoff of >120. b Not observed for >5 occupncy, with n verge ngle >149 nd distnce of <3.4 Å. S11 of S25
12 Tble S3. Percent occupncy, verge distnce nd verge ngle of the hydrogen-bonding interctions between the primer strnd, nd the plm or thumb domin during 40 ns MD simultions of the Dpo4 ternry complex for the repliction of DNA, xdna or ydse. Active Site Bse Pir Prmeter da349(op1) Lys193(NζH) dt350(op1) Thr190(NH) dt350(op1) Thr190(OγH) dt350(op2) Ile189(NH) dt350(op1) Lys221(NζH) dg352(op1) Lys152(NζH) Ser103(Oγ) dg352(o3'h) dg:dctp Å dt:datp Å dxa:dttp Å dya:dttp Å dxg:dctp Å dyg:dctp Å dxc:dgtp Å dyc:dgtp Å dxt:datp Å dyt:datp Å Hydrogen-bonding occupncies re bsed on distnce cutoff of <3.4 Å nd n ngle cutoff of >120. b Not observed for >5 occupncy, with n verge ngle >149 nd distnce of <3.4 Å. S12 of S25
13 Tble S4. Coordintion of the ctlytic nd binding Mg 2+ ions during 40 ns MD simultions of the Dpo4 ternry complex for the repliction of DNA, xdna or ydse. Active Site Bse Pir Ctlytic Mg 2+ ion Binding Mg 2+ ion Primer(O3 ) Glu106(Oε) b Asp7(Oδ1) dntp(oα2) Asp105(Oδ1) Wt(O) Asp7(Oδ2) Phe8(O) Asp105(Oδ2) dntp(oα2) dntp(oβ2) dntp(oγ1) dg:dctp dt:dttp , dxa:dttp , dya:dttp dxg:dctp dyg:dctp dxt:datp dyt:datp dxc:dgtp dyc:dgtp S13 of S25 Percentge of the simultion tht the distnce between Mg 2+ nd the coordinting tom is <2.5 Å. See Figure 3b for the coordintion of the Mg 2+ ions. b Occupncy of the side chin oxygen toms re listed seprtely if both shre coordintion to Mg 2+. Tble S5. Hydrogen-bonding occupncy nd verge geometry for the n 1 dc:dg bse pir during 40 ns MD simultions of the Dpo4 ternry complex for the repliction of DNA, xdna or ydse. Active Site Bse Pir C1 C1 b dc(n4h) dg(o6) dc(n3) dg(n1h) dc(o2) dg(n2h) Occupncy Averge Geometry c Occupncy Averge Geometry c Occupncy Averge Geometry c dg:dctp 10.7 ± 0.2 Å Å (163.7 ) Å (165.4 ) Å (164.2 ) dt:datp 10.6 ± 0.2 Å Å (163.5 ) Å (165.3 ) Å (163.6 ) dxa:dttp 10.8 ± 0.2 Å Å (162.8 ) Å (165.1 ) Å (162.9 ) dya:dttp 10.7 ± 0.2 Å Å (163.3 ) Å (164.4 ) Å (158.8 ) dxg:dctp 10.8 ± 0.2 Å Å (163.4 ) Å (165.8 ) Å (163.6 ) dyg:dctp 10.8 ± 0.2 Å Å (162.3 ) Å (165.5 ) Å (161.8 ) dxt:datp 10.7 ± 0.2 Å Å (161.9 ) Å (165.2 ) Å (161.9 ) dyt:datp 10.7 ± 0.2 Å Å (161.1 ) Å (163.3 ) Å (159.8 ) dxc:dgtp 10.7 ± 0.2 Å Å (161.3 ) Å (164.4 ) Å (163.8 ) dyc:dgtp 10.7 ± 0.2 Å Å (163.3 ) Å (165.2 ) Å (163.1 ) Hydrogen-bonding occupncies re bsed on distnce cutoff of <3.4 Å nd n ngle cutoff of >120. b Averge nd stndrd devition of the distnce between dc(c1 ) nd dg(c1 ) in the n-1 bse pir. c Averge distnce nd ngle (in prentheses) for ech hydrogen-bonding interction.
14 S14 of S25 Tble S6. Averge MM/GBSA binding energy (kcl mol 1 ) between individul residues nd the DNA over 40 ns MD simultions of the Dpo4 ternry complex for the repliction of DNA, xdna or ydse. c Active Site Bse Pir dg346 Arg298 dc347 Ser297 dc356 Arg247 dc356 Lys 78 dc356 Lys275 da357 Lys275 da357 Arg242 dt358 Arg242 dt358 Arg240 dc359 Arg240 dg:dctp 8.8 ± ± ± ± ± ± ± ± ± ± 1.2 dt:datp 9.5 ± ± ± ± ± ± ± ± ± ± 3.1 dxa:dttp 10.0 ± ± ± ± ± ± ± ± ± ± 4.8 dya:dttp 9.8 ± ± ± ± ± ± ± ± ± ± 4.3 dxg:dctp 10.0 ± ± ± ± ± ± ± ± ± ± 4.2 dyg:dctp 12.7 ± ± ± ± ± ± ± ± ± ± 3.1 dxt:datp 11.4 ± ± ± ± ± ± ± ± ± ± 4.3 dyt:datp 9.7 ± ± ± ± ± ± ± ± ± ± 1 dxc:dgtp 9.6 ± ± ± ± ± ± ± ± ± ± 3.5 dyc:dgtp 9.5 ± ± ± ± ± ± ± ± ± ± 1.2 Only residues hving n interction energy >5 kcl mol 1 in t lest one of the simultions hve been included. See Figure S11 for the numbering of the DNA helix. b Interction energy is for the DNA (including dntp) lignd binding to the Dpo4 receptor. c See Tble S1 for contribution of the ternry complex to dn nd dntp binding.
15 Tble S7. Percent occupncy, verge distnce nd verge ngle of the hydrogen-bonding interctions between the templte strnd nd the finger, plm or thumb domin during 40 ns MD simultions of the Dpo4 ternry complex for the repliction of DNA, xdna or ydse. Active Site Bse Pir dg:dctp dt:datp dxa:dttp dya:dttp dxg:dctp dyg:dctp dxc:dgtp dyc:dgtp dxt:datp dyt:datp Prmeter Gly58(O) dc353(n4h) Glu63(Oε) dc353(n4h) dn(op1) Ser34(OγH) 46 dn(op1) Ser40(OγH) S15 of S25 dc356(op1) Lys78(NζH) dg360(op1) Lys221(NζH) dc361(op1) Al220(NH) Å Å Å Å Å Å Å Å Å Å Hydrogen-bonding occupncies re bsed on distnce cutoff of <3.4 Å, n ngle cutoff of >120 nd MM/GBSA energy cutoff of 5 kcl mol 1. See Figure S11 for numbering of the DNA helix. b Not observed with >5 occupncy, with n verge ngle >149 nd distnce of <3.4 Å.
16 Tble S8. Percent occupncy, verge distnce nd verge ngle of the hydrogen-bonding interctions occurring between the templte strnd (dn or the n+1 dc) nd the little finger domin during 40 ns MD simultions of the Dpo4 ternry complex for the repliction of DNA, xdna or ydse. S16 of S25 Active Site Bse Pir Prmeter dn(o1) Arg331(Nη2H) dn(op2) Arg331(Nη2H) dn(op1) Arg331(Nη2H) dc355(op2) Arg332(NεH) dc355(op1) Thr250(NH) dc355(op2) Thr250(OγH) dc355(op1) Arg247(NηH) dg:dctp Å dt:datp Å dxa:dttp Å dya:dttp Å dxg:dctp Å dyg:dctp Å dxc:dgtp Å dyc:dgtp Å dxt:datp Å dyt:datp Å Hydrogen-bonding occupncies re bsed on distnce cutoff of <3.4 Å, n ngle cutoff of >120 nd MM/GBSA energy cutoff of 5 kcl mol 1. See Figure S11 for numbering of the DNA helix. b Not observed with >5 occupncy, with n verge ngle >149 nd distnce of <3.4 Å.
17 S17 of S25 Tble S9. Bckbone RMSD for the domin over 40 ns MD simultions of the Dpo4 ternry complex for the repliction of DNA, xdna or ydse.,b Active Site Bse Pir Enzyme Plm Domin Finger Domin Thumb Domin Little Finger Domin Tether Finger Loop dg:dctp 1.0 ± ± ± ± ± ± ± 0.2 dt:datp 1.1 ± ± ± ± ± ± ± 0.7 dxa:dttp 0.9 ± ± ± ± ± ± ± 0.2 dya:dttp 1.0 ± ± ± ± ± ± ± 0.2 dxg:dctp 1.1 ± ± ± ± ± ± ± 0.2 dyg:dctp 1.0 ± ± ± ± ± ± ± 0.2 dxt:datp 1.1 ± ± ± ± ± ± ± 0.2 dyt:datp 1.0 ± ± ± ± ± ± ± 0.2 dxc:dgtp 1.1 ± ± ± ± ± ± ± 0.2 dyc:dgtp 1.0 ± ± ± ± ± ± ± 0.2 Simultion Cα RMSD reltive to the representtive structure for the simultion. Initil lignment is bsed on the entire enzyme. b Domin residues re: plm domin (residues 1 10 nd ), finger domin (residues 11 77), thumb domin (residues ), little finger domin (residues ), tether (residues ), nd finger loop (residues 41 46). Tble S10. Bckbone RMSD for ech domin over 40 ns MD simultions of the Dpo4 ternry complex for the repliction of n xdna or ydse reltive to the repliction of nturl DNA.,b Active Site Bse Pir Comprison Enzyme Plm Domin Finger Domin Thumb Domin Little Finger Domin Tether Finger Loop dxa:dttp vs. dg:dctp 1.2 ± ± ± ± ± ± ± 0.2 dya:dttp vs. dg:dctp 1.1 ± ± ± ± ± ± ± 0.2 dxg:dctp vs. dg:dctp 1.2 ± ± ± ± ± ± ± 0.2 dyg:dctp vs. dg:dctp 1.2 ± ± ± ± ± ± ± 0.2 dxt:datp vs. dt:datp 1.3 ± ± ± ± ± ± ± 0.2 dyt:datp vs. dt:datp 1.2 ± ± ± ± ± ± ± 0.2 dxc:dgtp vs. dt:datp 1.3 ± ± ± ± ± ± ± 0.2 dyc:dgtp vs. dt:datp 1.3 ± ± ± ± ± ± ± 0.1 Simultion Cα RMSD reltive to the representtive structure from the corresponding nturl DNA simultion. Initil lignment is bsed on the entire enzyme. b Domin residues re: plm domin (residues 1 10 nd ), finger domin (residues 11 77), thumb domin (residues ), little finger domin (residues ), tether (residues ), nd finger loop (residues 41 46).
18 Active Site Bse Pir dg:dctp dt:datp dxa:dttp dya:dttp dxg:dctp dyg:dctp dxc:dgtp dyc:dgtp dxt:datp dyt:datp Tble S11. Percent occupncy, verge distnce nd verge ngle of the hydrogen-bonding interctions between the templte strnd (not dn or the n+1 dc) nd the little finger domin during 40 ns MD simultions of the Dpo4 ternry complex for the repliction of DNA, xdna or ydse. Prmeter dc356(op1) Lys275(NζH) dc356(op2) Ile248(NH) dc356(op1) Arg247(Nη1H) dc356(op1) Arg247(NεH) dc356(o3') Lys275(NζH) 45 da357(op2) Gly246(NH) da357(op1) Gly246(NH) da357(op2) Arg336(Nη1H) da357(o5') Arg336(Nη2H) Å Å Å Å Å Å Å Å Å Å Hydrogen-bonding occupncies re bsed on distnce cutoff of <3.4 Å, n ngle cutoff of >120 nd MM/GBSA energy cutoff of 5 kcl mol 1. See Figure S11 for the numbering of DNA helix. b Not observed with >5 occupncy, n verge ngle >149 nd hydrogen-bond distnce of <3.4 Å. S18 of S25 dt358(op2) Ser244(OγH)
19 Tble S12. Percent occupncy, verge distnce nd verge ngle of the hydrogen-bonding interctions occurring between the primer strnd nd the little finger domin during 40 ns MD simultions of the Dpo4 ternry complex for the repliction of DNA, xdna or ydse. Active Site Bse Pir dg:dctp dt:datp dxa:dttp dya:dttp dxg:dctp dyg:dctp dxc:dgtp dyc:dgtp dxt:datp dyt:datp Prmeter dc346(op2) Gly299(NH) dc346(op1) Arg298(Nη1H) dc347(op2) Ser297(NH) dc347(op1) Arg298(Nη1H) dc347(op2) Ser297(OγH) Å Å Å Å Å Å Å Å Å Å Hydrogen-bonding occupncies re bsed on distnce cutoff of <3.4 Å, n ngle cutoff of >120 nd MM/GBSA energy cutoff of 5 kcl mol 1. See Figure S11 for the numbering of DNA helix. b Not observed with >5 occupncy, with n verge ngle <149 nd hydrogen bond distnce of <3.4 Å. S19 of S25
20 Tble S13. Percent occupncy, verge distnce nd verge ngle of the hydrogen-bonding interctions between the templte strnd nd the tether domin during 40 ns MD simultions of the Dpo4 ternry complex for the repliction of DNA, xdna or ydse. Active Site Bse Pir Prmeter da357(op1) Arg242(Nη1H) dt358(op1) L ys243(nh) dt358(op1) Arg242(Nη1H) dt358(op1) A rg242(nεh) dc359(op1) A rg240(nηh) dc359(op2) A rg240(nηh) dc359(op2) L ys243(nζh) S20 of S25 dg360(op1) L ys221(nζh) dg:dctp Å dt:datp Å dxa:dttp Å dya:dttp Å dxg:dctp Å dyg:dctp Å dxc:dgtp Å dyc:dgtp Å dxt:datp Å dyt:datp Å Hydrogen-bonding occupncies re bsed on distnce cutoff of <3.4 Å, n ngle cutoff of >120 nd MM/GBSA energy cutoff of 5 kcl mol 1. See Figure S11 for the numbering of DNA helix. b Not observed with >5 occupncy, with n verge ngle >149 nd distnce of <3.4 Å.
21 S21 of S25 Tble S14. Reltive pirwise MM/GBSA energies (kcl mol 1 ) between individul residues in the finger or plm domins nd DNA in the Dpo4 ternry complex for the repliction of n xdna or ydse compred to Dse. Active Site Bse Pir b dntp Thr45 dntp Arg51 Finger c Plm d Mg 2+ ions dn Ser34 dn Ser40 Totl e dntp Tyr10 dntp Lys159 dc356 Lys78 Totl e dntp Binding Mg 2+ dntp Ctlytic Mg 2+ dxa:dttp dya:dttp dxg:dctp dyg:dctp dxt:datp dyt:datp dxc:dgtp dyc:dgtp Interction energies represent the DNA (including dntp) lignd binding to the Dpo4 receptor. See Figure S11 for numbering of DNA helix. b Energies for the (x,y)- purines re reltive to the dg:dctp simultion, while energies for the (x,y)-pyrimidines re reltive to the dt:datp simultion. c Finger domin includes residues d Plm domin includes residues 1-10 nd e Sum of the energy chnges listed for ech domin. Totl e Tble S15. Reltive pirwise MM/GBSA energies (kcl mol 1 ) between individul residues in the little finger domin or tether nd DNA in the Dpo4 ternry repliction complex for the repliction of n xdna or ydse compred to Dse. Active Site Bse Pir b dc347 Ser297 Little Finger c dc356 dg346 Arg298 da357 Lys275 Arg247 dc356 Lys275 Tether d Totl d dc359 Arg240 dt358 Arg240 da357 Arg242 dxa:dttp dya:dttp dxg:dctp dyg:dctp dxt:datp dyt:datp dxc:dgtp dyc:dgtp Interction energies represent the DNA (including dntp) lignd binding to the Dpo4 receptor. See Figure S11 for numbering of DNA helix. b Energies for the (x,y)- purines re reltive to the dg:dctp simultion, while energies for the (x,y)-pyrimidines re reltive to the dt:datp simultion. c Little finger domin includes residues d Tether domin includes residues e Sum of the energy chnges listed for ech domin. dt358 Arg242 Totl d
22 Tble S16. Prtil chrges nd AMBER tom types for dxa. Atom Atom Type Chrge P P O1P O O2P O O5' OS O3' OS C9 CB N13 N* C8 CB C10 CA C12 CK N11 NB C7 CM C4 CA H10 HA H12 H C5 CA H7 HA N3 NC C6 CA C2 CQ N1 NC N6 N H2 H H61 H H62 H C1' CT O4' OS H1' H C2' CT C4' CT C3' CT H2' HC H2'' HC C5' CI H4' H H3' H H5' H H5'' H Tble S17. Prtil chrges nd AMBER (GAFF) tom types for dxc. Atom Atom Type Chrge P P O1P O O2P O O5' OS O3' OS C9 CA C8 CA C10 CA H9 HA C7 CA H8 HA C6 CM C5 CM H7 HA N1 (n) C4 CA C2 C H1 H N3 NC N4 N O2 O H41 H H42 H C1' CT O4' OS H1' H C2' CT C4' CT C3' CT H2' HC H2'' HC C5' CI H4' H H3' H H5' H H5'' H Tble S18. Prtil chrges nd AMBER tom types for dxg. Atom Atom Type Chrge P P O1P O O2P O O5' OS O3' OS C9 CB N13 N* C8 CB C10 CM S22 of S25
23 C12 CK N11 NB C7 CM C4 CA H10 HA H12 H C5 CM H7 HA N3 NC C6 C C2 CA N1 NA O6 O N2 N H1 H H21 H H22 H C1' CT O4' OS H1' H C2' CT C4' CT C3' CT H2' HC C5' CI H4' H H3' H H5' H H5'' H H2'' HC Tble S19. Prtil chrges nd AMBER (GAFF) tom types for dxt. Atom Atom Type Chrge P P O1P O O2P O O5' OS O3' OS C9 CA C8 CA C10 CM H9 HA C7 CA C11 CT C6 CM C5 CM H7 HA H111 HC H112 HC H113 HC N1 (n) C4 C C2 C H1 H N3 n O4 O O2 O H3 H C1' CT O4' OS H1' H C2' CT C4' CT C3' CT H2'1 HC H2'2 HC C5' CI H4' H H7 H H5'1 H H5'2 H Tble S20. Prtil chrges nd AMBER tom types for dya. Atom Atom Type Chrge P P O1P O O2P O O5' OS O3' OS C8 CB N13 N* C7 CB C9 CA C12 CA C4 CA C11 C* C10 CA H9 HA H12 H C3 CA N5 NC H11 HA S23 of S25
24 H10 HA C2 CA C6 CQ N1 NC H2 H N6 N H61 H H62 H C1' CT O4' OS H1' H C2' CT C4' CT C3' CT H2' HC H2'' HC C5' CI H4' H H7 H H5' H H5'' H Tble S21. Prtil chrges nd AMBER tom types for dyc. Atom Atom Type Chrge P P O1P O O2P O O5' OS O3' OS C8 CA C9 CA C7 CA H8 HA C10 CA C6 CM C11 CT C1 CM H10 HA N5 NA H111 HC H112 HC H113 HC C2 C C4 CA H5 H N3 NC O2 O N4 N H41 H H41 H C1' CT O4' OS H1' H C2' CT C4' CT C3' CT H2' HC H2'' HC C5' CI H4' H H3' H H5' H H5'' H Tble S22. Prtil chrges nd AMBER (GAFF) tom types for dyg. Atom Atom Type Chrge P P O1P O O2P O O5' OS O3' OS C8 CB N13 N* C7 CB C9 CA C12 CA C4 CA C11 C* C10 CA H9 HA H12 H C3 CM N5 NC H11 HA H10 HA C2 CM C6 C N1 (n) N2 N O6 O H1 H H21 H S24 of S25
25 H22 H C1' CT O4' OS H1' H C2' CT C4' CT C3' CT H2' HC H2'' HC C5' CI H4' H H7 H H5' H H5'' H Tble S23. Prtil chrges nd AMBER (GAFF) tom types for dyt. Atom Atom Type Chrge P P O1P O O2P O O5' OS O3' OS C8 CA C9 CA C7 CM H8 HA C10 CA C6 CM H7 HA C1 CM H10 HA N5 (n) C2 C C4 C H5 H N3 (n) O2 O O4 O H3 H H1' H C1' CT O4' OS C2' CT C4' CT C3' CT H2' HC H2'' HC C5' CI H4' H H5 H H5' H H5'' H Tble S24. RMSD over 40 ns MD simultions of the Dpo4 ternry complex for the repliction of DNA, xdna or ydse. Active Site Bse Pir RMSD dg:dctp 1.3 ± 0.2 dt:datp 1.5 ± 0.3 dxa:dttp 1.3 ± 0.2 dya:dttp 1.3 ± 0.2 dxg:dctp 1.2 ± 0.2 dyg:dctp 1.4 ± 0.2 dxt:datp 1.2 ± 0.2 dyt:datp 1.1 ± 0.1 dxc:dgtp 1.2 ± 0.2 dyc:dgtp 1.6 ± 0.2 RMSD is reltive to the first frme in the respective simultion. S25 of S25
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