SMTL ID : 6ctr.1

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF (R & S isomers), beta, gamma dCTP analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: DNA (5'-D(P*GP*TP*CP*GP*G)-3')(Non-covalent)

DG-DT-DC-DG-DG.1: 18 residues within 4Å: Chain A: C.1, C.2, G.3, A.4, C.5 Chain C: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69 Ligands: NA.4 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.37, C:N.279, C:R.283, C:R.283, C:R.283 Water bridges: C:K.280 pi-Stacking: C:H.34

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain C: D.190, D.192 Ligands: NA.5, F3C.8, FF4.9 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H2O.5

3 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, I.106 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.105, C:I.106, C:I.106 NA.4: 5 residues within 4Å: Chain C: K.60, K.61, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.60, C:V.65 NA.5: 7 residues within 4Å: Chain B: A.10 Chain C: D.190, D.192, D.256 Ligands: MG.6, F3C.8, FF4.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.190

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 3 residues within 4Å: Chain C: N.294, T.297, R.299 Ligand excluded by PLIP

1 x F3C: 2'-deoxy-5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine(Non-covalent)

F3C.8: 20 residues within 4Å: Chain A: G.6 Chain B: A.10 Chain C: R.149, G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, T.273, G.274, S.275, D.276, N.279 Ligands: NA.5, MG.6, FF4.9 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:D.276 Hydrogen bonds: C:R.149, C:S.180, C:S.180, C:R.183, C:R.183, C:G.189, C:D.190, C:D.190, C:D.190, C:N.279 Water bridges: C:D.190, C:D.276, C:D.276, C:D.276, C:K.280 Halogen bonds: C:R.183

1 x FF4: 2'-deoxy-5'-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine(Non-covalent)

FF4.9: 20 residues within 4Å: Chain A: G.6 Chain B: A.10 Chain C: R.149, G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, T.273, G.274, S.275, D.276, N.279 Ligands: NA.5, MG.6, F3C.8 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:D.276 Hydrogen bonds: C:R.149, C:S.180, C:S.180, C:R.183, C:R.183, C:G.189, C:D.190, C:D.190, C:N.279 Water bridges: C:D.190, C:D.276, C:D.276, C:D.276, C:K.280

1 x DC: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

DC.10: 7 residues within 4Å: Chain C: I.174, T.176, L.194, T.196, K.262, Y.265, Y.266 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.174, C:Y.265 Hydrogen bonds: C:T.176, C:T.196, C:Y.265, C:Y.266 pi-Stacking: C:Y.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Batra, V.K. et al., Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs. Biochemistry (2018)

Release Date

2018-06-20

Peptides

DNA polymerase beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase beta

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