SMTL ID : 4rq8.1

Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine(8-oxoG) and dATP soaked with MnCl2 for 35 s

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: 19 residues within 4Å: Chain A: H.36, K.37, A.40, Y.41, L.64, P.65, G.66, V.67, G.68, T.69, K.70, I.71 Chain C: C.2, G.3, A.4, C.5 Ligands: NA.9, ACT.21, ACT.29 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.36, A:K.282, A:R.285

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.2: 11 residues within 4Å: Chain A: R.151, G.181, S.182, R.185, S.190, G.191, D.192, D.194 Chain B: A.11 Ligands: MN.5, MN.26 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.182, A:S.182, A:G.191, A:D.192 Water bridges: A:R.151, A:R.151, A:D.192 Salt bridges: A:R.151, A:R.185

6 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.3: 6 residues within 4Å: Chain A: D.192, D.194, D.258 Chain B: C.10, A.11 Ligands: MN.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.192, A:D.194, A:D.258, H2O.1 MN.4: 3 residues within 4Å: Chain A: E.11, H.339, H.341 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.339, A:H.341, H2O.1, H2O.1, H2O.1, H2O.1 MN.5: 5 residues within 4Å: Chain A: D.192, D.194 Chain B: A.11 Ligands: PPV.2, MN.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.192, A:D.194, H2O.1 MN.6: 1 residues within 4Å: Chain A: D.323 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.323, H2O.6, H2O.7, H2O.7 MN.7: 3 residues within 4Å: Chain A: K.50, H.338, H.340 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.50, A:H.338, A:H.340, H2O.7 MN.26: 2 residues within 4Å: Chain B: A.11 Ligands: PPV.2 No protein-ligand interaction detected (PLIP)

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

NA.8: 1 residues within 4Å: Chain A: H.342 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.342 NA.9: 4 residues within 4Å: Chain A: K.62, L.64, V.67 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.62, A:V.67 NA.10: 5 residues within 4Å: Chain A: T.103, V.105, S.106, I.108 Chain B: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.107, A:I.108, A:I.108 NA.11: 2 residues within 4Å: Chain A: H.287, E.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.290 Water bridges: A:H.287 NA.12: 1 residues within 4Å: Chain A: D.316 No protein-ligand interaction detected (PLIP) NA.13: 2 residues within 4Å: Chain A: D.147, H.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.147, A:H.254, A:H.254 NA.14: 1 residues within 4Å: Chain A: D.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.162 NA.27: 3 residues within 4Å: Chain C: G.6, G.7, C.8 No protein-ligand interaction detected (PLIP) NA.28: 1 residues within 4Å: Chain C: A.11 No protein-ligand interaction detected (PLIP)

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

CL.15: 3 residues within 4Å: Chain A: N.296, T.299, R.301 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain A: A.34, I.35, H.36, K.37 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: R.185, S.336, E.337 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain A: F.280, N.283 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain A: H.36, N.39 Chain C: C.5 Ligands: ACT.21 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain A: K.83, L.84, L.87, R.91 Ligand excluded by PLIP

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.21: 7 residues within 4Å: Chain A: N.39, A.40, K.43, K.282 Chain C: C.5 Ligands: DG-DT-DC-DG-DG.1, CL.19 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.39, A:A.40 Salt bridges: A:K.43, A:K.282 ACT.22: 2 residues within 4Å: Chain A: H.36 Chain C: C.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.36 Salt bridges: A:H.36 ACT.23: 3 residues within 4Å: Chain A: F.202, P.263, Y.298 No protein-ligand interaction detected (PLIP) ACT.24: 5 residues within 4Å: Chain A: Q.221, I.226, T.227, D.228, T.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.221 ACT.25: 2 residues within 4Å: Chain A: E.11, H.341 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.341 ACT.29: 4 residues within 4Å: Chain C: A.4, C.5 Ligands: DG-DT-DC-DG-DG.1, DG-DT-DC-DG-DG.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vyas, R. et al., Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography. J.Am.Chem.Soc. (2015)

Release Date

2015-04-15

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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