SMTL ID : 7k97.1

Human DNA polymerase beta dGDP product complex with Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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: 20 residues within 4Å: Chain A: E.17, H.25, K.26, A.29, Y.30, L.53, P.54, G.55, V.56, G.57, T.58, K.59, I.60, K.63 Chain C: C.1, C.2, G.3, A.4, C.5 Ligands: NA.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.271 Hydrogen bonds: A:R.274 Salt bridges: A:K.271 pi-Stacking: A:H.25

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

MN.2: 6 residues within 4Å: Chain A: D.181, D.183, D.247 Chain B: C.10, G.11 Ligands: MN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.181, A:D.183, A:D.247 MN.3: 5 residues within 4Å: Chain A: D.181, D.183 Chain B: G.11 Ligands: MN.2, PO4.11 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.181, A:D.183, H2O.2 MN.4: 2 residues within 4Å: Chain A: T.112, D.115 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.115 MN.5: 2 residues within 4Å: Chain A: H.276, E.279 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.276, A:E.279 MN.6: 1 residues within 4Å: Chain A: H.213 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.213 MN.9: 1 residues within 4Å: Chain B: G.4 No protein-ligand interaction detected (PLIP) MN.10: 2 residues within 4Å: Chain B: G.11 Ligands: PO4.11 No protein-ligand interaction detected (PLIP) MN.12: 1 residues within 4Å: Chain C: G.3 No protein-ligand interaction detected (PLIP)

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

NA.7: 5 residues within 4Å: Chain A: T.92, V.94, S.95, I.97 Chain B: G.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.94 NA.8: 4 residues within 4Å: Chain A: K.51, L.53, V.56 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.51, A:G.55, A:V.56

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.11: 8 residues within 4Å: Chain A: G.170, S.171, R.174, D.181, D.183 Chain B: G.11 Ligands: MN.3, MN.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.171, A:S.171 Water bridges: A:G.180, A:D.181 Salt bridges: A:R.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Varela, F.A. et al., Mechanism of Deoxyguanosine Diphosphate Insertion by Human DNA Polymerase beta. Biochemistry (2021)

Release Date

2021-02-03

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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