SMTL ID : 4f5q.1

Closed ternary complex of R283K DNA polymerase beta

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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: 17 residues within 4Å: Chain A: K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69 Chain C: C.1, C.2, G.3, A.4, C.5 Ligands: NA.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.280 pi-Stacking: A:H.34

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: D.190, D.192 Ligands: MN.3, 6CF.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H2O.1 MN.3: 6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain B: C.10 Ligands: MN.2, 6CF.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, A:D.256, H2O.3

1 x 6CF: 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine(Non-covalent)

6CF.4: 18 residues within 4Å: Chain A: G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, T.273, G.274, D.276, N.279 Chain B: C.10 Chain C: G.6, G.7 Ligands: MN.2, MN.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:D.276 Hydrogen bonds: A:R.149, A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:T.273, A:N.279

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

NA.5: 4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.65, A:V.65 NA.6: 6 residues within 4Å: Chain A: T.101, V.103, S.104, G.105, I.106 Chain B: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.103, A:G.105, A:I.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Freudenthal, B.D. et al., Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Structure (2012)

Release Date

2012-12-12

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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