SMTL ID : 4f5o.1

Open ternary complex of R283K DNA polymerase beta with a one metal bound dCTP analog

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: 16 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 B: C.1, C.2, G.3, A.4, C.5 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.34

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

6CF.2: 11 residues within 4Å: Chain A: G.179, S.180, R.183, S.188, G.189, D.190, Y.271, F.272 Chain B: G.6 Chain C: A.10 Ligands: MG.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.180, A:S.180, A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190 Water bridges: A:R.149, A:D.190, A:D.190

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.190 Ligands: 6CF.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.190, H2O.8, H2O.8, H2O.8

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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