SMTL ID : 4f5p.1

Open ternary mismatch complex of R283K DNA polymerase beta with a dATP analog

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: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69, K.72 Chain B: C.1, C.2, G.3, A.4, C.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.37 pi-Stacking: A:H.34

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.190, D.192 Ligands: F2A.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H2O.6

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

NA.3: 2 residues within 4Å: Chain A: T.101 Ligands: NA.4 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.27, A:N.28, A:T.101 NA.4: 6 residues within 4Å: Chain A: T.101, V.103, S.104, I.106 Chain C: G.9 Ligands: NA.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.105, A:I.106, A:I.106

1 x F2A: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine(Non-covalent)

F2A.5: 16 residues within 4Å: Chain A: R.149, G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, T.273, G.274, D.276 Chain B: G.6 Chain C: C.10 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:D.190, A:D.276 Water bridges: A:R.149, A:R.149, A:D.192, A:D.192 Salt bridges: A:R.149

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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