SMTL ID : 4php.1

Structure of human DNA polymerase beta complexed with T in the template base paired with incoming non-hydrolyzable GTP and MANGANESE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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: C.1, C.2, G.3, A.4, C.5 Chain C: K.26, A.29, Y.30, L.53, G.55, V.56, G.57, T.58, K.59, I.60, K.63 Ligands: NA.5 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.271 Hydrogen bonds: C:R.274 pi-Stacking: C:H.25

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

MN.2: 4 residues within 4Å: Chain C: D.181, D.183 Ligands: MN.3, XG4.6 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.181, C:D.183, H2O.4 MN.3: 6 residues within 4Å: Chain B: C.10 Chain C: D.181, D.183, D.247 Ligands: MN.2, XG4.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.181, C:D.183, C:D.247

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

NA.4: 5 residues within 4Å: Chain B: G.9 Chain C: T.92, V.94, S.95, I.97 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.94, C:G.96, C:I.97 NA.5: 4 residues within 4Å: Chain C: K.51, L.53, V.56 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.51, C:V.56

1 x XG4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine(Non-covalent)

XG4.6: 20 residues within 4Å: Chain A: T.6, G.7 Chain B: C.10 Chain C: G.170, S.171, R.174, S.179, G.180, D.181, D.183, Y.262, F.263, T.264, G.265, S.266, D.267, N.270, R.274 Ligands: MN.2, MN.3 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.171, C:S.171, C:S.171, C:R.174, C:R.174, C:G.180, C:D.181, C:N.270, C:R.274 Water bridges: C:D.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koag, M.C. et al., The spontaneous base substitution mechanisms of human DNA polymerase beta. To Be Published

Release Date

2015-05-06

Peptides

DNA polymerase beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase beta

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