SMTL ID : 4p2h.1

Structure of human DNA polymerase complexed with N7MG in the template opposite to incoming non-hydrolyzable TTP with manganese in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 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: 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 B: C.1, C.2, G.3, A.4, C.5 Ligands: NA.4 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.25

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

MN.2: 5 residues within 4Å: Chain A: D.181, D.183 Chain C: A.10 Ligands: MN.3, 1FZ.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.181, A:D.183, H2O.3 MN.3: 4 residues within 4Å: Chain A: D.181, D.183 Ligands: MN.2, 1FZ.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.181, A:D.183, H2O.2

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

NA.4: 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:L.53, A:G.55, A:V.56 NA.5: 5 residues within 4Å: Chain A: T.92, V.94, S.95, I.97 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.96, A:I.97, A:I.97

1 x 1FZ: 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine(Non-covalent)

1FZ.6: 18 residues within 4Å: Chain A: R.140, G.170, S.171, R.174, S.179, G.180, D.181, D.183, Y.262, F.263, G.265, S.266, D.267, N.270 Chain B: G.6 Chain C: A.10 Ligands: MN.2, MN.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.140, A:S.171, A:S.171, A:R.174, A:R.174, A:G.180, A:D.181, A:D.181, A:Y.262, A:D.267, A:D.267, A:N.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koag, M.C. et al., Transition-state destabilization reveals how human DNA polymerase beta proceeds across the chemically unstable lesion N7-methylguanine. Nucleic Acids Res. (2014)

Release Date

2014-06-25

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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