SMTL ID : 4lvs.1

DNA polymerase beta mismatched substrate complex with Mn2+, 2.5 min

Coordinates

PDB Format

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: 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 Chain C: C.1, C.2, G.3, A.4, C.5 Ligands: NA.7 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.230, A:K.230, A:T.233, A:T.233, A:K.234, A:K.234, A:K.234, A:K.234, A:Y.271, A:Y.271, A:R.283, A:R.283, A:G.105, A:G.107, A:G.107, A:S.109, A:A.110, A:R.258 Water bridges: A:H.34, A:N.133, A:H.134, A:T.101, A:T.101, A:V.103, A:I.106, A:S.109, A:S.109, A:D.190, A:D.190, A:R.254, A:R.254 pi-Stacking: A:H.34 Salt bridges: A:R.254

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.2: 20 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, S.275, D.276, N.279 Chain B: C.10 Chain C: G.6, G.7 Ligands: MN.3, MN.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.149, A:S.180, A:S.180, A:R.183, A:G.189, A:D.190 Salt bridges: A:R.183

6 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.3: 5 residues within 4Å: Chain A: D.190, D.192, D.256 Ligands: DTP.2, MN.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, A:D.256, H2O.1, H2O.6 MN.4: 4 residues within 4Å: Chain A: D.190, D.192 Ligands: DTP.2, MN.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H2O.1 MN.5: 1 residues within 4Å: Chain A: D.124 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.124, H2O.5, H2O.5, H2O.5, H2O.5 MN.8: 2 residues within 4Å: Chain B: G.4, A.5 No protein-ligand interaction detected (PLIP) MN.9: 1 residues within 4Å: Chain C: G.15 No protein-ligand interaction detected (PLIP) MN.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

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:G.105, A:I.106, A:I.106 NA.7: 5 residues within 4Å: Chain A: K.60, L.62, P.63, 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

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Freudenthal, B.D. et al., Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.) (2013)

Release Date

2013-09-04

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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