SMTL ID : 3rh5.1

DNA Polymerase Beta Mutant (Y271) with a dideoxy-terminated primer with an incoming deoxynucleotide (dCTP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: 5'-D(P*GP*TP*CP*GP*G)-3'(Non-covalent)

DG-DT-DC-DG-DG.1: 18 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 Ligands: NA.10, MN.17 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.279, A:R.283, A:R.283, A:R.283 Water bridges: A:N.37, A:K.280 Salt bridges: A:K.280 pi-Stacking: A:H.34

2 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.2: 18 residues within 4Å: Chain A: G.179, S.180, R.183, S.188, G.189, D.190, D.192, A.271, F.272, T.273, G.274, D.276, N.279 Chain B: G.6 Chain C: G.10 Ligands: MN.4, MN.5, MN.8 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:D.276 Hydrogen bonds: A:R.149, A:S.180, A:S.180, A:S.180, A:R.183, A:G.189, A:D.190, A:N.279 Water bridges: A:F.181, A:R.183, A:R.183, A:D.276 Salt bridges: A:R.183 DCP.3: 8 residues within 4Å: Chain A: I.174, A.175, T.176, T.196, K.262, Y.265, Y.266 Ligands: MN.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.174, A:Y.265 Hydrogen bonds: A:T.176, A:T.176, A:T.196, A:Y.265, A:Y.265, A:Y.266 Water bridges: A:R.182, A:Y.266 pi-Stacking: A:Y.265

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

MN.4: 4 residues within 4Å: Chain A: D.190, D.192 Ligands: DCP.2, MN.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H2O.1 MN.5: 5 residues within 4Å: Chain A: D.190, D.192, D.256 Ligands: DCP.2, MN.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.190, A:D.192, A:D.256 MN.6: 2 residues within 4Å: Chain A: D.145, H.252 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.145, A:H.252, H2O.2, H2O.2 MN.7: 1 residues within 4Å: Ligands: DCP.3 No protein-ligand interaction detected (PLIP) MN.8: 1 residues within 4Å: Ligands: DCP.2 No protein-ligand interaction detected (PLIP) MN.16: 2 residues within 4Å: Chain B: A.4, C.5 No protein-ligand interaction detected (PLIP) MN.17: 2 residues within 4Å: Ligands: DG-DT-DC-DG-DG.1, DG-DT-DC-DG-DG.1 No protein-ligand interaction detected (PLIP)

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

NA.9: 4 residues within 4Å: Chain A: T.101, V.103, I.106 Chain C: G.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.106, A:I.106 NA.10: 4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.60, A:V.65

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 3 residues within 4Å: Chain A: N.294, T.297, R.299 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: K.81, L.82, E.86, R.89 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: Q.159, T.176, V.177 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: E.329, P.330, K.331 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: A.32, I.33, H.34, K.35 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cavanaugh, N.A. et al., Molecular insights into DNA polymerase deterrents for ribonucleotide insertion. J.Biol.Chem. (2011)

Release Date

2011-07-06

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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