SMTL ID : 4ba9.2 (1 other biounit)

The structural basis for the coordination of Y-family Translesion DNA Polymerases by Rev1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

homo-tetramer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.53 Chain D: D.53 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Metal complexes: A:D.53, D:D.53 MG.2: 1 residues within 4Å: Chain A: D.106 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.106, H2O.1, H2O.1 MG.5: 2 residues within 4Å: Chain B: D.102, D.106 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.106, B:D.106, H2O.1, H2O.1 MG.8: 2 residues within 4Å: Chain B: D.53 Chain C: D.53 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Metal complexes: C:D.53, B:D.53 MG.9: 1 residues within 4Å: Chain C: D.106 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.106, H2O.2, H2O.2 MG.12: 2 residues within 4Å: Chain D: D.102, D.106 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.106, D:D.106, H2O.2, H2O.2

8 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 3 residues within 4Å: Chain A: H.3, H.5 Chain B: G.1 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.3, A:H.5, B:G.1 NI.4: 7 residues within 4Å: Chain A: D.11, E.57 Chain C: S.8, D.11, E.57, Q.61 Ligands: NI.11 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Metal complexes: C:D.11, C:E.57, C:E.57, A:D.11, A:E.57 NI.6: 3 residues within 4Å: Chain A: G.1 Chain B: H.3, H.5 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.3, B:H.5, A:G.1, H2O.1 NI.7: 6 residues within 4Å: Chain B: D.11, E.57 Chain D: D.11, E.57, Q.61 Ligands: NI.14 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Metal complexes: B:D.11, B:E.57, D:D.11, D:D.11, D:E.57 NI.10: 3 residues within 4Å: Chain C: H.3, H.5 Chain D: G.1 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Metal complexes: C:H.3, C:H.5, D:G.1 NI.11: 7 residues within 4Å: Chain A: S.8, D.11, E.57, Q.61 Chain C: D.11, E.57 Ligands: NI.4 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Metal complexes: C:D.11, C:E.57, A:D.11, A:E.57, A:E.57 NI.13: 3 residues within 4Å: Chain C: G.1 Chain D: H.3, H.5 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:H.3, D:H.5, C:G.1, H2O.2 NI.14: 6 residues within 4Å: Chain B: D.11, E.57, Q.61 Chain D: D.11, E.57 Ligands: NI.7 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Metal complexes: B:D.11, B:D.11, B:E.57, D:D.11, D:E.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grummitt, C.G. et al., The Structural Basis for the Coordination of Y- Family Translesion DNA Polymerases by Rev1. To be Published

Release Date

2013-09-25

Peptides

DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
E

D
F

DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1

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