SMTL ID : 3sjj.1

RB69 DNA Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the presence of Mn2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

monomer

Ligands

1 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.1: 17 residues within 4Å: Chain A: D.411, L.412, T.413, S.414, L.415, Y.416, R.482, K.560, N.564, T.622, D.623 Chain B: A.4, G.5 Chain C: C.13 Ligands: MN.2, MN.3, MN.7 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:S.414, A:L.415, A:Y.416, A:K.560, A:N.564, A:N.564 Water bridges: A:R.482 Salt bridges: A:R.482, A:K.560

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

MN.2: 5 residues within 4Å: Chain A: D.411, L.412, D.623 Ligands: DUP.1, MN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.411, A:L.412, A:D.623 MN.3: 5 residues within 4Å: Chain A: D.411, D.623 Chain C: C.13 Ligands: DUP.1, MN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.411, A:D.623, A:D.623, H2O.3, H2O.6 MN.4: 2 residues within 4Å: Chain A: E.716 Ligands: MN.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.716, H2O.3, H2O.3 MN.5: 2 residues within 4Å: Chain A: D.114, E.116 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.114, A:E.116 MN.6: 2 residues within 4Å: Chain A: E.160, E.161 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.160, H2O.1, H2O.1, H2O.3 MN.7: 4 residues within 4Å: Chain A: E.686, E.716 Ligands: DUP.1, MN.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.686, H2O.3, H2O.3, H2O.4 MN.8: 1 residues within 4Å: Chain A: E.172 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, S. et al., Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase. Biochemistry (2011)

Release Date

2011-10-12

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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