SMTL ID : 3uiq.1

RB69 DNA Polymerase Ternary Complex containing dUpNpp

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

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

DUP.1: 18 residues within 4Å: Chain A: D.411, L.412, S.414, L.415, Y.416, P.417, R.482, K.486, K.560, N.564, Y.567, T.622, D.623 Chain B: A.4, G.5 Chain C: C.13 Ligands: CA.2, CA.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:S.414, A:S.414, A:L.415, A:Y.416, A:K.560, A:N.564, A:D.623 Water bridges: A:R.482 Salt bridges: A:R.482, A:K.486, A:K.560

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.411, L.412, D.623 Ligands: DUP.1, CA.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.411, A:D.411, A:L.412, A:D.623 CA.3: 2 residues within 4Å: Chain A: E.660, D.684 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.660, A:D.684, H2O.10 CA.4: 5 residues within 4Å: Chain A: D.411, D.623 Chain C: C.13 Ligands: DUP.1, CA.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.411, A:D.623, H2O.13, H2O.13, H2O.13 CA.5: 2 residues within 4Å: Chain A: D.411, E.716 No protein-ligand interaction detected (PLIP) CA.6: 3 residues within 4Å: Chain A: N.505, N.507, K.531 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.505, A:K.531, H2O.9, H2O.17 CA.7: 1 residues within 4Å: Chain A: E.116 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.116, H2O.13, H2O.17, H2O.20, H2O.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, S. et al., Bidentate and tridentate metal-ion coordination states within ternary complexes of RB69 DNA polymerase. Protein Sci. (2012)

Release Date

2012-04-18

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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