SMTL ID : 3qnn.1

RB69 DNA Polymerase (Y567A) Ternary Complex with dGT Opposite 3tCo

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.1: 18 residues within 4Å: Chain A: D.411, L.412, T.413, S.414, L.415, Y.416, R.482, K.486, K.560, N.564, G.568, T.622, D.623 Chain B: X.4, G.5 Chain C: C.13 Ligands: CA.2, CA.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:S.414, A:L.415, A:Y.416, A:N.564, A:G.568 Water bridges: A:S.414, A:R.482, A:R.482, A:R.482, A:R.482, A:K.486, A:K.486, A:K.560, A:N.564 Salt bridges: A:R.482, A:K.486, A:K.560, A:K.560, A:K.560

7 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.411, L.412, D.623 Ligands: DGT.1, CA.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.411, A:D.411, A:L.412, A:D.623 CA.3: 6 residues within 4Å: Chain A: D.411, D.623, S.624 Chain C: C.13 Ligands: DGT.1, CA.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.411, A:D.623, H2O.22 CA.4: 3 residues within 4Å: Chain A: N.505, N.507, K.531 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:N.505, A:K.531, H2O.6, H2O.7, H2O.8 CA.5: 1 residues within 4Å: Chain A: E.116 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.116, A:E.116, H2O.1, H2O.22, H2O.23 CA.6: 2 residues within 4Å: Chain A: E.660, D.684 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.684, H2O.18, H2O.27 CA.7: 2 residues within 4Å: Chain A: A.789, D.792 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.792, H2O.27 CA.8: 1 residues within 4Å: Chain A: E.716 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.716, H2O.15, H2O.17, H2O.18, H2O.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, S. et al., Using a Fluorescent Cytosine Analogue tC(o) To Probe the Effect of the Y567 to Ala Substitution on the Preinsertion Steps of dNMP Incorporation by RB69 DNA Polymerase. Biochemistry (2012)

Release Date

2012-02-08

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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