SMTL ID : 4khn.1 (1 other biounit)

Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

monomer

Ligands

2 x XG4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine(Non-covalent)

XG4.1: 15 residues within 4Å: Chain A: Y.33, S.36, F.38, K.48, Y.49, R.59, G.84, M.85, D.95, F.370, K.374, N.377, K.378, V.379, I.380 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Y.33, A:K.48, A:Y.49, A:Y.49, A:M.85, A:D.95, A:K.374, A:K.378, A:K.378, A:I.380 Water bridges: A:S.36, A:R.59 pi-Stacking: A:F.38, A:F.38, A:F.370 XG4.11: 14 residues within 4Å: Chain A: L.415, Y.416, P.417, K.560, N.564, G.568, T.622, D.623 Chain B: C.4, G.5 Chain C: C.13 Ligands: CA.2, SO4.3, GOL.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:Y.416, A:K.560, A:N.564, A:N.564, A:G.568 Water bridges: A:L.415, A:A.567 Salt bridges: A:K.560

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: D.411, D.623 Ligands: XG4.11 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.623, H2O.1, H2O.9

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 7 residues within 4Å: Chain A: L.412, T.413, S.414, R.482, K.486, K.560 Ligands: XG4.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.414, A:S.414 Salt bridges: A:R.482, A:K.486, A:K.560 SO4.4: 5 residues within 4Å: Chain A: W.216, N.217, S.289, L.290, K.302 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.217, A:L.290, A:D.291 Salt bridges: A:K.302 SO4.5: 3 residues within 4Å: Chain A: G.637, E.638, S.639 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.639, A:S.639 SO4.6: 3 residues within 4Å: Chain A: K.48, Y.49, R.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.49 Salt bridges: A:R.59 SO4.7: 4 residues within 4Å: Chain A: H.105, V.110, D.335, I.341 3 PLIP interactions: 3 interactions with chain A Water bridges: A:I.341, A:N.342 Salt bridges: A:H.105

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: F.282, I.557, K.560, L.561, N.564 Ligands: XG4.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.564 GOL.9: 4 residues within 4Å: Chain A: F.650, K.653, F.654, R.658 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.650, A:R.658

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

NA.10: 6 residues within 4Å: Chain A: Y.619, D.621, K.706, Y.708 Chain C: A.12, C.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.619, A:Y.619, A:D.621, A:K.706

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jacewicz, A. et al., A Remote Palm Domain Residue of RB69 DNA Polymerase Is Critical for Enzyme Activity and Influences the Conformation of the Active Site. Plos One (2013)

Release Date

2013-10-09

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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