SMTL ID : 2pyj.2 (1 other biounit)

Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

monomer

Ligands

17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: T.8, A.9, C.10 Chain B: G.5 Ligand excluded by PLIP EDO.2: 4 residues within 4Å: Chain B: G.9, C.10 Chain C: R.496, K.575 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain C: R.491, D.503, F.526, T.542, F.543 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain C: I.504, M.506, E.515, K.525 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain C: V.210, Y.265, T.356 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain C: T.368, T.372, K.478, K.479, L.480 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain C: N.251, K.371, K.379, P.477 Ligands: DGT.5 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain C: E.375, G.376, K.379 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain C: E.334, E.338, W.436, Y.439 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain C: R.227, T.301, I.302, Q.303, D.332, R.438 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain C: L.262, P.282 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain C: H.3, M.4 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain C: E.33, L.178, K.182 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain C: Y.29, S.36, E.37, Y.38 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain C: L.123, F.128, P.129 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain C: T.372, K.478 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain C: S.260, R.261, W.436 Ligand excluded by PLIP

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

MN.3: 5 residues within 4Å: Chain C: D.249, V.250, D.458 Ligands: MG.4, DGT.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.249, C:V.250, C:D.458

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: C.10 Chain C: D.249, D.458 Ligands: MN.3, DGT.5 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.249, C:D.458, H2O.5, H2O.7

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

DGT.5: 19 residues within 4Å: Chain A: C.10 Chain B: C.4, G.5 Chain C: D.249, V.250, N.251, S.252, L.253, Y.254, P.255, K.371, K.383, N.387, Y.390, T.457, D.458 Ligands: MN.3, MG.4, EDO.10 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:Y.254 Hydrogen bonds: C:S.252, C:L.253, C:Y.254, C:N.387 Water bridges: C:D.249, C:D.249, C:V.250, C:N.251, C:S.252, C:K.371, C:K.383, C:K.383, C:N.387 Salt bridges: C:K.371, C:K.371, C:K.383, C:K.383, C:K.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berman, A.J. et al., Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases. Embo J. (2007)

Release Date

2007-07-17

Peptides

DNA polymerase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
B

DNA polymerase

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