SMTL ID : 2pyj.1 (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

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

EDO.1: 6 residues within 4Å: Chain A: T.4, G.5 Chain C: K.402, F.414, R.415, L.416 Ligand excluded by PLIP EDO.2: 4 residues within 4Å: Chain A: G.5, C.6 Chain C: F.414, Q.560 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain B: T.6, A.7 Chain C: K.305 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain B: G.12, T.13 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain C: I.474, G.481, Y.482 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain C: K.274, Y.275, H.284, Q.286, L.333, K.337, Y.347 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain C: R.308 Ligands: EDO.11 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain C: R.306, S.307, R.308 Ligands: EDO.10 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain C: N.62, K.64, P.558 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain C: N.62, L.123, F.128, P.129 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain C: I.202, K.206, L.359 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain C: Q.380, K.383 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain C: S.551, R.552, M.554 Ligands: EDO.23 Ligand excluded by PLIP EDO.17: 1 residues within 4Å: Chain C: I.323 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain C: Q.183, K.366, W.367 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain C: L.253, Q.257, T.440, G.481 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain A: G.5, C.6 Chain C: K.64, I.94, G.98, W.100, K.402, F.414 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: C.6, T.7 Chain C: K.64, M.97, G.98 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain C: I.40, G.41, N.42, E.46 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain C: G.549, F.550, S.551, R.552 Ligands: EDO.16 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain C: W.81, T.92, I.93, I.94, G.401, K.402, E.420 Ligand excluded by PLIP

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

MN.5: 5 residues within 4Å: Chain C: D.249, V.250, D.458 Ligands: MG.6, DGT.7 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.6: 5 residues within 4Å: Chain A: C.10 Chain C: D.249, D.458 Ligands: MN.5, DGT.7 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.249, C:D.458, H2O.10, H2O.16

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

DGT.7: 18 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.5, MG.6 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:Y.254 Hydrogen bonds: C:N.251, C:S.252, C:L.253, C:Y.254, C:N.387 Water bridges: C:D.249, C:D.249, C:K.371, C:K.383, C:K.383 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
A

DNA polymerase

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