SMTL ID : 2pyl.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain C: D.249, V.250, D.458 Ligands: MG.2, TTP.3 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.249, C:D.458, H2O.4, H2O.14, H2O.14 MG.2: 4 residues within 4Å: Chain C: D.249, D.458 Ligands: MG.1, TTP.3 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.249, C:D.458, H2O.14

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.3: 14 residues within 4Å: Chain A: A.11 Chain B: A.3, T.4 Chain C: S.252, L.253, Y.254, P.255, K.371, K.383, N.387, Y.390, D.458 Ligands: MG.1, MG.2 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Y.254 Hydrogen bonds: C:S.252, C:L.253, C:Y.254, C:N.387, C:D.458 Water bridges: C:K.371, C:K.371, C:Q.380, C:Q.380, C:K.383, C:K.383 Salt bridges: C:K.371, C:K.371, C:K.383, C:K.383, C:K.383

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

EDO.4: 3 residues within 4Å: Chain C: I.158, P.160 Ligands: EDO.7 No protein-ligand interaction detected (PLIP) EDO.5: 5 residues within 4Å: Chain C: A.256, Q.257, S.260, T.440, G.481 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.257, C:S.260, C:S.260, C:R.261 EDO.6: 3 residues within 4Å: Chain C: K.80, P.87, N.88 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.80, C:K.80, C:N.88 EDO.7: 5 residues within 4Å: Chain C: I.40, G.41, N.42, I.158 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.40, C:I.158 Water bridges: C:K.39 EDO.8: 5 residues within 4Å: Chain C: Y.59, Y.120, D.186, R.187, M.188 1 PLIP interactions: 1 interactions with chain C Water bridges: C:M.188 EDO.9: 5 residues within 4Å: Chain B: A.3 Chain C: K.124, T.189, A.190, G.191 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.189, C:A.190, C:G.191 Water bridges: C:L.123

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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