SMTL ID : 3py8.1

Crystal structure of a mutant of the large fragment of DNA polymerase I from thermus aquaticus in a closed ternary complex with DNA and ddCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

1 x DCT: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE(Non-covalent)

DCT.1: 17 residues within 4Å: Chain A: R.281, D.318, Y.319, S.320, Q.321, K.322, E.323, H.347, R.367, K.371, F.375, D.493 Chain B: C.12 Chain C: G.4, G.5 Ligands: MN.3, MG.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:E.323, A:F.375, A:F.375 Hydrogen bonds: A:R.281, A:Q.321, A:K.322 Water bridges: A:R.367, A:R.367, A:K.371, A:K.371, A:K.371, A:K.371 Salt bridges: A:H.347, A:R.367, A:K.371, A:K.371, A:K.371

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: T.252, Y.253, P.256, P.287, N.288, N.291 Chain C: C.9, C.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.288, A:N.291 Water bridges: A:Y.253, A:D.286 GOL.7: 1 residues within 4Å: Chain A: E.140 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.140

5 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.3: 5 residues within 4Å: Chain A: D.318, Y.319, D.493 Ligands: DCT.1, MG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493 MN.5: 2 residues within 4Å: Chain A: E.170, E.173 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.170, A:E.173, H2O.5, H2O.7, H2O.12 MN.6: 1 residues within 4Å: Chain A: H.151 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.151, H2O.8, H2O.9, H2O.9, H2O.13 MN.8: 1 residues within 4Å: Chain B: G.7 No protein-ligand interaction detected (PLIP) MN.9: 1 residues within 4Å: Chain C: G.5 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: D.318, D.493 Chain B: C.12 Ligands: DCT.1, MN.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:D.493, H2O.7, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Obeid, S. et al., Learning from Directed Evolution: Thermus aquaticus DNA Polymerase Mutants with Translesion Synthesis Activity. Chembiochem (2011)

Release Date

2011-06-15

Peptides

DNA polymerase I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I

Related Entries With Identical Sequence