SMTL ID : 3po5.1

Structure of a mutant of the large fragment of DNA polymerase I from Thermus Auqaticus in complex with an abasic site and ddATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.318, Y.319 Ligands: DDS.4 No protein-ligand interaction detected (PLIP)

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 3 residues within 4Å: Chain A: R.21, W.26, L.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.21, A:W.26 PGE.3: 7 residues within 4Å: Chain A: T.252, Y.253, P.256, P.287, N.288 Chain C: C.6, C.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.288, A:N.288

1 x DDS: 2',3'-dideoxyadenosine triphosphate(Non-covalent)

DDS.4: 9 residues within 4Å: Chain A: R.295, Q.321, H.347, K.371, F.375, Y.379, D.493 Chain B: A.12 Ligands: MG.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.295, A:Q.321, A:Q.321 Water bridges: A:R.295, A:R.295, A:K.322 Salt bridges: A:H.347, A:H.347, A:K.371, A:K.371, A:K.371

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain B: C.6, G.7, G.8 Chain C: C.6 No protein-ligand interaction detected (PLIP)

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

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