SMTL ID : 3po4.1

Structure of a mutant of the large fragment of DNA polymerase I from Thermus aquaticus in complex with a blunt-ended DNA and ddATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 2 residues within 4Å: Chain A: D.318 Ligands: DDS.4 No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain A: E.494 Chain B: A.12 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 1 residues within 4Å: Chain A: E.215 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.215

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: W.136, F.432, Y.519 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.519, A:Y.519 Water bridges: A:R.133

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

DDS.4: 10 residues within 4Å: Chain A: R.295, Q.321, H.347, R.367, K.371, F.375, Y.379, D.493 Chain B: A.12 Ligands: MG.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.375 Hydrogen bonds: A:Q.321, A:Q.321 Water bridges: A:R.295, A:R.295, A:R.295, A:R.295, A:K.322, A:K.371, A:K.371, A:D.493, A:E.528 Salt bridges: A:H.347, A:H.347, A:R.367, A:K.371, A:K.371, A:K.371 pi-Stacking: A:F.375, A:F.375

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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