SMTL ID : 4dsk.1

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with duplex DNA, PPi and Calcium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

monomer

Ligands

4 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: G.14 Ligands: POP.2, CA.3 2 PLIP interactions: 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.1, POP.2 CA.3: 5 residues within 4Å: Chain A: G.14 Chain C: D.533, E.534 Ligands: CA.1, POP.2 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.533, C:E.534, POP.2 CA.4: 2 residues within 4Å: Chain C: L.561, V.563 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:L.561, H2O.5, H2O.7, H2O.8, H2O.12 CA.5: 2 residues within 4Å: Chain C: D.57, Q.59 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.57, H2O.2, H2O.11

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.2: 6 residues within 4Å: Chain A: G.14 Chain C: D.356, Y.357, D.533 Ligands: CA.1, CA.3 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.356

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gan, J.H. et al., Biochemical and structural insights into the fidelity of bacillus stearothermophilus DNA polymerase. To be Published

Release Date

2013-03-27

Peptides

DNA polymerase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase

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