SMTL ID : 2ago.1

Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

monomer

Ligands

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

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.2: 5 residues within 4Å: Chain A: G.14 Chain C: S.103, D.105, E.106 Ligands: POP.6 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.105, H2O.2 MG.4: 2 residues within 4Å: Chain C: A.181, I.186 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:A.181, C:I.186, H2O.3, H2O.3, H2O.4 MG.5: 1 residues within 4Å: Chain C: D.294 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.294, C:D.294

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain C: D.7, F.8, D.105, K.159 Ligands: POP.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.7, C:F.8, C:D.105, POP.6

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

POP.6: 12 residues within 4Å: Chain A: G.14 Chain C: D.7, F.8, D.9, Y.10, F.11, T.45, R.51, D.105, K.159 Ligands: MG.2, CA.3 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Y.10, C:F.11 Water bridges: C:Y.12, C:T.45, C:S.103 Salt bridges: C:R.51, C:K.159, C:K.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vaisman, A. et al., Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. Embo J. (2005)

Release Date

2005-09-06

Peptides

DNA polymerase IV: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase IV

Related Entries With Identical Sequence