SMTL ID : 1d5a.1

CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK. DEPOSITION OF SECOND NATIVE STRUCTURE AT 2.4 ANGSTROM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: P.94, R.97, D.113 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.97 SO4.2: 5 residues within 4Å: Chain A: Y.7, P.90, Q.91, P.115, F.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.7, A:Q.91, A:F.116 SO4.3: 3 residues within 4Å: Chain A: G.131, R.335, R.482 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.131 Water bridges: A:R.335 Salt bridges: A:R.335, A:R.482 SO4.4: 6 residues within 4Å: Chain A: Y.405, K.406, S.407, K.487, N.491 Ligands: SO4.9 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.405, A:S.407, A:N.491 Water bridges: A:L.408, A:L.408 Salt bridges: A:K.406, A:K.487 SO4.5: 6 residues within 4Å: Chain A: Y.402, F.545, E.580, Y.583, Y.594, T.604 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.594 SO4.6: 1 residues within 4Å: Chain A: K.188 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.188 Salt bridges: A:K.188 SO4.7: 2 residues within 4Å: Chain A: K.464, K.468 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Q.461, A:K.468, A:K.468 Salt bridges: A:K.464, A:K.468 SO4.8: 2 residues within 4Å: Chain A: E.609, Q.623 No protein-ligand interaction detected (PLIP) SO4.9: 5 residues within 4Å: Chain A: K.406, R.460, K.464, K.487 Ligands: SO4.4 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.464 Salt bridges: A:K.406, A:R.460, A:K.464, A:K.487

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 5 residues within 4Å: Chain A: D.141, I.142, E.143, D.315 Ligands: MG.11 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.141, A:D.315 MG.11: 2 residues within 4Å: Chain A: D.141 Ligands: MG.10 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Crystal structure of an archaebacterial DNA polymerase. Structure Fold.Des. (1999)

Release Date

2000-03-24

Peptides

PROTEIN (DNA POLYMERASE): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PROTEIN (DNA POLYMERASE)