SMTL ID : 4r8z.1

Crystal Structure of PA4781 HD-GYP domain from Pseudomonas aeruginosa at 2.2A resolution showing a bi-metallic Ni ion center

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

4 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 3 residues within 4Å: Chain A: H.30, H.70, D.71 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.30, A:H.70, A:D.71, H2O.1, H2O.1, H2O.1 NI.2: 4 residues within 4Å: Chain A: D.71, H.99, H.131, H.132 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.71, A:H.99, A:H.131, A:H.132, H2O.1, H2O.1 NI.4: 4 residues within 4Å: Chain B: D.71, H.99, H.131, H.132 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.71, B:H.99, B:H.131, B:H.132, H2O.4, H2O.4 NI.5: 3 residues within 4Å: Chain B: H.30, H.70, D.71 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.30, B:H.70, B:D.71, H2O.5, H2O.5, H2O.5

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: V.210, R.213 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain B: R.213 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rinaldo, S. et al., Structural basis of functional diversification of the HD-GYP domain revealed by the Pseudomonas aeruginosa PA4781 protein, which displays an unselective bimetallic binding site. J.Bacteriol. (2015)

Release Date

2015-03-04

Peptides

Cyclic di-GMP phosphodiesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cyclic di-GMP phosphodiesterase