SMTL ID : 7bz3.1

The mutant variant of PNGM-1. H257 was substituted for alanine to study substrate binding.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.94, H.95, D.209, H.278 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.94, A:H.95, A:D.209, A:H.278, H2O.1 ZN.2: 6 residues within 4Å: Chain A: H.90, H.92, H.95, H.187, D.209 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.90, A:H.92, A:H.187, A:D.209, H2O.1 ZN.3: 5 residues within 4Å: Chain B: D.94, H.95, D.209, H.278 Ligands: ZN.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.94, B:H.95, B:D.209, B:H.278, H2O.10 ZN.4: 5 residues within 4Å: Chain B: H.90, H.92, H.187, D.209 Ligands: ZN.3 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.90, B:H.92, B:H.187, B:D.209, H2O.10 ZN.5: 5 residues within 4Å: Chain C: D.94, H.95, D.209, H.278 Ligands: ZN.6 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.94, C:H.95, C:D.209, C:H.278, H2O.21 ZN.6: 6 residues within 4Å: Chain C: H.90, H.92, H.95, H.187, D.209 Ligands: ZN.5 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.90, C:H.92, C:H.187, C:D.209, H2O.21 ZN.7: 5 residues within 4Å: Chain D: D.94, H.95, D.209, H.278 Ligands: ZN.8 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.94, D:H.95, D:D.209, D:H.278, H2O.28 ZN.8: 6 residues within 4Å: Chain D: H.90, H.92, H.95, H.187, D.209 Ligands: ZN.7 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.90, D:H.92, D:H.187, D:D.209, H2O.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, Y.S. et al., Structural Study of Metal Binding and Coordination in Ancient Metallo-beta-Lactamase PNGM-1 Variants. Int J Mol Sci (2020)

Release Date

2021-04-28

Peptides

Metallo-beta-lactamase PNGM-1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Metallo-beta-lactamase PNGM-1