SMTL ID : 6kns.1 (3 other biounits)

Crystal structure of the metallo-beta-lactamase fold protein YhfI from Bacillus subtilis (space group I4122)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 1 residues within 4Å: Chain A: E.238 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.238, A:E.238, H2O.2 CA.2: 3 residues within 4Å: Chain A: D.34, K.57, D.59 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.34, A:K.57, A:D.59, H2O.1 CA.5: 1 residues within 4Å: Chain B: E.238 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.238, B:E.238, H2O.6 CA.6: 3 residues within 4Å: Chain B: D.34, K.57, D.59 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.34, B:K.57, B:D.59, H2O.5

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: H.65, D.69, H.70, D.161, H.217 Ligands: ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.69, A:H.70, A:D.161, A:H.217 ZN.4: 5 residues within 4Å: Chain A: H.65, H.67, H.140, D.161 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.65, A:H.67, A:H.140, A:D.161 ZN.7: 6 residues within 4Å: Chain B: H.65, D.69, H.70, D.161, H.217 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.69, B:H.70, B:D.161, B:H.217 ZN.8: 5 residues within 4Å: Chain B: H.65, H.67, H.140, D.161 Ligands: ZN.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.65, B:H.67, B:H.140, B:D.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Na, H.W. et al., Structural and biochemical analyses of the metallo-beta-lactamase fold protein YhfI from Bacillus subtilis. Biochem.Biophys.Res.Commun. (2019)

Release Date

2019-09-18

Peptides

Putative metal-dependent hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Putative metal-dependent hydrolase

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