SMTL ID : 6ck1.1

Crystal structure of Paracoccus denitrificans AztD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.124, H.167, H.218 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.124, A:H.167, A:H.218, H2O.8 ZN.2: 4 residues within 4Å: Chain A: H.99, H.102, D.104, H.408 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.102, A:D.104, A:D.104, A:H.408 ZN.3: 3 residues within 4Å: Chain B: H.124, H.167, H.218 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.124, B:H.167, B:H.218, H2O.16 ZN.4: 4 residues within 4Å: Chain B: H.99, H.102, D.104, H.408 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.102, B:D.104, B:H.408 ZN.5: 3 residues within 4Å: Chain C: H.124, H.167, H.218 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.124, C:H.167, C:H.218, H2O.24 ZN.6: 2 residues within 4Å: Chain C: D.104, H.408 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.104, C:D.104, C:H.408 ZN.8: 4 residues within 4Å: Chain D: H.99, H.102, D.104, H.408 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.99, D:H.102, D:D.104, D:D.104, D:H.408 ZN.9: 3 residues within 4Å: Chain D: H.124, H.167, H.218 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.124, D:H.167, D:H.218, H2O.32

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 5 residues within 4Å: Chain C: G.209, N.210, L.211, A.212, Y.247 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neupane, D.P. et al., Crystal structures of AztD provide mechanistic insights into direct zinc transfer between proteins. Commun Biol (2019)

Release Date

2019-03-06

Peptides

A1B2F4 protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
D

A1B2F4 protein