SMTL ID : 7lrv.1

Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in the presence of Ni(II)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 18 residues within 4Å: Chain A: L.3, E.4, M.7, L.10, N.11, M.33, P.45, P.46, F.61, G.64, F.65, L.68, H.97, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:L.3, A:M.7, A:L.10, A:L.10, A:N.11, A:P.45, A:F.61, A:F.65, A:F.65, A:F.65, A:L.68 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEC.3: 16 residues within 4Å: Chain B: L.3, E.4, M.7, L.10, N.11, M.33, P.45, P.46, F.61, G.64, F.65, H.97, C.98, C.101, H.102, R.106 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:M.7, B:P.45, B:F.61, B:F.65, B:F.65, B:F.65 Hydrogen bonds: B:E.4 pi-Stacking: B:H.102 pi-Cation interactions: B:R.106 Metal complexes: B:H.102

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

NI.2: 5 residues within 4Å: Chain A: H.60, H.100, H.104 Chain B: H.67, H.71 6 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.60, A:H.100, A:H.104, B:H.67, B:H.71, H2O.8 NI.4: 5 residues within 4Å: Chain A: H.67, H.71 Chain B: H.60, H.100, H.104 6 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.60, B:H.100, B:H.104, A:H.67, A:H.71, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choi, T.S. et al., Structure-guided metal selectivity in malleable protein interfacemediated by single disulfide bond. To Be Published

Release Date

2022-02-23

Peptides

Soluble cytochrome b562: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

Soluble cytochrome b562

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