SMTL ID : 8drl.1

Zn(II)-bound B2 dimer (H60/H100/H104) formed in Cu(II)//Zn(II) (M1 // M2) condition

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 17 residues within 4Å: Chain A: L.3, E.4, M.7, E.8, L.10, N.11, M.33, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, R.106 Ligands: ZN.4 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:L.3, A:M.7, A:L.10, A:N.11, A:F.61, A:F.65, A:F.65, A:F.65, A:L.68, A:R.106 Metal complexes: A:H.102 HEC.5: 17 residues within 4Å: Chain B: L.3, E.4, M.7, E.8, L.10, N.11, M.33, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, R.106 Ligands: ZN.8 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:L.3, B:M.7, B:L.10, B:N.11, B:F.61, B:F.65, B:F.65, B:F.65, B:L.68, B:R.106 Metal complexes: B:H.102

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.60, H.100 Chain B: H.60, H.100 Ligands: ZN.6 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.60, A:H.60, H2O.4, H2O.9 ZN.3: 5 residues within 4Å: Chain A: H.63 Chain B: E.57, H.60, H.104, Y.105 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Metal complexes: B:E.57, B:E.57, B:H.60, B:H.104, A:H.63 ZN.4: 3 residues within 4Å: Chain A: E.4, E.8 Ligands: HEC.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.4, A:E.8 ZN.6: 5 residues within 4Å: Chain A: H.60, H.100 Chain B: H.60, H.100 Ligands: ZN.2 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.60, A:H.60, H2O.4, H2O.9 ZN.7: 5 residues within 4Å: Chain A: E.57, H.60, H.104, Y.105 Chain B: H.63 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Metal complexes: B:H.63, A:E.57, A:E.57, A:H.60, A:H.104 ZN.8: 3 residues within 4Å: Chain B: E.4, E.8 Ligands: HEC.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.4, B:E.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choi, T.S. et al., Design of a Flexible, Zn-Selective Protein Scaffold that Displays Anti-Irving-Williams Behavior. J.Am.Chem.Soc. (2022)

Release Date

2022-10-12

Peptides

Soluble cytochrome b562: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Soluble cytochrome b562

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