SMTL ID : 7dgl.1

The Ni-bound dimeric structure of K78H/G80A/H82A myoglobin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 19 residues within 4Å: Chain A: L.89, S.92, H.93, H.97, I.99, Y.103, L.104, I.107, F.138 Chain B: T.39, K.42, F.43, K.45, H.64, V.67, V.68, A.71, L.72 Ligands: O.4 22 PLIP interactions: 8 interactions with chain B, 13 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:F.43, B:F.43, B:F.43, B:V.67, B:V.68, B:A.71, A:L.89, A:I.99, A:I.99, A:Y.103, A:L.104, A:I.107, A:F.138 Water bridges: B:H.64, A:P.88 Salt bridges: B:K.45, A:H.93, A:H.97 Hydrogen bonds: A:S.92 pi-Stacking: A:H.97 Metal complexes: A:H.93, O.4 HEM.5: 19 residues within 4Å: Chain A: T.39, K.42, F.43, K.45, H.64, V.67, V.68, A.71, L.72 Chain B: L.89, S.92, H.93, H.97, I.99, Y.103, L.104, I.107, F.138 Ligands: O.2 20 PLIP interactions: 8 interactions with chain A, 11 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.43, A:F.43, A:F.43, A:V.67, A:V.68, A:A.71, A:L.72, B:L.89, B:H.97, B:I.99, B:Y.103, B:I.107, B:F.138 Salt bridges: A:K.45, B:H.93, B:H.97 Hydrogen bonds: B:S.92 pi-Stacking: B:H.97 Metal complexes: B:H.93, O.2

2 x O: OXYGEN ATOM(Non-covalent)

O.2: 4 residues within 4Å: Chain A: H.64, V.68 Chain B: H.93 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.64 O.4: 5 residues within 4Å: Chain A: H.93 Chain B: F.43, H.64, V.68 Ligands: HEM.1 No protein-ligand interaction detected (PLIP)

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

NI.3: 3 residues within 4Å: Chain A: H.81, E.85 Chain B: H.78 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.81, A:E.85, B:H.78, H2O.2, H2O.4, H2O.5 NI.6: 3 residues within 4Å: Chain A: H.78 Chain B: H.81, E.85 6 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:H.81, B:E.85, A:H.78, H2O.4, H2O.4, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagao, S. et al., Rational design of metal-binding sites in domain-swapped myoglobin dimers. J.Inorg.Biochem. (2021)

Release Date

2021-02-17

Peptides

Myoglobin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Myoglobin

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