SMTL ID : 8xbj.1

The X-ray structure of F46C myoglobin with a covalently linked Ni-complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

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

HEM.1: 16 residues within 4Å: Chain A: T.39, K.42, F.43, H.64, T.67, V.68, A.71, L.89, S.92, H.93, H.97, I.99, Y.103, L.104, I.107, F.138 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:F.43, A:T.67, A:V.68, A:A.71, A:L.89, A:L.89, A:I.99, A:I.99, A:Y.103, A:L.104, A:I.107, A:F.138 Hydrogen bonds: A:S.92 Water bridges: A:H.97 Salt bridges: A:H.64, A:H.93, A:H.97 pi-Stacking: A:H.97 Metal complexes: A:H.93, H2O.3

2 x Y6C: 4-oxidanylidene-4-(1,10-phenanthrolin-5-ylamino)but-2-enoic acid(Covalent)

Y6C.2: 9 residues within 4Å: Chain A: F.43, D.44, R.45, C.46, K.50, D.60, H.64 Ligands: Y6C.3, NI.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.43, A:F.43, A:D.44 Hydrogen bonds: A:R.45 Water bridges: A:D.44 Salt bridges: A:K.50 Y6C.3: 7 residues within 4Å: Chain A: R.45, C.46, H.48, L.49, K.50, E.54 Ligands: Y6C.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:H.48, A:K.50 Hydrogen bonds: A:H.48 Salt bridges: A:K.50 pi-Stacking: A:H.48

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

NI.4: 3 residues within 4Å: Chain A: D.60, H.64 Ligands: Y6C.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.60, A:H.64, H2O.1, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, Y.W. et al., The X-ray structure of F46C myoglobin with a covalently linked Ni-complex. To Be Published

Release Date

2024-12-11

Peptides

Myoglobin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Myoglobin

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