SMTL ID : 5ut7.1

Wild-type sperm whale myoglobin with nitrite

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: T.40, K.43, F.44, R.46, H.65, T.68, V.69, A.72, L.90, S.93, H.94, H.98, I.100, Y.104, L.105, I.108, F.139 Ligands: NO2.2 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:F.44, A:F.44, A:F.44, A:V.69, A:V.69, A:A.72, A:L.90, A:L.90, A:I.100, A:Y.104, A:L.105, A:I.108, A:F.139, A:F.139 Hydrogen bonds: A:S.93 Water bridges: A:P.89, A:S.93, A:H.98 Salt bridges: A:R.46, A:H.65, A:H.94, A:H.98 pi-Stacking: A:H.94 Metal complexes: A:H.94

7 x NO2: NITRITE ION(Non-covalent)

NO2.2: 6 residues within 4Å: Chain A: L.30, F.44, H.65, V.69, H.94 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) NO2.3: 1 residues within 4Å: Chain A: S.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.4 Water bridges: A:G.6 NO2.4: 5 residues within 4Å: Chain A: R.32, S.36, E.110, A.111, H.114 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.32 NO2.5: 5 residues within 4Å: Chain A: H.83, E.84, L.87, D.142 Ligands: GOL.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.142 NO2.8: 3 residues within 4Å: Chain A: Q.92, S.93, K.97 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.92 Water bridges: A:S.93 NO2.9: 3 residues within 4Å: Chain A: V.67, T.68, T.71 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.68 NO2.10: 2 residues within 4Å: Chain A: G.125, A.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.126 Water bridges: A:D.127

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 2 residues within 4Å: Chain A: A.16, K.17 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.17, A:K.17 Salt bridges: A:K.17 SO4.7: 2 residues within 4Å: Chain A: S.4, E.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.5 Water bridges: A:G.6 SO4.12: 1 residues within 4Å: Chain A: R.32 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.32

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 4 residues within 4Å: Chain A: H.82, H.83, E.84 Ligands: NO2.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.84, A:E.84 Water bridges: A:H.82, A:A.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, B. et al., Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets. Biochemistry (2018)

Release Date

2018-02-28

Peptides

Myoglobin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Myoglobin

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