SMTL ID : 5uta.1

Sperm whale myoglobin H64Q with nitrite

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

monomer

Ligands

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

HEM.1: 20 residues within 4Å: Chain A: T.40, K.43, F.44, R.46, Q.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: NO2.3, NO2.10, NO2.15 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:F.44, A:F.44, A:F.44, A:T.68, A:V.69, A:A.72, A:L.90, A:L.90, A:I.100, A:Y.104, A:I.108, A:F.139 Hydrogen bonds: A:S.93 Water bridges: A:P.89, A:H.98 Salt bridges: A:R.46, A:H.94, A:H.98 pi-Stacking: A:H.94, A:H.98 pi-Cation interactions: A:H.94 Metal complexes: A:H.94

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

SO4.2: 3 residues within 4Å: Chain A: T.52, E.53, A.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.53, A:A.54 SO4.11: 1 residues within 4Å: Chain A: R.32 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.32

10 x NO2: NITRITE ION(Non-covalent)

NO2.3: 5 residues within 4Å: Chain A: L.30, F.44, Q.65, V.69 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.65 NO2.4: 5 residues within 4Å: Chain A: R.32, S.36, E.110, A.111, H.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.32 Water bridges: A:E.110 NO2.5: 3 residues within 4Å: Chain A: I.31, R.32, K.35 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.32, A:R.32 Water bridges: A:R.32 NO2.6: 3 residues within 4Å: Chain A: K.141, A.144, A.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.141 NO2.7: 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 NO2.8: 6 residues within 4Å: Chain A: W.8, L.77, H.83, A.135, L.138, F.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.83, A:F.139 NO2.9: 5 residues within 4Å: Chain A: H.83, E.84, L.87, D.142, K.146 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.142 NO2.10: 8 residues within 4Å: Chain A: L.105, I.108, S.109, I.112, L.136, F.139, R.140 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) NO2.12: 3 residues within 4Å: Chain A: Q.92, S.93, K.97 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.93 NO2.15: 7 residues within 4Å: Chain A: L.90, H.94, L.105, F.139, I.143, Y.147 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.147

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 4 residues within 4Å: Chain A: A.58, S.59, E.60, D.61 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.60, A:D.61, A:D.61 GOL.14: 6 residues within 4Å: Chain A: N.123, F.124, G.125, A.126, D.127, A.128 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.125, A:A.126, A:D.127, A:A.128 Water bridges: A:P.121, A:G.122

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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