SMTL ID : 2vry.1 (1 other biounit)

Mouse Neuroglobin with heme iron in the reduced ferrous state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-hexamer

Ligands

6 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 15 residues within 4Å: Chain A: L.34, L.44, F.45, Y.47, H.67, K.70, V.71, V.74, Y.91, L.95, H.99, V.102, V.104, F.109, V.112 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:L.34, A:F.45, A:F.45, A:K.70, A:K.70, A:V.71, A:V.74, A:V.74, A:V.74, A:L.95, A:V.102, A:V.104, A:V.104, A:F.109, A:V.112, A:V.112 Hydrogen bonds: A:Y.47 Water bridges: A:K.70, A:K.70 Salt bridges: A:K.70, A:K.98 pi-Stacking: A:H.67 Metal complexes: A:H.67, A:H.99 HEM.4: 15 residues within 4Å: Chain B: L.34, L.44, F.45, Y.47, H.67, K.70, V.71, V.74, Y.91, L.95, H.99, V.102, V.104, F.109, V.112 24 PLIP interactions: 24 interactions with chain B, Hydrophobic interactions: B:L.34, B:F.45, B:F.45, B:K.70, B:K.70, B:V.71, B:V.74, B:V.74, B:V.74, B:L.95, B:V.102, B:V.104, B:V.104, B:F.109, B:V.112, B:V.112 Hydrogen bonds: B:Y.47 Water bridges: B:K.70, B:K.70 Salt bridges: B:K.70, B:K.98 pi-Stacking: B:H.67 Metal complexes: B:H.67, B:H.99 HEM.7: 15 residues within 4Å: Chain C: L.34, L.44, F.45, Y.47, H.67, K.70, V.71, V.74, Y.91, L.95, H.99, V.102, V.104, F.109, V.112 24 PLIP interactions: 24 interactions with chain C, Hydrophobic interactions: C:L.34, C:F.45, C:F.45, C:K.70, C:K.70, C:V.71, C:V.74, C:V.74, C:V.74, C:L.95, C:V.102, C:V.104, C:V.104, C:F.109, C:V.112, C:V.112 Hydrogen bonds: C:Y.47 Water bridges: C:K.70, C:K.70 Salt bridges: C:K.70, C:K.98 pi-Stacking: C:H.67 Metal complexes: C:H.67, C:H.99 HEM.10: 15 residues within 4Å: Chain D: L.34, L.44, F.45, Y.47, H.67, K.70, V.71, V.74, Y.91, L.95, H.99, V.102, V.104, F.109, V.112 25 PLIP interactions: 25 interactions with chain D, Hydrophobic interactions: D:L.34, D:F.45, D:F.45, D:K.70, D:K.70, D:V.71, D:V.74, D:V.74, D:V.74, D:L.95, D:V.102, D:V.104, D:V.104, D:F.109, D:V.112, D:V.112 Hydrogen bonds: D:Y.47, D:Y.47 Water bridges: D:K.70, D:K.70 Salt bridges: D:K.70, D:K.98 pi-Stacking: D:H.67 Metal complexes: D:H.67, D:H.99 HEM.13: 15 residues within 4Å: Chain E: L.34, L.44, F.45, Y.47, H.67, K.70, V.71, V.74, Y.91, L.95, H.99, V.102, V.104, F.109, V.112 25 PLIP interactions: 25 interactions with chain E, Hydrophobic interactions: E:L.34, E:F.45, E:F.45, E:K.70, E:K.70, E:V.71, E:V.74, E:V.74, E:V.74, E:L.95, E:V.102, E:V.104, E:V.104, E:F.109, E:V.112, E:V.112 Hydrogen bonds: E:Y.47, E:Y.47 Water bridges: E:K.70, E:K.70 Salt bridges: E:K.70, E:K.98 pi-Stacking: E:H.67 Metal complexes: E:H.67, E:H.99 HEM.16: 15 residues within 4Å: Chain F: L.34, L.44, F.45, Y.47, H.67, K.70, V.71, V.74, Y.91, L.95, H.99, V.102, V.104, F.109, V.112 25 PLIP interactions: 25 interactions with chain F, Hydrophobic interactions: F:L.34, F:F.45, F:F.45, F:K.70, F:K.70, F:V.71, F:V.74, F:V.74, F:V.74, F:L.95, F:V.102, F:V.104, F:V.104, F:F.109, F:V.112, F:V.112 Hydrogen bonds: F:Y.47, F:Y.47 Water bridges: F:K.70, F:K.70 Salt bridges: F:K.70, F:K.98 pi-Stacking: F:H.67 Metal complexes: F:H.67, F:H.99

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

SO4.2: 5 residues within 4Å: Chain A: S.22, P.23, L.24, E.25, R.69 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:L.24, A:E.25 Water bridges: A:E.25, A:E.25, E:E.25, E:E.25 Salt bridges: A:R.69 SO4.3: 6 residues within 4Å: Chain A: L.24, P.62, L.65, D.66, R.69 Chain E: E.25 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.69 SO4.5: 5 residues within 4Å: Chain B: S.22, P.23, L.24, E.25, R.69 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:L.24, B:E.25 Water bridges: B:E.25, B:E.25, D:E.25, D:E.25 Salt bridges: B:R.69 SO4.6: 6 residues within 4Å: Chain B: L.24, P.62, L.65, D.66, R.69 Chain D: E.25 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.69 SO4.8: 5 residues within 4Å: Chain C: S.22, P.23, L.24, E.25, R.69 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:L.24, C:E.25 Water bridges: C:E.25, C:E.25, F:E.25, F:E.25 Salt bridges: C:R.69 SO4.9: 6 residues within 4Å: Chain C: L.24, P.62, L.65, D.66, R.69 Chain F: E.25 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.69 SO4.11: 5 residues within 4Å: Chain D: S.22, P.23, L.24, E.25, R.69 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:L.24, D:E.25, D:E.25 Water bridges: D:E.25, D:E.25, B:E.25, B:E.25 Salt bridges: D:R.69 SO4.12: 6 residues within 4Å: Chain B: E.25 Chain D: L.24, P.62, L.65, D.66, R.69 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.66 Salt bridges: D:R.69 SO4.14: 5 residues within 4Å: Chain E: S.22, P.23, L.24, E.25, R.69 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:L.24, E:E.25, E:E.25 Water bridges: E:E.25, E:E.25, A:E.25, A:E.25 Salt bridges: E:R.69 SO4.15: 6 residues within 4Å: Chain A: E.25 Chain E: L.24, P.62, L.65, D.66, R.69 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.66 Salt bridges: E:R.69 SO4.17: 5 residues within 4Å: Chain F: S.22, P.23, L.24, E.25, R.69 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain F Water bridges: C:E.25, C:E.25, F:E.25, F:E.25 Hydrogen bonds: F:L.24, F:E.25, F:E.25 Salt bridges: F:R.69 SO4.18: 6 residues within 4Å: Chain C: E.25 Chain F: L.24, P.62, L.65, D.66, R.69 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.66 Salt bridges: F:R.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arcovito, A. et al., An X-Ray Diffraction and X-Ray Absorption Spectroscopy Joint Study of Neuroglobin. Arch.Biochem.Biophys. (2008)

Release Date

2008-05-06

Peptides

NEUROGLOBIN: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

NEUROGLOBIN

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