SMTL ID : 3pi3.2 (2 other biounits)

Crystallographic Structure of HbII-oxy from Lucina pectinata at pH 5.0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 20 residues within 4Å: Chain A: T.41, P.44, F.45, L.48, Q.66, V.69, F.70, M.74, M.94, L.97, H.98, R.101, I.103, D.107, L.108, A.111, Y.112 Chain B: K.93, L.97 Ligands: OXY.2 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:P.44, A:F.45, A:F.45, A:F.45, A:V.69, A:F.70, A:I.103, A:L.108, A:Y.112, A:Y.112 Water bridges: A:L.48, A:H.98, B:K.96, B:K.96 Salt bridges: A:H.98, A:R.101, B:K.93, B:K.96 pi-Stacking: A:F.70 Metal complexes: A:H.98 HEM.3: 19 residues within 4Å: Chain A: K.93, L.97 Chain B: T.41, P.44, F.45, L.48, Q.66, V.69, F.70, M.74, M.94, L.97, H.98, R.101, I.103, L.108, A.111, Y.112 Ligands: OXY.4 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:T.41, B:P.44, B:P.44, B:F.45, B:F.45, B:F.45, B:V.69, B:F.70, B:F.70, B:I.103, B:Y.112 Hydrogen bonds: B:L.48 Water bridges: B:H.98, A:K.96, A:K.96 Salt bridges: B:H.98, B:R.101, A:K.93, A:K.96 pi-Cation interactions: B:R.101 Metal complexes: B:H.98 HEM.5: 20 residues within 4Å: Chain C: T.41, P.44, F.45, L.48, Q.66, V.69, F.70, M.74, M.94, L.97, H.98, R.101, I.103, D.107, L.108, A.111, Y.112 Chain D: K.93, L.97 Ligands: OXY.6 20 PLIP interactions: 16 interactions with chain C, 4 interactions with chain D, Hydrophobic interactions: C:P.44, C:F.45, C:F.45, C:F.45, C:V.69, C:F.70, C:I.103, C:L.108, C:Y.112, C:Y.112 Water bridges: C:L.48, C:H.98, D:K.96, D:K.96 Salt bridges: C:H.98, C:R.101, D:K.93, D:K.96 pi-Stacking: C:F.70 Metal complexes: C:H.98 HEM.7: 19 residues within 4Å: Chain C: K.93, L.97 Chain D: T.41, P.44, F.45, L.48, Q.66, V.69, F.70, M.74, M.94, L.97, H.98, R.101, I.103, L.108, A.111, Y.112 Ligands: OXY.8 21 PLIP interactions: 17 interactions with chain D, 4 interactions with chain C, Hydrophobic interactions: D:T.41, D:P.44, D:P.44, D:F.45, D:F.45, D:F.45, D:V.69, D:F.70, D:F.70, D:I.103, D:Y.112 Hydrogen bonds: D:L.48 Water bridges: D:H.98, C:K.96, C:K.96 Salt bridges: D:H.98, D:R.101, C:K.93, C:K.96 pi-Cation interactions: D:R.101 Metal complexes: D:H.98

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 5 residues within 4Å: Chain A: Y.31, F.45, Q.66, F.70 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.31, A:Y.31, A:Q.66 OXY.4: 5 residues within 4Å: Chain B: Y.31, F.45, Q.66, F.70 Ligands: HEM.3 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.31, B:Y.31, B:Q.66 OXY.6: 5 residues within 4Å: Chain C: Y.31, F.45, Q.66, F.70 Ligands: HEM.5 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.31, C:Q.66 OXY.8: 5 residues within 4Å: Chain D: Y.31, F.45, Q.66, F.70 Ligands: HEM.7 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.31, D:Q.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nieves-Marrero, C.A. et al., pH-dependence crystallographic studies of the oxygen carrier hemoglobin II from Lucina pectinata. To be Published

Release Date

2011-11-09

Peptides

Hemoglobin II: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Hemoglobin II

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