SMTL ID : 3pt7.1

Structure of HbII-III-Oxy from Lucina pectinata at pH 5.0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

2 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 23 PLIP interactions: 19 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:T.41, A:P.44, A:P.44, A:F.45, A:F.45, A:V.69, A:F.70, A:I.103, A:L.108, A:A.111, A:Y.112, A:Y.112 Water bridges: A:L.48, A:M.94, A:H.98, B:K.96, B:K.96 Salt bridges: A:H.98, A:R.101, B:K.93, B:K.96 pi-Cation interactions: A:R.101 Metal complexes: A:H.98 HEM.3: 20 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, E.107, L.108, G.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:I.103, B:L.108, B:Y.112 Water bridges: B:S.47, B:L.48, B:H.98, A:K.96, A:K.96 Salt bridges: B:H.98, B:R.101, A:K.93, A:K.96 Metal complexes: B:H.98

2 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.31, A:Q.66 OXY.4: 4 residues within 4Å: Chain B: Y.31, F.45, Q.66 Ligands: HEM.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.31, B:Q.66

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain B: Q.92, K.96, F.147 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.92, A:S.47, A:K.62 Water bridges: B:K.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruiz-Martinez, C.R. et al., New Crystallographic Structure of HbII-III-Oxy and CN forms from Lucina pectinata. To be Published

Release Date

2011-12-07

Peptides

Hemoglobin II: A
Hemoglobin III: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hemoglobin II

Hemoglobin III

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