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SMTL ID : 1qsi.1

MAGNESIUM(II)-AND ZINC(II)-PROTOPORPHYRIN IX'S STABILIZE THE LOWEST OXYGEN AFFINITY STATE OF HUMAN HEMOGLOBIN EVEN MORE STRONGLY THAN DEOXYHEME

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1:

17 residues within 4Å:

Chain A: Y.42, F.43, H.45, F.46, H.58, K.61, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136
Ligands: CMO.2

17 PLIP interactions:

17 interactions with chain A,

Hydrophobic interactions: A:Y.42, A:F.43, A:A.65, A:L.83, A:L.86, A:L.91, A:L.91, A:V.93, A:V.93, A:F.98, A:F.98, A:L.101, A:L.136
Salt bridges: A:H.45, A:H.58, A:K.61
Metal complexes: A:H.87

HEM.4:

20 residues within 4Å:

Chain C: M.32, T.39, Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136
Ligands: CMO.5

19 PLIP interactions:

18 interactions with chain C, 1 Ligand-Ligand interactions

Hydrophobic interactions: C:F.43, C:V.62, C:A.65, C:L.83, C:L.86, C:L.91, C:L.91, C:V.93, C:V.93, C:F.98, C:F.98, C:L.101, C:L.136
Water bridges: C:H.58
Salt bridges: C:H.45, C:H.58, C:K.61
Metal complexes: C:H.87, CMO.5

2 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.2:	5 residues within 4Å: Chain A: L.29, H.58, V.62, H.87 Ligands: HEM.1 No protein-ligand interaction detected (PLIP)
CMO.5:	4 residues within 4Å: Chain C: H.58, V.62, H.87 Ligands: HEM.4 No protein-ligand interaction detected (PLIP)

2 x HEG: PROTOPORPHYRIN IX CONTAINING MG(Non-covalent)

HEG.3:

16 residues within 4Å:

Chain B: L.31, F.41, F.42, H.63, K.66, V.67, A.70, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141

21 PLIP interactions:

21 interactions with chain B,

Hydrophobic interactions: B:L.31, B:F.41, B:F.41, B:F.42, B:F.42, B:F.42, B:K.66, B:K.66, B:V.67, B:L.88, B:L.88, B:L.91, B:L.96, B:V.98, B:V.98, B:F.103, B:L.106, B:L.141
Salt bridges: B:K.66
pi-Stacking: B:H.63
Metal complexes: B:H.92

HEG.6:

17 residues within 4Å:

Chain D: L.31, F.41, F.42, H.63, K.66, V.67, A.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141

17 PLIP interactions:

17 interactions with chain D,

Hydrophobic interactions: D:L.31, D:F.41, D:F.41, D:F.42, D:F.42, D:K.66, D:V.67, D:L.88, D:L.91, D:L.96, D:V.98, D:N.102, D:F.103, D:L.106, D:L.141
pi-Stacking: D:H.63
Metal complexes: D:H.92

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Miyazaki, G. et al., Magnesium(II) and zinc(II)-protoporphyrin IX's stabilize the lowest oxygen affinity state of human hemoglobin even more strongly than deoxyheme. J.Mol.Biol. (1999)

Release Date

1999-07-02

Peptides

PROTEIN (HEMOGLOBIN ALPHA CHAIN): AC
PROTEIN (HEMOGLOBIN BETA CHAIN): BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

PROTEIN (HEMOGLOBIN ALPHA CHAIN)

Toggle Identical (AC)

PROTEIN (HEMOGLOBIN BETA CHAIN)

Toggle Identical (BD)

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