SMTL ID : 2w72.1

DEOXYGENATED STRUCTURE OF A DISTAL SITE HEMOGLOBIN MUTANT PLUS XE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.07 Å

Oligo State

hetero-1-2-1-mer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: Y.29, M.32, Y.42, F.43, F.46, Q.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: XE.9 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:Y.42, A:F.43, A:K.61, A:V.62, A:V.62, A:L.83, A:L.86, A:L.91, A:L.91, A:V.93, A:V.93, A:N.97, A:F.98, A:L.101, A:L.101, A:L.136 Water bridges: A:Q.58, A:K.61 Salt bridges: A:K.61, A:K.61 Metal complexes: A:H.87 HEM.12: 17 residues within 4Å: Chain B: Y.28, F.41, F.42, F.45, Q.63, K.66, V.67, A.70, F.85, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: XE.16 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:F.41, B:F.41, B:F.42, B:F.42, B:F.42, B:V.67, B:F.85, B:L.96, B:L.96, B:V.98, B:V.98, B:L.141 Water bridges: B:K.66, B:K.95, B:K.95 pi-Stacking: B:Y.28 Metal complexes: B:H.92 HEM.18: 20 residues within 4Å: Chain C: Y.29, M.32, Y.42, F.43, H.45, F.46, Q.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: XE.26 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:F.43, C:F.43, C:K.61, C:V.62, 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:L.101, C:L.101, C:L.136 Water bridges: C:K.61 Salt bridges: C:H.45, C:K.61, C:K.61 Metal complexes: C:H.87 HEM.28: 19 residues within 4Å: Chain D: Y.28, F.41, F.42, Q.63, K.66, V.67, A.70, F.71, F.85, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: XE.30 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:F.41, D:F.41, D:F.42, D:K.66, D:K.66, D:V.67, D:F.71, D:F.85, D:L.88, D:L.91, D:L.96, D:L.96, D:V.98, D:V.98, D:F.103, D:L.106, D:L.141 Water bridges: D:K.66 Salt bridges: D:K.66 pi-Stacking: D:Y.28 Metal complexes: D:H.92

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

SO4.2: 2 residues within 4Å: Chain A: F.36, L.100 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Water bridges: A:T.38, A:T.38, A:T.38, D:R.104 SO4.3: 5 residues within 4Å: Chain A: K.16, L.113, P.114, A.115, E.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.115, A:E.116 Salt bridges: A:K.16 SO4.4: 4 residues within 4Å: Chain A: A.5, N.9, A.120 Chain B: P.51 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.9 Water bridges: A:N.9 SO4.13: 6 residues within 4Å: Chain B: M.1, L.78, D.79, N.80, L.81, K.82 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.1, B:L.81, B:K.82 Water bridges: B:N.80 SO4.14: 3 residues within 4Å: Chain B: E.26, H.116, H.117 4 PLIP interactions: 4 interactions with chain B Water bridges: B:E.26, B:H.116 Salt bridges: B:H.116, B:H.117 SO4.19: 3 residues within 4Å: Chain C: F.36, P.37, T.38 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.38 SO4.20: 4 residues within 4Å: Chain A: R.141 Chain C: M.1, K.127, A.130 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:M.1 Water bridges: C:S.131 Salt bridges: A:R.141 SO4.29: 5 residues within 4Å: Chain C: P.119 Chain D: E.26, R.30, M.55, H.116 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.26 Water bridges: D:E.26, D:R.30, D:R.30 Salt bridges: D:R.30, D:H.116

15 x XE: XENON(Non-covalent)(Covalent)

XE.5: 2 residues within 4Å: Chain A: W.14, F.128 No protein-ligand interaction detected (PLIP) XE.6: 4 residues within 4Å: Chain A: W.14, A.21, G.25, L.105 No protein-ligand interaction detected (PLIP) XE.7: 6 residues within 4Å: Chain A: F.43, F.46, L.48, Q.54, V.55, Q.58 No protein-ligand interaction detected (PLIP) XE.8: 2 residues within 4Å: Chain A: A.28, V.62 No protein-ligand interaction detected (PLIP) XE.9: 4 residues within 4Å: Chain A: L.101, S.102, L.129 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) XE.10: 3 residues within 4Å: Chain A: A.13, L.113, E.116 No protein-ligand interaction detected (PLIP) XE.16: 3 residues within 4Å: Chain B: F.103, V.134 Ligands: HEM.12 No protein-ligand interaction detected (PLIP) XE.17: 6 residues within 4Å: Chain B: G.24, Y.28, G.64, V.67, L.68, L.106 No protein-ligand interaction detected (PLIP) XE.23: 2 residues within 4Å: Chain C: W.14, F.128 No protein-ligand interaction detected (PLIP) XE.24: 5 residues within 4Å: Chain C: F.43, F.46, Q.54, V.55, Q.58 No protein-ligand interaction detected (PLIP) XE.25: 5 residues within 4Å: Chain C: A.28, V.62, L.101, L.105 Ligands: XE.26 No protein-ligand interaction detected (PLIP) XE.26: 4 residues within 4Å: Chain C: L.101, L.129 Ligands: HEM.18, XE.25 No protein-ligand interaction detected (PLIP) XE.27: 2 residues within 4Å: Chain C: A.13, E.116 No protein-ligand interaction detected (PLIP) XE.30: 4 residues within 4Å: Chain D: F.103, G.107, V.134 Ligands: HEM.28 No protein-ligand interaction detected (PLIP) XE.31: 6 residues within 4Å: Chain D: G.24, A.27, Y.28, V.67, L.68, L.106 No protein-ligand interaction detected (PLIP)

3 x K: POTASSIUM ION(Non-covalent)

K.11: 1 residues within 4Å: Chain D: W.37 No protein-ligand interaction detected (PLIP) K.15: 3 residues within 4Å: Chain B: A.62, K.65, K.66 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.62, H2O.9 K.22: 3 residues within 4Å: Chain C: L.100, H.103 Chain D: N.108 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.21: 2 residues within 4Å: Chain A: A.130 Chain C: R.141 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Water bridges: C:T.137, C:S.138, C:R.141, C:R.141, C:R.141, C:R.141, A:K.127 Salt bridges: C:R.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Savino, C. et al., Pattern of Cavities in Globins: The Case of Human Hemoglobin. Biopolymers (2009)

Release Date

2009-04-28

Peptides

HUMAN HEMOGLOBIN A: A
HUMAN HEMOGLOBIN A: BD
HUMAN HEMOGLOBIN A: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

HUMAN HEMOGLOBIN A

HUMAN HEMOGLOBIN A

HUMAN HEMOGLOBIN A

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