SMTL ID : 3f7l.1

X-ray Crystal Structure of Alvinella pompejana Cu,Zn Superoxide Dismutase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.99 Å

Oligo State

homo-dimer

Ligands

2 x CU1: COPPER (I) ION(Non-covalent)

CU1.1: 6 residues within 4Å: Chain A: H.44, H.46, H.61, V.116, H.118 Ligands: CU.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.44, A:H.46, A:H.118 CU1.13: 6 residues within 4Å: Chain B: H.44, H.46, H.61, V.116, H.118 Ligands: CU.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.44, B:H.46, B:H.118

2 x CU: COPPER (II) ION(Non-covalent)

CU.2: 5 residues within 4Å: Chain A: H.44, H.46, H.61, H.118 Ligands: CU1.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.44, A:H.46, A:H.118, H2O.1, H2O.1 CU.14: 5 residues within 4Å: Chain B: H.44, H.46, H.61, H.118 Ligands: CU1.13 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.44, B:H.46, B:H.118, H2O.14, H2O.14

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.61, H.69, H.78, D.81 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.61, A:H.69, A:H.78, A:D.81, A:D.81 ZN.15: 4 residues within 4Å: Chain B: H.61, H.69, H.78, D.81 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.61, B:H.69, B:H.78, B:D.81, B:D.81

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: G.88, E.89, D.90, G.91, K.92 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.88, A:D.90, A:G.91, A:K.92, A:K.92 NA.16: 5 residues within 4Å: Chain B: G.88, E.89, D.90, G.91, K.92 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.88, B:D.90, B:G.91, B:K.92, B:K.92

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 3 residues within 4Å: Chain A: P.72, E.73, L.124 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.124 Hydrogen bonds: A:E.73 Water bridges: A:N.84 ACY.6: 1 residues within 4Å: Chain A: E.89 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.89 Water bridges: A:E.89 ACY.17: 3 residues within 4Å: Chain B: P.72, E.73, L.124 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.124 Hydrogen bonds: B:E.73 Water bridges: B:N.84 ACY.18: 1 residues within 4Å: Chain B: E.89 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.89 Water bridges: B:E.89

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

SO4.7: 5 residues within 4Å: Chain A: N.53, G.54, C.55, T.56, R.141 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:C.55, A:T.56 Water bridges: A:D.11, A:D.11, A:T.56, A:T.56, A:R.141 SO4.8: 3 residues within 4Å: Chain A: D.74, E.75, N.76 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.75, A:N.76 Water bridges: A:D.74, A:D.74, A:R.126, A:R.126 SO4.9: 4 residues within 4Å: Chain A: E.47, F.48, R.113 Chain B: I.149 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.47 Water bridges: A:R.113, A:R.113, A:R.113 Salt bridges: A:R.113 SO4.10: 1 residues within 4Å: Chain A: N.76 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.76 Water bridges: A:E.68, A:E.68, A:N.76, A:N.76 SO4.11: 3 residues within 4Å: Chain A: H.129, E.130 Ligands: SO4.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.130 Water bridges: A:Q.131, A:N.137 Salt bridges: A:H.129 SO4.12: 5 residues within 4Å: Chain A: H.129, E.130, Q.131, N.137 Ligands: SO4.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.130, A:Q.131 Water bridges: A:E.130, A:Q.131, A:N.137 Salt bridges: A:H.129 SO4.19: 5 residues within 4Å: Chain B: N.53, G.54, C.55, T.56, R.141 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:C.55, B:T.56, B:T.56 Water bridges: B:D.11, B:D.11, B:D.11, B:T.56, B:R.141 SO4.20: 3 residues within 4Å: Chain B: D.74, E.75, N.76 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.75, B:N.76 Water bridges: B:D.74, B:E.75, B:R.126 SO4.21: 4 residues within 4Å: Chain A: I.149 Chain B: E.47, F.48, R.113 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.113, B:R.113, B:R.113 Salt bridges: B:R.113 SO4.22: 1 residues within 4Å: Chain B: N.76 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.76 Water bridges: B:E.68, B:E.68, B:N.76, B:N.76 SO4.23: 3 residues within 4Å: Chain B: H.129, E.130 Ligands: SO4.24 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.130 Water bridges: B:Q.131, B:N.137 Salt bridges: B:H.129 SO4.24: 5 residues within 4Å: Chain B: H.129, E.130, Q.131, N.137 Ligands: SO4.23 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.130, B:Q.131 Water bridges: B:E.130, B:Q.131, B:N.137 Salt bridges: B:H.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, D.S. et al., Superoxide Dismutase from the Eukaryotic Thermophile Alvinella pompejana: Structures, Stability, Mechanism, and Insights into Amyotrophic Lateral Sclerosis. J.Mol.Biol. (2009)

Release Date

2009-02-10

Peptides

Copper,Zinc Superoxide Dismutase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Copper,Zinc Superoxide Dismutase

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