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Copper in PDB 3f7l: X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase

Enzymatic activity of X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase

All present enzymatic activity of X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase, PDB code: 3f7l was solved by D.S.Shin, M.Didonato, D.P.Barondeau, E.D.Getzoff, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 0.99
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 62.493, 62.493, 163.191, 90.00, 90.00, 120.00
R / Rfree (%) 11.2 / 13.8

Other elements in 3f7l:

The structure of X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Sodium (Na) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase (pdb code 3f7l). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase, PDB code: 3f7l:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 3f7l

Go back to Copper Binding Sites List in 3f7l
Copper binding site 1 out of 2 in the X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:7.2
occ:0.80
CU A:CU202 1.1 11.8 0.2
NE2 A:HIS46 1.9 7.8 1.0
NE2 A:HIS118 2.0 7.8 1.0
ND1 A:HIS44 2.0 7.9 1.0
CE1 A:HIS46 2.9 7.5 1.0
CD2 A:HIS118 2.9 8.0 1.0
CD2 A:HIS46 3.0 7.5 1.0
CE1 A:HIS44 3.0 8.0 1.0
CG A:HIS44 3.0 7.8 1.0
CE1 A:HIS118 3.0 8.0 1.0
NE2 A:HIS61 3.3 9.9 1.0
CB A:HIS44 3.3 8.2 1.0
O A:HOH300 3.6 20.7 1.0
CD2 A:HIS61 3.6 9.7 1.0
O A:HOH301 3.7 10.7 0.6
CB A:VAL116 3.9 7.7 1.0
ND1 A:HIS46 4.1 7.5 1.0
CG1 A:VAL116 4.1 8.7 1.0
CG A:HIS118 4.1 7.2 1.0
CG A:HIS46 4.1 7.3 1.0
N A:HIS44 4.1 6.9 1.0
NE2 A:HIS44 4.1 8.4 1.0
CD2 A:HIS44 4.2 8.6 1.0
CE1 A:HIS61 4.2 8.3 1.0
ND1 A:HIS118 4.2 8.0 1.0
CA A:HIS44 4.2 7.0 1.0
O A:VAL116 4.3 7.6 1.0
O A:HIS44 4.6 7.5 1.0
CG2 A:VAL116 4.7 8.6 1.0
CG A:HIS61 4.7 8.0 1.0
C A:HIS44 4.7 6.6 1.0
C A:VAL116 4.8 7.0 1.0
CA A:VAL116 4.9 7.0 1.0
C A:PHE43 4.9 7.2 1.0
ND1 A:HIS61 5.0 7.2 1.0

Copper binding site 2 out of 2 in 3f7l

Go back to Copper Binding Sites List in 3f7l
Copper binding site 2 out of 2 in the X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:11.8
occ:0.20
CU A:CU1201 1.1 7.2 0.8
ND1 A:HIS44 1.9 7.9 1.0
NE2 A:HIS118 2.2 7.8 1.0
NE2 A:HIS61 2.3 9.9 1.0
NE2 A:HIS46 2.4 7.8 1.0
CE1 A:HIS44 2.7 8.0 1.0
O A:HOH301 2.8 10.7 0.6
O A:HOH300 2.8 20.7 1.0
CD2 A:HIS61 2.9 9.7 1.0
CE1 A:HIS46 3.0 7.5 1.0
CG A:HIS44 3.0 7.8 1.0
CE1 A:HIS118 3.0 8.0 1.0
CE1 A:HIS61 3.2 8.3 1.0
CD2 A:HIS118 3.3 8.0 1.0
CD2 A:HIS46 3.5 7.5 1.0
CB A:HIS44 3.6 8.2 1.0
NE2 A:HIS44 3.8 8.4 1.0
CD2 A:HIS44 4.0 8.6 1.0
CG A:HIS61 4.0 8.0 1.0
ND1 A:HIS61 4.2 7.2 1.0
ND1 A:HIS118 4.2 8.0 1.0
ND1 A:HIS46 4.2 7.5 1.0
CG A:HIS118 4.3 7.2 1.0
CG A:HIS46 4.5 7.3 1.0
O A:HOH302 4.6 13.7 0.9
CA A:HIS44 4.8 7.0 1.0
N A:HIS44 4.8 6.9 1.0
O A:HOH303 4.8 11.5 1.0
CB A:VAL116 4.9 7.7 1.0
O A:THR135 4.9 9.5 1.0
CG1 A:VAL116 5.0 8.7 1.0

Reference:

D.S.Shin, M.Didonato, D.P.Barondeau, G.L.Hura, C.Hitomi, J.A.Berglund, E.D.Getzoff, S.C.Cary, J.A.Tainer. Superoxide Dismutase From the Eukaryotic Thermophile Alvinella Pompejana: Structures, Stability, Mechanism, and Insights Into Amyotrophic Lateral Sclerosis. J.Mol.Biol. V. 385 1534 2009.
ISSN: ISSN 0022-2836
PubMed: 19063897
DOI: 10.1016/J.JMB.2008.11.031
Page generated: Wed Oct 28 14:23:50 2020
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