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Copper in PDB 3f7k: X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex

Enzymatic activity of X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex

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

Protein crystallography data

The structure of X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex, PDB code: 3f7k 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 / 1.35
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 62.563, 62.563, 163.745, 90.00, 90.00, 120.00
R / Rfree (%) 12.8 / 17.6

Other elements in 3f7k:

The structure of X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex 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 An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex (pdb code 3f7k). 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 An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex, PDB code: 3f7k:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 3f7k

Go back to Copper Binding Sites List in 3f7k
Copper binding site 1 out of 2 in the X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex


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 An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:11.1
occ:0.92
CU A:CU202 1.0 9.0 0.1
NE2 A:HIS46 1.9 10.9 1.0
NE2 A:HIS118 2.0 10.9 1.0
ND1 A:HIS44 2.0 11.5 1.0
CE1 A:HIS46 2.9 11.2 1.0
CD2 A:HIS118 2.9 11.7 1.0
CD2 A:HIS46 3.0 10.3 1.0
CE1 A:HIS44 3.0 12.0 1.0
CG A:HIS44 3.0 11.2 1.0
CE1 A:HIS118 3.1 11.5 1.0
NE2 A:HIS61 3.4 13.0 1.0
CB A:HIS44 3.4 11.5 1.0
O2 A:PEO209 3.5 35.7 1.0
CD2 A:HIS61 3.7 13.7 1.0
O A:HOH301 3.8 20.3 1.0
CB A:VAL116 3.9 10.7 1.0
ND1 A:HIS46 4.1 11.3 1.0
CG1 A:VAL116 4.1 11.9 1.0
N A:HIS44 4.1 10.6 1.0
CG A:HIS46 4.1 10.2 1.0
NE2 A:HIS44 4.1 11.8 1.0
CG A:HIS118 4.1 11.2 1.0
ND1 A:HIS118 4.2 11.2 1.0
CD2 A:HIS44 4.2 12.4 1.0
CA A:HIS44 4.2 10.4 1.0
O A:VAL116 4.2 11.4 1.0
CE1 A:HIS61 4.3 12.9 1.0
O A:HIS44 4.6 11.4 1.0
O1 A:PEO209 4.6 35.6 1.0
CG2 A:VAL116 4.7 11.8 1.0
C A:HIS44 4.7 10.0 1.0
CG A:HIS61 4.7 13.2 1.0
C A:VAL116 4.8 10.6 1.0
CA A:VAL116 4.9 10.1 1.0
C A:PHE43 4.9 11.2 1.0
ND1 A:HIS61 5.0 11.7 1.0

Copper binding site 2 out of 2 in 3f7k

Go back to Copper Binding Sites List in 3f7k
Copper binding site 2 out of 2 in the X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex


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 An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:9.0
occ:0.08
CU A:CU1201 1.0 11.1 0.9
ND1 A:HIS44 1.9 11.5 1.0
NE2 A:HIS118 2.3 10.9 1.0
NE2 A:HIS46 2.3 10.9 1.0
NE2 A:HIS61 2.4 13.0 1.0
CE1 A:HIS44 2.6 12.0 1.0
O2 A:PEO209 2.7 35.7 1.0
CD2 A:HIS61 2.9 13.7 1.0
CG A:HIS44 3.0 11.2 1.0
CE1 A:HIS46 3.0 11.2 1.0
O A:HOH301 3.0 20.3 1.0
CE1 A:HIS118 3.1 11.5 1.0
CD2 A:HIS118 3.3 11.7 1.0
CE1 A:HIS61 3.4 12.9 1.0
CD2 A:HIS46 3.5 10.3 1.0
CB A:HIS44 3.6 11.5 1.0
NE2 A:HIS44 3.8 11.8 1.0
CD2 A:HIS44 3.9 12.4 1.0
CG A:HIS61 4.0 13.2 1.0
O1 A:PEO209 4.0 35.6 1.0
ND1 A:HIS61 4.2 11.7 1.0
ND1 A:HIS46 4.2 11.3 1.0
ND1 A:HIS118 4.2 11.2 1.0
CG A:HIS118 4.3 11.2 1.0
CG A:HIS46 4.5 10.2 1.0
CA A:HIS44 4.7 10.4 1.0
N A:HIS44 4.7 10.6 1.0
CB A:VAL116 4.8 10.7 1.0
O A:HOH302 4.9 25.0 1.0
CG1 A:VAL116 4.9 11.9 1.0
O A:HOH303 5.0 16.8 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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