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Copper in PDB 3kh4: Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit

Enzymatic activity of Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit

All present enzymatic activity of Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit, PDB code: 3kh4 was solved by E.M.Gazdag, W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.69 / 3.50
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 112.188, 112.188, 428.268, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 20.8

Other elements in 3kh4:

The structure of Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit (pdb code 3kh4). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit, PDB code: 3kh4:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3kh4

Go back to Copper Binding Sites List in 3kh4
Copper binding site 1 out of 6 in the Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu154

b:1.0
occ:1.00
 NE2 A:HIS120 2.1 72.2 1.0
ND1 A:HIS46 2.1 70.1 1.0
NE2 A:HIS48 2.4 71.5 1.0
NE2 A:HIS63 2.7 80.7 1.0
CE1 A:HIS120 2.8 74.8 1.0
CE1 A:HIS48 3.0 73.5 1.0
CE1 A:HIS46 3.0 72.2 1.0
CG A:HIS46 3.1 67.6 1.0
CD2 A:HIS120 3.2 70.4 1.0
CE1 A:HIS63 3.4 79.4 1.0
CD2 A:HIS63 3.4 80.2 1.0
CB A:HIS46 3.5 65.5 1.0
CD2 A:HIS48 3.6 70.7 1.0
ND1 A:HIS120 3.9 73.9 1.0
CG A:HIS120 4.1 70.3 1.0
NE2 A:HIS46 4.1 71.3 1.0
ND1 A:HIS48 4.2 73.0 1.0
CD2 A:HIS46 4.2 70.2 1.0
ND1 A:HIS63 4.2 78.6 1.0
CG A:HIS63 4.3 78.0 1.0
CG A:HIS48 4.5 70.7 1.0
CA A:HIS46 4.8 64.3 1.0
N A:HIS46 4.8 63.5 1.0
CB A:VAL118 4.9 64.4 1.0
CG1 A:VAL118 4.9 65.5 1.0

Copper binding site 2 out of 6 in 3kh4

Go back to Copper Binding Sites List in 3kh4
Copper binding site 2 out of 6 in the Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu154

b:0.4
occ:1.00
 NE2 B:HIS120 2.2 77.2 1.0
NE2 B:HIS48 2.4 75.0 1.0
CE1 B:HIS120 2.5 80.0 1.0
ND1 B:HIS46 2.6 75.8 1.0
NE2 B:HIS63 2.7 87.0 1.0
CE1 B:HIS48 2.7 76.9 1.0
CD2 B:HIS63 3.3 85.7 1.0
CD2 B:HIS120 3.4 75.4 1.0
CE1 B:HIS46 3.4 78.8 1.0
CE1 B:HIS63 3.5 86.0 1.0
CG B:HIS46 3.6 73.0 1.0
CD2 B:HIS48 3.7 73.4 1.0
ND1 B:HIS120 3.7 79.5 1.0
ND1 B:HIS48 4.0 75.6 1.0
CB B:HIS46 4.0 69.8 1.0
CG B:HIS120 4.1 75.7 1.0
CG B:HIS63 4.3 83.3 1.0
ND1 B:HIS63 4.4 84.6 1.0
CG B:HIS48 4.5 72.7 1.0
NE2 B:HIS46 4.5 78.3 1.0
CD2 B:HIS46 4.7 76.4 1.0
CG1 B:VAL118 5.0 67.6 1.0
NE B:ARG143 5.0 87.3 1.0

Copper binding site 3 out of 6 in 3kh4

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Copper binding site 3 out of 6 in the Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu154

b:0.7
occ:1.00
 NE2 C:HIS120 2.2 86.3 1.0
NE2 C:HIS48 2.4 84.5 1.0
ND1 C:HIS46 2.4 83.5 1.0
NE2 C:HIS63 2.6 93.8 1.0
CE1 C:HIS120 2.7 88.9 1.0
CE1 C:HIS48 2.8 86.4 1.0
CE1 C:HIS46 3.2 85.8 1.0
CD2 C:HIS120 3.3 84.8 1.0
CD2 C:HIS63 3.3 93.2 1.0
CE1 C:HIS63 3.4 92.5 1.0
CG C:HIS46 3.4 80.9 1.0
CD2 C:HIS48 3.6 83.4 1.0
CB C:HIS46 3.8 78.7 1.0
ND1 C:HIS120 3.8 88.6 1.0
ND1 C:HIS48 4.0 85.6 1.0
CG C:HIS120 4.2 85.0 1.0
CG C:HIS63 4.2 90.9 1.0
ND1 C:HIS63 4.2 91.5 1.0
NE2 C:HIS46 4.3 84.9 1.0
CG C:HIS48 4.4 83.0 1.0
CD2 C:HIS46 4.4 83.7 1.0
CB C:VAL118 5.0 77.8 1.0
CG1 C:VAL118 5.0 79.3 1.0

Copper binding site 4 out of 6 in 3kh4

Go back to Copper Binding Sites List in 3kh4
Copper binding site 4 out of 6 in the Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu154

b:0.5
occ:1.00
 NE2 D:HIS120 2.1 79.8 1.0
ND1 D:HIS46 2.1 76.3 1.0
NE2 D:HIS48 2.6 77.8 1.0
CE1 D:HIS120 2.6 82.9 1.0
NE2 D:HIS63 2.7 86.9 1.0
CE1 D:HIS46 2.9 78.8 1.0
CE1 D:HIS48 3.0 80.0 1.0
CD2 D:HIS120 3.1 78.1 1.0
CG D:HIS46 3.2 73.4 1.0
CE1 D:HIS63 3.4 85.1 1.0
CD2 D:HIS63 3.4 86.2 1.0
CB D:HIS46 3.7 70.8 1.0
ND1 D:HIS120 3.7 82.9 1.0
CD2 D:HIS48 3.7 76.5 1.0
CG D:HIS120 4.0 78.9 1.0
NE2 D:HIS46 4.1 77.7 1.0
CD2 D:HIS46 4.2 76.0 1.0
ND1 D:HIS48 4.2 79.2 1.0
ND1 D:HIS63 4.3 83.9 1.0
CG D:HIS63 4.3 83.5 1.0
CG D:HIS48 4.6 76.4 1.0
CA D:HIS46 4.9 69.4 1.0
N D:HIS46 5.0 68.9 1.0
CG1 D:VAL118 5.0 72.7 1.0
O D:THR137 5.0 83.9 1.0

Copper binding site 5 out of 6 in 3kh4

Go back to Copper Binding Sites List in 3kh4
Copper binding site 5 out of 6 in the Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu154

b:0.3
occ:1.00
 NE2 E:HIS120 2.2 82.0 1.0
NE2 E:HIS48 2.3 80.8 1.0
ND1 E:HIS46 2.4 79.1 1.0
NE2 E:HIS63 2.7 92.8 1.0
CE1 E:HIS120 2.7 85.7 1.0
CE1 E:HIS48 2.7 84.0 1.0
CE1 E:HIS46 3.2 81.5 1.0
CD2 E:HIS63 3.3 92.7 1.0
CD2 E:HIS120 3.3 79.3 1.0
CG E:HIS46 3.4 75.8 1.0
CE1 E:HIS63 3.4 90.8 1.0
CD2 E:HIS48 3.5 79.2 1.0
CB E:HIS46 3.7 73.0 1.0
ND1 E:HIS120 3.9 85.0 1.0
ND1 E:HIS48 3.9 83.2 1.0
CG E:HIS120 4.2 80.1 1.0
CG E:HIS63 4.2 90.2 1.0
ND1 E:HIS63 4.2 90.1 1.0
CG E:HIS48 4.3 79.6 1.0
NE2 E:HIS46 4.3 80.3 1.0
CD2 E:HIS46 4.4 78.5 1.0
CB E:VAL118 4.9 71.2 1.0
CG1 E:VAL118 4.9 73.3 1.0
CA E:HIS46 5.0 70.6 1.0

Copper binding site 6 out of 6 in 3kh4

Go back to Copper Binding Sites List in 3kh4
Copper binding site 6 out of 6 in the Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in Leishmania Tarantolae; P6522 Crystal Form Containing 6 Chains in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu154

b:0.6
occ:1.00
 NE2 F:HIS120 2.0 73.7 1.0
ND1 F:HIS46 2.2 71.9 1.0
NE2 F:HIS48 2.5 72.4 1.0
CE1 F:HIS120 2.6 75.9 1.0
NE2 F:HIS63 2.8 81.9 1.0
CE1 F:HIS48 3.0 74.0 1.0
CE1 F:HIS46 3.0 74.1 1.0
CD2 F:HIS120 3.1 72.1 1.0
CG F:HIS46 3.3 69.6 1.0
CE1 F:HIS63 3.5 80.8 1.0
CD2 F:HIS63 3.5 81.2 1.0
CD2 F:HIS48 3.7 71.9 1.0
CB F:HIS46 3.7 67.5 1.0
ND1 F:HIS120 3.7 75.1 1.0
CG F:HIS120 4.0 71.8 1.0
NE2 F:HIS46 4.2 73.7 1.0
ND1 F:HIS48 4.2 73.3 1.0
CD2 F:HIS46 4.3 72.6 1.0
ND1 F:HIS63 4.4 79.8 1.0
CG F:HIS63 4.4 78.9 1.0
CG F:HIS48 4.6 71.3 1.0
CG1 F:VAL118 4.9 66.3 1.0
CB F:VAL118 4.9 65.6 1.0
CA F:HIS46 5.0 66.6 1.0
N F:HIS46 5.0 65.9 1.0

Reference:

E.M.Gazdag, I.C.Cirstea, R.Breitling, J.Lukes, W.Blankenfeldt, K.Alexandrov. Purification and Crystallization of Human Cu/Zn Superoxide Dismutase Recombinantly Produced in the Protozoan Leishmania Tarentolae. Acta Crystallogr.,Sect.F V. 66 871 2010.
ISSN: ESSN 1744-3091
PubMed: 20693657
DOI: 10.1107/S1744309110019330
Page generated: Wed Jul 31 01:14:09 2024

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