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Zinc 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:

Copper (Cu) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3kh4

Go back to Zinc Binding Sites List in 3kh4
Zinc 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 Zinc with other atoms in the Zn 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:Zn155

b:72.8
occ:1.00
 OD1 A:ASP83 1.8 70.2 1.0
ND1 A:HIS63 2.1 78.6 1.0
ND1 A:HIS71 2.1 75.7 1.0
ND1 A:HIS80 2.2 77.5 1.0
CG A:ASP83 2.7 71.2 1.0
OD2 A:ASP83 2.9 73.7 1.0
CG A:HIS63 2.9 78.0 1.0
CE1 A:HIS71 3.0 73.9 1.0
CE1 A:HIS63 3.0 79.4 1.0
CG A:HIS80 3.0 78.0 1.0
CE1 A:HIS80 3.1 80.3 1.0
CG A:HIS71 3.2 77.8 1.0
CB A:HIS63 3.3 77.3 1.0
CB A:HIS80 3.4 76.8 1.0
CB A:HIS71 3.7 80.8 1.0
O A:LYS136 3.7 80.3 1.0
NE2 A:HIS63 3.9 80.7 1.0
CD2 A:HIS63 4.0 80.2 1.0
CA A:HIS71 4.1 82.6 1.0
CB A:ASP83 4.1 70.2 1.0
NE2 A:HIS80 4.1 82.6 1.0
CD2 A:HIS80 4.1 81.3 1.0
NE2 A:HIS71 4.1 74.2 1.0
CD2 A:HIS71 4.3 76.6 1.0
CA A:ASP83 4.6 68.6 1.0
CA A:HIS80 4.7 78.8 1.0
N A:HIS80 4.7 80.4 1.0
N A:GLY72 4.8 81.1 1.0
C A:LYS136 4.8 81.8 1.0
CA A:HIS63 4.8 76.8 1.0
N A:ASP83 4.9 68.9 1.0
C A:HIS71 5.0 82.8 1.0

Zinc binding site 2 out of 6 in 3kh4

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Zinc 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 Zinc with other atoms in the Zn 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:Zn155

b:78.1
occ:1.00
 OD1 B:ASP83 1.8 76.2 1.0
ND1 B:HIS80 2.1 83.3 1.0
ND1 B:HIS71 2.2 84.1 1.0
ND1 B:HIS63 2.2 84.6 1.0
CG B:ASP83 2.6 77.6 1.0
OD2 B:ASP83 2.7 80.3 1.0
CG B:HIS80 2.9 83.3 1.0
CE1 B:HIS80 3.0 86.5 1.0
CE1 B:HIS71 3.0 82.5 1.0
CG B:HIS63 3.1 83.3 1.0
CE1 B:HIS63 3.1 86.0 1.0
CG B:HIS71 3.2 87.3 1.0
CB B:HIS80 3.3 81.3 1.0
CB B:HIS63 3.4 81.8 1.0
CB B:HIS71 3.6 90.3 1.0
O B:LYS136 3.7 88.2 1.0
CD2 B:HIS80 4.0 87.0 1.0
CA B:HIS71 4.0 91.4 1.0
NE2 B:HIS80 4.0 88.8 1.0
CB B:ASP83 4.0 76.4 1.0
NE2 B:HIS63 4.1 87.0 1.0
CD2 B:HIS63 4.1 85.7 1.0
NE2 B:HIS71 4.2 84.0 1.0
CD2 B:HIS71 4.3 86.9 1.0
CA B:HIS80 4.5 83.2 1.0
N B:HIS80 4.6 85.7 1.0
CA B:ASP83 4.6 73.9 1.0
N B:GLY72 4.7 90.3 1.0
C B:LYS136 4.8 90.7 1.0
C B:HIS71 4.9 92.4 1.0
CA B:HIS63 4.9 80.3 1.0
N B:ASP83 4.9 73.3 1.0
N B:HIS71 5.0 94.8 1.0

Zinc binding site 3 out of 6 in 3kh4

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Zinc 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 Zinc with other atoms in the Zn 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:Zn155

b:95.3
occ:1.00
 OD1 C:ASP83 1.8 83.4 1.0
ND1 C:HIS71 2.0 89.2 1.0
ND1 C:HIS63 2.1 91.5 1.0
ND1 C:HIS80 2.3 90.8 1.0
CG C:ASP83 2.7 84.6 1.0
CE1 C:HIS71 2.9 87.3 1.0
OD2 C:ASP83 2.9 87.0 1.0
CE1 C:HIS63 2.9 92.5 1.0
CG C:HIS63 3.0 90.9 1.0
CG C:HIS80 3.1 91.5 1.0
CE1 C:HIS80 3.2 93.8 1.0
CG C:HIS71 3.2 91.3 1.0
CB C:HIS63 3.4 90.2 1.0
CB C:HIS80 3.5 90.2 1.0
O C:LYS136 3.6 93.5 1.0
CB C:HIS71 3.6 94.4 1.0
NE2 C:HIS63 3.9 93.8 1.0
CD2 C:HIS63 4.0 93.2 1.0
CA C:HIS71 4.0 96.2 1.0
NE2 C:HIS71 4.1 87.7 1.0
CB C:ASP83 4.1 83.5 1.0
NE2 C:HIS80 4.2 96.5 1.0
CD2 C:HIS80 4.2 95.3 1.0
CD2 C:HIS71 4.2 90.1 1.0
CA C:ASP83 4.6 81.8 1.0
C C:LYS136 4.7 95.3 1.0
N C:GLY72 4.7 94.6 1.0
CA C:HIS80 4.7 92.6 1.0
N C:HIS80 4.8 94.2 1.0
N C:ASP83 4.9 82.2 1.0
CA C:HIS63 4.9 89.4 1.0
C C:HIS71 4.9 96.4 1.0

Zinc binding site 4 out of 6 in 3kh4

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Zinc 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 Zinc with other atoms in the Zn 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:Zn155

b:68.8
occ:1.00
 OD1 D:ASP83 1.8 74.9 1.0
ND1 D:HIS71 2.0 81.6 1.0
ND1 D:HIS63 2.1 83.9 1.0
ND1 D:HIS80 2.3 82.7 1.0
CG D:ASP83 2.7 75.9 1.0
CE1 D:HIS71 2.8 79.8 1.0
CE1 D:HIS63 2.9 85.1 1.0
OD2 D:ASP83 2.9 78.5 1.0
CG D:HIS63 2.9 83.5 1.0
CG D:HIS71 3.1 84.1 1.0
CE1 D:HIS80 3.1 86.0 1.0
CG D:HIS80 3.2 83.0 1.0
CB D:HIS63 3.4 82.6 1.0
CB D:HIS80 3.5 81.3 1.0
CB D:HIS71 3.6 87.2 1.0
O D:LYS136 3.6 87.4 1.0
NE2 D:HIS63 3.8 86.9 1.0
CD2 D:HIS63 3.9 86.2 1.0
NE2 D:HIS71 4.0 80.7 1.0
CA D:HIS71 4.0 88.4 1.0
CB D:ASP83 4.1 74.6 1.0
NE2 D:HIS80 4.1 88.4 1.0
CD2 D:HIS71 4.1 83.3 1.0
CD2 D:HIS80 4.2 86.6 1.0
C D:LYS136 4.7 89.4 1.0
CA D:ASP83 4.7 72.7 1.0
N D:GLY72 4.7 86.5 1.0
CA D:HIS80 4.8 83.1 1.0
N D:HIS80 4.8 84.8 1.0
CA D:HIS63 4.9 82.2 1.0
C D:HIS71 4.9 88.5 1.0
N D:ASP83 5.0 72.9 1.0

Zinc binding site 5 out of 6 in 3kh4

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Zinc 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 Zinc with other atoms in the Zn 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:Zn155

b:93.0
occ:1.00
 OD1 E:ASP83 1.9 81.5 1.0
ND1 E:HIS80 2.1 92.5 1.0
ND1 E:HIS71 2.1 89.1 1.0
ND1 E:HIS63 2.3 90.1 1.0
CG E:ASP83 2.7 82.5 1.0
OD2 E:ASP83 2.8 86.1 1.0
CE1 E:HIS80 2.9 97.0 1.0
CG E:HIS80 2.9 93.0 1.0
CE1 E:HIS71 3.0 86.0 1.0
CG E:HIS63 3.1 90.2 1.0
CG E:HIS71 3.1 92.7 1.0
CE1 E:HIS63 3.2 90.8 1.0
CB E:HIS80 3.3 89.9 1.0
CB E:HIS63 3.4 89.7 1.0
CB E:HIS71 3.5 97.6 1.0
O E:LYS136 3.6 96.8 1.0
CA E:HIS71 3.9 99.6 1.0
NE2 E:HIS80 3.9 0.4 1.0
CD2 E:HIS80 3.9 98.3 1.0
CD2 E:HIS63 4.1 92.7 1.0
NE2 E:HIS63 4.1 92.8 1.0
NE2 E:HIS71 4.2 87.0 1.0
CB E:ASP83 4.2 79.9 1.0
CD2 E:HIS71 4.2 91.1 1.0
CA E:HIS80 4.6 92.4 1.0
N E:HIS80 4.6 94.5 1.0
C E:LYS136 4.7 99.7 1.0
N E:GLY72 4.7 95.9 1.0
CA E:ASP83 4.8 76.9 1.0
C E:HIS71 4.8 99.3 1.0
N E:HIS71 4.9 0.9 1.0
CA E:HIS63 4.9 88.7 1.0

Zinc binding site 6 out of 6 in 3kh4

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Zinc 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 Zinc with other atoms in the Zn 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:Zn155

b:74.7
occ:1.00
 OD1 F:ASP83 1.8 72.0 1.0
ND1 F:HIS71 1.9 77.6 1.0
ND1 F:HIS63 2.2 79.8 1.0
ND1 F:HIS80 2.3 78.7 1.0
CG F:ASP83 2.6 73.2 1.0
OD2 F:ASP83 2.8 75.6 1.0
CE1 F:HIS71 2.8 76.0 1.0
CE1 F:HIS63 2.9 80.8 1.0
CG F:HIS71 3.0 79.5 1.0
CG F:HIS63 3.1 78.9 1.0
CE1 F:HIS80 3.1 81.1 1.0
CG F:HIS80 3.2 79.3 1.0
CB F:HIS80 3.5 78.2 1.0
CB F:HIS63 3.5 78.3 1.0
CB F:HIS71 3.5 82.3 1.0
O F:LYS136 3.6 81.2 1.0
NE2 F:HIS71 3.9 76.5 1.0
NE2 F:HIS63 3.9 81.9 1.0
CA F:HIS71 4.0 84.0 1.0
CD2 F:HIS63 4.0 81.2 1.0
CB F:ASP83 4.0 72.6 1.0
CD2 F:HIS71 4.1 78.7 1.0
NE2 F:HIS80 4.1 83.5 1.0
CD2 F:HIS80 4.2 82.6 1.0
N F:GLY72 4.6 83.0 1.0
CA F:ASP83 4.7 71.0 1.0
C F:LYS136 4.7 82.6 1.0
CA F:HIS80 4.7 80.4 1.0
N F:HIS80 4.7 82.0 1.0
C F:HIS71 4.9 84.5 1.0
N F:ASP83 5.0 71.3 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 Dec 16 04:30:09 2020

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