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Zinc in PDB 2vr8: Crystal Structure of G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution

Enzymatic activity of Crystal Structure of G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution

All present enzymatic activity of Crystal Structure of G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution, PDB code: 2vr8 was solved by S.Antonyuk, X.Cao, S.V.Seetharaman, L.J.Whitson, A.B.Taylor, S.P.Holloway, R.W.Strange, P.A.Doucette, A.Tiwari, L.J.Hayward, S.Padua, J.A.Cohlberg, J.Selverstone Valentine, S.S.Hasnain, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.36
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 34.210, 56.647, 74.714, 90.00, 102.14, 90.00
R / Rfree (%) 11.3 / 15.3

Other elements in 2vr8:

The structure of Crystal Structure of G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution (pdb code 2vr8). 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 G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution, PDB code: 2vr8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2vr8

Go back to Zinc Binding Sites List in 2vr8
Zinc binding site 1 out of 6 in the Crystal Structure of G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution


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 G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1157

b:11.8
occ:0.35
CU A:CU1156 1.1 10.2 0.2
NE2 A:HIS120 1.9 11.4 1.0
O1 A:SO41159 2.1 9.9 0.5
NE2 A:HIS48 2.1 11.1 1.0
O A:HOH2265 2.2 25.6 0.5
ND1 A:HIS46 2.3 15.8 1.0
CE1 A:HIS120 2.6 10.8 1.0
CE1 A:HIS48 2.7 10.7 1.0
CD2 A:HIS120 3.1 10.3 1.0
CE1 A:HIS46 3.1 12.1 1.0
NE2 A:HIS63 3.2 12.5 1.0
S A:SO41159 3.3 9.9 0.5
CD2 A:HIS48 3.3 10.8 1.0
CG A:HIS46 3.4 11.1 1.0
O2 A:SO41159 3.6 10.8 0.5
CD2 A:HIS63 3.6 12.5 1.0
CB A:HIS46 3.8 11.4 1.0
ND1 A:HIS120 3.8 9.9 1.0
ND1 A:HIS48 4.0 9.9 1.0
CG A:HIS120 4.0 8.7 1.0
O4 A:SO41159 4.2 11.7 0.5
O3 A:SO41159 4.2 11.8 0.5
CG A:HIS48 4.3 9.4 1.0
CE1 A:HIS63 4.3 10.1 1.0
O A:HOH2269 4.3 12.1 0.3
NE2 A:HIS46 4.3 13.1 1.0
O A:HOH2241 4.3 20.1 0.7
CG1 A:VAL118 4.4 8.4 1.0
CD2 A:HIS46 4.5 12.4 1.0
O A:HOH2268 4.5 12.4 0.3
CB A:VAL118 4.5 8.3 1.0
NE A:ARG143 4.8 9.8 1.0
CG A:HIS63 4.8 11.7 1.0

Zinc binding site 2 out of 6 in 2vr8

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Zinc binding site 2 out of 6 in the Crystal Structure of G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution


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 G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1158

b:9.5
occ:0.60
OD1 A:ASP83 2.0 9.0 1.0
ND1 A:HIS63 2.0 9.6 1.0
ND1 A:HIS71 2.0 10.1 1.0
ND1 A:HIS80 2.1 8.3 1.0
CG A:ASP83 2.8 8.7 1.0
OD2 A:ASP83 2.9 9.5 1.0
CE1 A:HIS71 2.9 8.3 1.0
CE1 A:HIS80 2.9 8.9 1.0
CE1 A:HIS63 2.9 10.1 1.0
CG A:HIS63 3.1 11.7 1.0
CG A:HIS80 3.1 8.3 1.0
CG A:HIS71 3.2 10.0 1.0
CB A:HIS63 3.5 10.4 1.0
CB A:HIS80 3.5 7.8 1.0
CB A:HIS71 3.7 9.1 1.0
CA A:HIS71 4.0 9.5 1.0
NE2 A:HIS80 4.0 10.0 1.0
NE2 A:HIS71 4.1 10.0 1.0
NE2 A:HIS63 4.1 12.5 1.0
O A:LYS136 4.1 12.8 1.0
CD2 A:HIS80 4.1 10.1 1.0
CD2 A:HIS63 4.2 12.5 1.0
CB A:ASP83 4.2 8.4 1.0
CD2 A:HIS71 4.2 9.8 1.0
CA A:ASP83 4.7 9.6 1.0
N A:HIS80 4.7 9.2 1.0
CA A:HIS80 4.8 8.6 1.0
O A:HOH2239 4.8 20.4 1.0
N A:GLY72 4.8 9.6 1.0
N A:ASP83 4.9 8.9 1.0
C A:HIS71 4.9 10.1 1.0
N A:HIS71 5.0 9.3 1.0
CA A:HIS63 5.0 10.3 1.0

Zinc binding site 3 out of 6 in 2vr8

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Zinc binding site 3 out of 6 in the Crystal Structure of G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution


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 G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1160

b:12.8
occ:0.70
N A:SCN1162 1.9 12.2 1.0
N A:SCN1161 1.9 10.8 1.0
OE1 A:GLU24 2.0 10.4 1.0
CD A:GLU24 2.7 10.9 1.0
OE2 A:GLU24 2.7 12.2 1.0
C A:SCN1162 3.0 12.2 1.0
C A:SCN1161 3.0 10.9 1.0
CG A:GLU24 4.1 11.1 1.0
O A:HOH2062 4.1 18.6 1.0
S A:SCN1161 4.8 11.0 1.0
S A:SCN1162 4.8 16.6 1.0
O A:HOH2060 5.0 12.6 0.5

Zinc binding site 4 out of 6 in 2vr8

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Zinc binding site 4 out of 6 in the Crystal Structure of G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution


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 G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1157

b:11.1
occ:0.35
CU F:CU1156 1.1 12.6 0.2
NE2 F:HIS120 1.9 11.3 1.0
O1 F:SO41159 2.0 9.5 0.7
NE2 F:HIS48 2.1 10.8 1.0
ND1 F:HIS46 2.3 14.3 1.0
CE1 F:HIS120 2.7 11.6 1.0
CE1 F:HIS48 2.7 10.1 1.0
CD2 F:HIS120 3.1 11.8 1.0
CE1 F:HIS46 3.1 14.1 1.0
S F:SO41159 3.2 11.9 0.7
NE2 F:HIS63 3.3 13.3 1.0
CD2 F:HIS48 3.3 10.8 1.0
CG F:HIS46 3.4 11.4 1.0
O2 F:SO41159 3.5 14.0 0.7
CD2 F:HIS63 3.7 12.3 1.0
CB F:HIS46 3.7 11.9 1.0
ND1 F:HIS120 3.9 11.7 1.0
ND1 F:HIS48 4.0 9.4 1.0
O4 F:SO41159 4.1 14.7 0.7
CG F:HIS120 4.1 9.9 1.0
O3 F:SO41159 4.2 11.8 0.7
O F:HOH2250 4.2 9.5 0.3
CG F:HIS48 4.3 8.9 1.0
NE2 F:HIS46 4.3 12.5 1.0
CE1 F:HIS63 4.3 9.9 1.0
O F:HOH2224 4.4 11.3 0.5
CG1 F:VAL118 4.4 9.4 1.0
CD2 F:HIS46 4.4 13.4 1.0
CB F:VAL118 4.5 7.7 1.0
NE F:ARG143 4.7 10.2 1.0
CG F:HIS63 4.9 11.2 1.0

Zinc binding site 5 out of 6 in 2vr8

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Zinc binding site 5 out of 6 in the Crystal Structure of G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution


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 G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1158

b:10.9
occ:0.65
OD1 F:ASP83 2.0 9.5 1.0
ND1 F:HIS63 2.0 10.4 1.0
ND1 F:HIS80 2.0 9.2 1.0
ND1 F:HIS71 2.1 10.0 1.0
CG F:ASP83 2.8 9.9 1.0
OD2 F:ASP83 2.9 10.7 1.0
CE1 F:HIS71 2.9 10.0 1.0
CE1 F:HIS80 2.9 9.7 1.0
CE1 F:HIS63 2.9 9.9 1.0
CG F:HIS63 3.1 11.2 1.0
CG F:HIS80 3.1 9.9 1.0
CG F:HIS71 3.2 9.7 1.0
CB F:HIS63 3.4 11.1 1.0
CB F:HIS80 3.5 9.4 1.0
CB F:HIS71 3.7 9.3 1.0
CA F:HIS71 4.0 10.4 1.0
NE2 F:HIS80 4.1 10.7 1.0
NE2 F:HIS71 4.1 10.2 1.0
NE2 F:HIS63 4.1 13.3 1.0
O F:LYS136 4.1 12.6 1.0
CD2 F:HIS80 4.1 10.2 1.0
CD2 F:HIS63 4.2 12.3 1.0
CB F:ASP83 4.2 9.6 1.0
CD2 F:HIS71 4.2 10.5 1.0
CA F:ASP83 4.7 9.6 1.0
N F:HIS80 4.7 9.5 1.0
CA F:HIS80 4.8 8.5 1.0
O F:HOH2222 4.8 19.1 1.0
N F:ASP83 4.8 9.5 1.0
N F:GLY72 4.9 11.6 1.0
N F:HIS71 5.0 11.1 1.0
CA F:HIS63 5.0 10.3 1.0
C F:HIS71 5.0 11.2 1.0

Zinc binding site 6 out of 6 in 2vr8

Go back to Zinc Binding Sites List in 2vr8
Zinc binding site 6 out of 6 in the Crystal Structure of G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution


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 G85R Als Mutant of Human Cu,Zn Superoxide Dismutase (Cuznsod) at 1.36 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1160

b:13.3
occ:0.70
N F:SCN1162 1.9 13.0 1.0
N F:SCN1161 1.9 14.5 1.0
OE1 F:GLU24 1.9 13.8 1.0
CD F:GLU24 2.7 13.0 1.0
OE2 F:GLU24 2.8 16.0 1.0
C F:SCN1162 3.0 10.7 1.0
C F:SCN1161 3.0 14.2 1.0
CG F:GLU24 4.1 12.5 1.0
O F:HOH2048 4.2 18.7 0.5
S F:SCN1162 4.7 10.6 1.0
S F:SCN1161 4.8 19.5 1.0
O F:HOH2049 4.8 17.6 1.0

Reference:

X.Cao, S.Antonyuk, S.V.Seetharaman, L.J.Whitson, A.B.Taylor, S.P.Holloway, R.W.Strange, P.A.Doucette, A.Tiwari, L.J.Hayward, S.Padua, J.A.Cohlberg, J.Selverstone Valentine, S.S.Hasnain, P.J.Hart. Structures of the G85R Variant of SOD1 in Familial Amyotrophic Lateral Sclerosis. J.Biol.Chem. V. 283 16169 2008.
ISSN: ISSN 0021-9258
PubMed: 18378676
DOI: 10.1074/JBC.M801522200
Page generated: Thu Oct 29 08:16:19 2020
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