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Zinc in PDB 3gqf: Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q

Enzymatic activity of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q

All present enzymatic activity of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q:
1.15.1.1;

Protein crystallography data

The structure of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q, PDB code: 3gqf was solved by D.D.Winkler, J.P.Schuermann, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.07 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 112.576, 194.331, 143.179, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.2

Other elements in 3gqf:

The structure of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q also contains other interesting chemical elements:

Calcium (Ca) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q (pdb code 3gqf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q, PDB code: 3gqf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3gqf

Go back to Zinc Binding Sites List in 3gqf
Zinc binding site 1 out of 6 in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn155

b:28.7
occ:1.00
 OD1 A:ASP83 1.9 25.4 1.0
ND1 A:HIS80 2.1 26.9 1.0
ND1 A:HIS63 2.1 26.0 1.0
ND1 A:HIS71 2.1 26.8 1.0
CG A:ASP83 2.8 25.4 1.0
CE1 A:HIS80 2.9 25.9 1.0
OD2 A:ASP83 3.0 26.8 1.0
CE1 A:HIS71 3.0 28.4 1.0
CE1 A:HIS63 3.1 25.6 1.0
CG A:HIS63 3.1 25.9 1.0
CG A:HIS80 3.2 26.9 1.0
CG A:HIS71 3.2 29.4 1.0
CB A:HIS63 3.5 27.4 1.0
CB A:HIS71 3.6 30.6 1.0
CB A:HIS80 3.6 28.0 1.0
CA A:HIS71 3.9 31.2 1.0
O A:LYS136 4.0 31.2 1.0
NE2 A:HIS80 4.1 26.2 1.0
NE2 A:HIS71 4.2 28.3 1.0
CB A:ASP83 4.2 24.5 1.0
CD2 A:HIS80 4.2 27.0 1.0
NE2 A:HIS63 4.2 24.2 1.0
CD2 A:HIS63 4.3 24.8 1.0
CD2 A:HIS71 4.3 28.4 1.0
CA A:ASP83 4.7 24.9 1.0
N A:HIS80 4.7 29.4 1.0
N A:GLY72 4.8 31.0 1.0
CA A:HIS80 4.8 28.0 1.0
C A:HIS71 4.9 31.1 1.0
N A:HIS71 4.9 32.1 1.0
N A:ASP83 4.9 25.1 1.0
C A:LYS136 5.0 31.3 1.0
CA A:HIS63 5.0 27.8 1.0

Zinc binding site 2 out of 6 in 3gqf

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Zinc binding site 2 out of 6 in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn155

b:25.5
occ:1.00
 OD1 B:ASP83 1.9 20.6 1.0
ND1 B:HIS80 2.0 21.8 1.0
ND1 B:HIS63 2.1 20.7 1.0
ND1 B:HIS71 2.2 25.1 1.0
CG B:ASP83 2.7 22.3 1.0
CE1 B:HIS80 2.9 22.2 1.0
OD2 B:ASP83 2.9 21.0 1.0
CE1 B:HIS63 3.0 21.0 1.0
CG B:HIS63 3.1 22.9 1.0
CG B:HIS80 3.1 23.7 1.0
CE1 B:HIS71 3.2 24.6 1.0
CG B:HIS71 3.3 26.9 1.0
CB B:HIS63 3.4 24.4 1.0
CB B:HIS71 3.6 29.0 1.0
CB B:HIS80 3.6 25.0 1.0
CA B:HIS71 3.9 29.7 1.0
NE2 B:HIS80 4.0 21.7 1.0
NE2 B:HIS63 4.1 20.2 1.0
CD2 B:HIS80 4.2 21.3 1.0
CB B:ASP83 4.2 22.3 1.0
CD2 B:HIS63 4.2 21.2 1.0
O B:LYS136 4.3 30.5 1.0
NE2 B:HIS71 4.3 23.4 1.0
CD2 B:HIS71 4.4 23.5 1.0
CA B:ASP83 4.7 22.7 1.0
N B:HIS80 4.7 26.9 1.0
CA B:THR137 4.8 28.7 1.0
CA B:HIS80 4.8 25.6 1.0
N B:GLY72 4.8 29.5 1.0
N B:HIS71 4.9 30.7 1.0
C B:HIS71 4.9 29.9 1.0
CA B:HIS63 5.0 25.1 1.0
N B:ASP83 5.0 22.9 1.0

Zinc binding site 3 out of 6 in 3gqf

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Zinc binding site 3 out of 6 in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn155

b:32.5
occ:1.00
 OD1 C:ASP83 1.9 24.8 1.0
ND1 C:HIS63 2.1 27.7 1.0
ND1 C:HIS80 2.1 27.7 1.0
ND1 C:HIS71 2.3 31.9 1.0
CG C:ASP83 2.8 26.9 1.0
OD2 C:ASP83 2.9 28.6 1.0
CE1 C:HIS80 2.9 26.0 1.0
CE1 C:HIS63 3.0 28.0 1.0
CG C:HIS63 3.1 28.5 1.0
CG C:HIS80 3.2 28.3 1.0
CE1 C:HIS71 3.3 31.4 1.0
CG C:HIS71 3.4 32.5 1.0
CB C:HIS63 3.4 28.8 1.0
CB C:HIS71 3.6 33.0 1.0
CB C:HIS80 3.7 29.8 1.0
CA C:HIS71 3.9 33.0 1.0
NE2 C:HIS80 4.1 26.9 1.0
O C:LYS136 4.1 33.7 1.0
NE2 C:HIS63 4.2 26.8 1.0
CD2 C:HIS63 4.2 27.6 1.0
CB C:ASP83 4.2 26.1 1.0
CD2 C:HIS80 4.2 27.2 1.0
NE2 C:HIS71 4.4 31.2 1.0
CD2 C:HIS71 4.5 31.5 1.0
CA C:ASP83 4.7 26.0 1.0
N C:HIS80 4.7 31.1 1.0
N C:GLY72 4.8 32.4 1.0
CA C:HIS80 4.8 29.4 1.0
N C:HIS71 4.9 34.1 1.0
C C:HIS71 4.9 32.9 1.0
CA C:HIS63 4.9 29.1 1.0
N C:ASP83 5.0 26.5 1.0

Zinc binding site 4 out of 6 in 3gqf

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Zinc binding site 4 out of 6 in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn155

b:29.6
occ:1.00
 OD1 D:ASP83 1.8 26.2 1.0
ND1 D:HIS80 2.0 27.5 1.0
ND1 D:HIS63 2.1 27.9 1.0
ND1 D:HIS71 2.2 30.0 1.0
CG D:ASP83 2.7 27.5 1.0
CE1 D:HIS80 2.8 27.0 1.0
OD2 D:ASP83 2.9 28.5 1.0
CE1 D:HIS63 3.0 29.3 1.0
CG D:HIS63 3.1 27.5 1.0
CE1 D:HIS71 3.1 28.4 1.0
CG D:HIS80 3.2 28.0 1.0
CG D:HIS71 3.3 30.6 1.0
CB D:HIS63 3.4 28.2 1.0
CB D:HIS71 3.6 31.4 1.0
CB D:HIS80 3.7 29.0 1.0
CA D:HIS71 4.0 31.9 1.0
NE2 D:HIS80 4.0 27.2 1.0
CB D:ASP83 4.1 25.4 1.0
NE2 D:HIS63 4.2 28.3 1.0
CD2 D:HIS80 4.2 27.5 1.0
CD2 D:HIS63 4.2 27.8 1.0
NE2 D:HIS71 4.3 29.9 1.0
O D:LYS136 4.3 32.2 1.0
CD2 D:HIS71 4.4 30.7 1.0
CA D:ASP83 4.6 25.4 1.0
N D:HIS80 4.7 30.6 1.0
CA D:THR137 4.8 30.2 1.0
N D:ASP83 4.8 25.5 1.0
CA D:HIS80 4.8 29.1 1.0
N D:GLY72 4.9 31.3 1.0
C D:HIS71 4.9 31.8 1.0
CA D:HIS63 5.0 27.9 1.0
O D:THR137 5.0 29.6 1.0
N D:HIS71 5.0 32.7 1.0

Zinc binding site 5 out of 6 in 3gqf

Go back to Zinc Binding Sites List in 3gqf
Zinc binding site 5 out of 6 in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn155

b:26.6
occ:1.00
 OD1 E:ASP83 2.0 20.1 1.0
ND1 E:HIS63 2.0 21.9 1.0
ND1 E:HIS80 2.1 24.5 1.0
ND1 E:HIS71 2.2 27.1 1.0
CG E:ASP83 2.8 23.1 1.0
CE1 E:HIS80 2.9 24.2 1.0
OD2 E:ASP83 3.0 22.6 1.0
CE1 E:HIS63 3.0 24.2 1.0
CG E:HIS63 3.0 25.4 1.0
CE1 E:HIS71 3.1 26.4 1.0
CG E:HIS80 3.1 25.1 1.0
CG E:HIS71 3.3 28.3 1.0
CB E:HIS63 3.3 25.9 1.0
CB E:HIS80 3.6 25.5 1.0
CB E:HIS71 3.7 29.2 1.0
CA E:HIS71 4.0 30.0 1.0
NE2 E:HIS80 4.1 23.9 1.0
NE2 E:HIS63 4.1 25.1 1.0
CD2 E:HIS63 4.2 23.1 1.0
CD2 E:HIS80 4.2 22.9 1.0
CB E:ASP83 4.2 23.5 1.0
O E:LYS136 4.3 30.4 1.0
NE2 E:HIS71 4.3 26.4 1.0
CD2 E:HIS71 4.4 27.8 1.0
CA E:ASP83 4.7 23.8 1.0
N E:HIS80 4.7 27.0 1.0
CA E:HIS80 4.8 26.5 1.0
CA E:THR137 4.8 29.1 1.0
N E:GLY72 4.8 29.9 1.0
N E:ASP83 4.9 24.1 1.0
CA E:HIS63 4.9 26.8 1.0
C E:HIS71 4.9 30.1 1.0

Zinc binding site 6 out of 6 in 3gqf

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Zinc binding site 6 out of 6 in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn155

b:23.1
occ:1.00
 OD1 F:ASP83 1.9 18.4 1.0
ND1 F:HIS80 2.1 23.0 1.0
ND1 F:HIS63 2.1 21.9 1.0
ND1 F:HIS71 2.2 23.3 1.0
CG F:ASP83 2.7 21.4 1.0
OD2 F:ASP83 2.9 19.1 1.0
CE1 F:HIS80 3.0 21.8 1.0
CE1 F:HIS71 3.1 23.9 1.0
CG F:HIS63 3.1 23.9 1.0
CE1 F:HIS63 3.1 21.9 1.0
CG F:HIS80 3.1 24.1 1.0
CG F:HIS71 3.2 26.7 1.0
CB F:HIS63 3.4 24.9 1.0
CB F:HIS80 3.5 25.4 1.0
CB F:HIS71 3.6 27.9 1.0
CA F:HIS71 3.9 28.8 1.0
O F:LYS136 4.1 30.2 1.0
NE2 F:HIS80 4.1 22.5 1.0
CB F:ASP83 4.2 21.1 1.0
CD2 F:HIS80 4.2 23.3 1.0
NE2 F:HIS63 4.2 21.1 1.0
NE2 F:HIS71 4.2 23.6 1.0
CD2 F:HIS63 4.2 22.2 1.0
CD2 F:HIS71 4.3 25.6 1.0
CA F:ASP83 4.7 22.5 1.0
N F:HIS80 4.7 26.4 1.0
CA F:HIS80 4.7 25.5 1.0
N F:GLY72 4.8 28.6 1.0
N F:ASP83 4.9 22.2 1.0
N F:HIS71 4.9 29.9 1.0
C F:HIS71 4.9 28.7 1.0
CA F:HIS63 4.9 25.3 1.0
C F:LYS136 5.0 30.1 1.0

Reference:

D.D.Winkler, J.P.Schuermann, X.Cao, S.P.Holloway, D.R.Borchelt, M.C.Carroll, J.B.Proescher, V.C.Culotta, P.J.Hart. Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q. Biochemistry V. 48 3436 2009.
ISSN: ISSN 0006-2960
PubMed: 19227972
DOI: 10.1021/BI8021735
Page generated: Thu Oct 24 13:51:31 2024

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