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:
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
Mono view
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
Go back to
Zinc Binding Sites List in 3gqf
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
Go back to
Zinc Binding Sites List in 3gqf
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
Go back to
Zinc Binding Sites List in 3gqf
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
Go back to
Zinc Binding Sites List in 3gqf
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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