Zinc in PDB 7t8e: G93A Mutant of Human SOD1 in P21 Space Group
Enzymatic activity of G93A Mutant of Human SOD1 in P21 Space Group
All present enzymatic activity of G93A Mutant of Human SOD1 in P21 Space Group:
1.15.1.1;
Protein crystallography data
The structure of G93A Mutant of Human SOD1 in P21 Space Group, PDB code: 7t8e
was solved by
K.Amporndanai,
S.S.Hasnain,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.24 /
1.40
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
38.74,
68.21,
51.08,
90,
105.63,
90
|
R / Rfree (%)
|
19.9 /
22.9
|
Zinc Binding Sites:
The binding sites of Zinc atom in the G93A Mutant of Human SOD1 in P21 Space Group
(pdb code 7t8e). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
G93A Mutant of Human SOD1 in P21 Space Group, PDB code: 7t8e:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 7t8e
Go back to
Zinc Binding Sites List in 7t8e
Zinc binding site 1 out
of 4 in the G93A Mutant of Human SOD1 in P21 Space Group
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of G93A Mutant of Human SOD1 in P21 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn201
b:14.3
occ:1.00
|
ND1
|
A:HIS63
|
2.0
|
12.9
|
1.0
|
ND1
|
A:HIS80
|
2.0
|
14.7
|
1.0
|
OD1
|
A:ASP83
|
2.0
|
15.7
|
1.0
|
ND1
|
A:HIS71
|
2.1
|
16.1
|
1.0
|
CG
|
A:ASP83
|
2.8
|
14.1
|
1.0
|
OD2
|
A:ASP83
|
2.8
|
14.7
|
1.0
|
CE1
|
A:HIS80
|
2.9
|
15.1
|
1.0
|
CE1
|
A:HIS63
|
2.9
|
15.6
|
1.0
|
CE1
|
A:HIS71
|
2.9
|
15.2
|
1.0
|
HB2
|
A:HIS80
|
3.0
|
14.2
|
1.0
|
HE1
|
A:HIS80
|
3.0
|
15.3
|
1.0
|
CG
|
A:HIS63
|
3.0
|
14.4
|
1.0
|
HE1
|
A:HIS71
|
3.0
|
15.6
|
1.0
|
CG
|
A:HIS80
|
3.1
|
14.9
|
1.0
|
HE1
|
A:HIS63
|
3.1
|
15.2
|
1.0
|
HA
|
A:HIS71
|
3.2
|
18.0
|
1.0
|
CG
|
A:HIS71
|
3.2
|
16.6
|
1.0
|
HB3
|
A:HIS63
|
3.2
|
13.8
|
1.0
|
HB2
|
A:HIS63
|
3.3
|
13.8
|
1.0
|
HB2
|
A:HIS71
|
3.4
|
17.3
|
1.0
|
CB
|
A:HIS63
|
3.4
|
14.0
|
1.0
|
CB
|
A:HIS80
|
3.5
|
13.7
|
1.0
|
CB
|
A:HIS71
|
3.6
|
17.3
|
1.0
|
CA
|
A:HIS71
|
3.9
|
18.0
|
1.0
|
H
|
A:HIS80
|
3.9
|
15.3
|
1.0
|
O
|
A:LYS136
|
3.9
|
25.2
|
1.0
|
HB3
|
A:HIS80
|
4.0
|
14.2
|
1.0
|
NE2
|
A:HIS80
|
4.0
|
16.3
|
1.0
|
NE2
|
A:HIS63
|
4.1
|
16.8
|
1.0
|
H
|
A:GLY72
|
4.1
|
18.2
|
1.0
|
NE2
|
A:HIS71
|
4.1
|
15.8
|
1.0
|
CD2
|
A:HIS63
|
4.1
|
15.8
|
1.0
|
CD2
|
A:HIS80
|
4.1
|
15.2
|
1.0
|
CB
|
A:ASP83
|
4.2
|
13.7
|
1.0
|
CD2
|
A:HIS71
|
4.3
|
16.4
|
1.0
|
HA
|
A:ASP83
|
4.3
|
13.8
|
1.0
|
HA
|
A:THR137
|
4.6
|
23.0
|
1.0
|
HB3
|
A:HIS71
|
4.6
|
17.3
|
1.0
|
HB3
|
A:ASP83
|
4.6
|
13.8
|
1.0
|
N
|
A:HIS80
|
4.7
|
15.0
|
1.0
|
CA
|
A:ASP83
|
4.7
|
13.7
|
1.0
|
CA
|
A:HIS80
|
4.7
|
14.6
|
1.0
|
N
|
A:GLY72
|
4.8
|
18.2
|
1.0
|
HB2
|
A:ASP83
|
4.8
|
13.8
|
1.0
|
HE2
|
A:HIS80
|
4.8
|
30.0
|
0.0
|
HE2
|
A:HIS63
|
4.9
|
30.0
|
0.0
|
N
|
A:HIS71
|
4.9
|
18.4
|
1.0
|
C
|
A:LYS136
|
4.9
|
25.1
|
1.0
|
C
|
A:HIS71
|
4.9
|
18.2
|
1.0
|
HE2
|
A:HIS71
|
4.9
|
30.0
|
0.0
|
CA
|
A:HIS63
|
4.9
|
12.9
|
1.0
|
O
|
A:HOH381
|
5.0
|
23.1
|
1.0
|
N
|
A:ASP83
|
5.0
|
13.8
|
1.0
|
|
Zinc binding site 2 out
of 4 in 7t8e
Go back to
Zinc Binding Sites List in 7t8e
Zinc binding site 2 out
of 4 in the G93A Mutant of Human SOD1 in P21 Space Group
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of G93A Mutant of Human SOD1 in P21 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn203
b:17.6
occ:0.40
|
NE2
|
A:HIS120
|
1.6
|
18.5
|
1.0
|
O3
|
A:SO4204
|
2.2
|
40.6
|
1.0
|
NE2
|
A:HIS48
|
2.2
|
14.3
|
1.0
|
CE1
|
A:HIS120
|
2.3
|
19.8
|
1.0
|
ND1
|
A:HIS46
|
2.4
|
18.8
|
1.0
|
HE1
|
A:HIS120
|
2.5
|
19.3
|
1.0
|
HE2
|
A:HIS63
|
2.6
|
30.0
|
0.0
|
CD2
|
A:HIS120
|
2.7
|
17.8
|
1.0
|
HE1
|
A:HIS48
|
2.9
|
14.3
|
1.0
|
CE1
|
A:HIS48
|
2.9
|
14.3
|
1.0
|
HB2
|
A:HIS46
|
3.1
|
14.9
|
1.0
|
HD2
|
A:HIS120
|
3.1
|
18.1
|
1.0
|
O
|
A:HOH303
|
3.1
|
27.2
|
1.0
|
NE2
|
A:HIS63
|
3.2
|
16.8
|
1.0
|
CE1
|
A:HIS46
|
3.3
|
17.9
|
1.0
|
CD2
|
A:HIS48
|
3.4
|
14.1
|
1.0
|
HE1
|
A:HIS46
|
3.4
|
18.3
|
1.0
|
ND1
|
A:HIS120
|
3.4
|
18.8
|
1.0
|
S
|
A:SO4204
|
3.4
|
38.8
|
1.0
|
CG
|
A:HIS46
|
3.4
|
16.6
|
1.0
|
HD2
|
A:HIS63
|
3.5
|
15.6
|
1.0
|
CG
|
A:HIS120
|
3.6
|
18.1
|
1.0
|
O1
|
A:SO4204
|
3.7
|
40.0
|
1.0
|
HD2
|
A:HIS48
|
3.7
|
14.0
|
1.0
|
CD2
|
A:HIS63
|
3.7
|
15.8
|
1.0
|
CB
|
A:HIS46
|
3.7
|
15.3
|
1.0
|
HB
|
A:VAL118
|
3.8
|
12.7
|
1.0
|
HG11
|
A:VAL118
|
3.9
|
13.1
|
1.0
|
ND1
|
A:HIS48
|
4.1
|
14.1
|
1.0
|
HD1
|
A:HIS120
|
4.1
|
30.0
|
0.0
|
HB3
|
A:HIS46
|
4.2
|
14.9
|
1.0
|
HG12
|
A:VAL118
|
4.2
|
13.1
|
1.0
|
O4
|
A:SO4204
|
4.2
|
43.0
|
1.0
|
HG2
|
A:ARG143
|
4.3
|
16.8
|
1.0
|
CE1
|
A:HIS63
|
4.4
|
15.6
|
1.0
|
CG
|
A:HIS48
|
4.4
|
13.7
|
1.0
|
O2
|
A:SO4204
|
4.4
|
42.4
|
1.0
|
CG1
|
A:VAL118
|
4.4
|
13.2
|
1.0
|
NE2
|
A:HIS46
|
4.5
|
18.9
|
1.0
|
CB
|
A:VAL118
|
4.5
|
12.8
|
1.0
|
CD2
|
A:HIS46
|
4.6
|
18.9
|
1.0
|
HE
|
A:ARG143
|
4.6
|
17.5
|
1.0
|
HB3
|
A:ALA140
|
4.6
|
24.1
|
1.0
|
HE1
|
A:HIS63
|
4.7
|
15.2
|
1.0
|
HD1
|
A:HIS48
|
4.8
|
30.0
|
0.0
|
HG22
|
A:VAL118
|
4.9
|
12.7
|
1.0
|
H
|
A:HIS46
|
4.9
|
12.8
|
1.0
|
NE
|
A:ARG143
|
4.9
|
17.5
|
1.0
|
CG
|
A:HIS63
|
5.0
|
14.4
|
1.0
|
CA
|
A:HIS46
|
5.0
|
12.8
|
1.0
|
|
Zinc binding site 3 out
of 4 in 7t8e
Go back to
Zinc Binding Sites List in 7t8e
Zinc binding site 3 out
of 4 in the G93A Mutant of Human SOD1 in P21 Space Group
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of G93A Mutant of Human SOD1 in P21 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn201
b:13.8
occ:1.00
|
ND1
|
F:HIS80
|
2.0
|
14.4
|
1.0
|
OD1
|
F:ASP83
|
2.0
|
12.9
|
1.0
|
ND1
|
F:HIS63
|
2.0
|
14.8
|
1.0
|
ND1
|
F:HIS71
|
2.1
|
15.1
|
1.0
|
CG
|
F:ASP83
|
2.7
|
13.0
|
1.0
|
OD2
|
F:ASP83
|
2.8
|
12.2
|
1.0
|
CE1
|
F:HIS80
|
2.9
|
15.7
|
1.0
|
CE1
|
F:HIS71
|
2.9
|
14.6
|
1.0
|
HB2
|
F:HIS80
|
3.0
|
13.0
|
1.0
|
CE1
|
F:HIS63
|
3.0
|
16.4
|
1.0
|
HE1
|
F:HIS80
|
3.0
|
15.5
|
1.0
|
HE1
|
F:HIS71
|
3.0
|
14.7
|
1.0
|
CG
|
F:HIS80
|
3.1
|
13.9
|
1.0
|
CG
|
F:HIS63
|
3.1
|
15.7
|
1.0
|
HE1
|
F:HIS63
|
3.1
|
16.5
|
1.0
|
CG
|
F:HIS71
|
3.2
|
15.1
|
1.0
|
HA
|
F:HIS71
|
3.2
|
16.0
|
1.0
|
HB3
|
F:HIS63
|
3.2
|
14.7
|
1.0
|
HB2
|
F:HIS63
|
3.3
|
14.7
|
1.0
|
HB2
|
F:HIS71
|
3.4
|
15.5
|
1.0
|
CB
|
F:HIS63
|
3.4
|
14.8
|
1.0
|
CB
|
F:HIS80
|
3.5
|
12.9
|
1.0
|
CB
|
F:HIS71
|
3.6
|
15.5
|
1.0
|
CA
|
F:HIS71
|
3.9
|
15.9
|
1.0
|
H
|
F:HIS80
|
3.9
|
13.0
|
1.0
|
O
|
F:LYS136
|
4.0
|
24.0
|
1.0
|
NE2
|
F:HIS80
|
4.0
|
16.3
|
1.0
|
HB3
|
F:HIS80
|
4.0
|
13.0
|
1.0
|
H
|
F:GLY72
|
4.1
|
15.9
|
1.0
|
CD2
|
F:HIS80
|
4.1
|
14.9
|
1.0
|
NE2
|
F:HIS71
|
4.1
|
14.7
|
1.0
|
NE2
|
F:HIS63
|
4.1
|
18.5
|
1.0
|
CD2
|
F:HIS63
|
4.2
|
17.2
|
1.0
|
CB
|
F:ASP83
|
4.2
|
12.9
|
1.0
|
CD2
|
F:HIS71
|
4.2
|
14.7
|
1.0
|
HA
|
F:ASP83
|
4.3
|
12.6
|
1.0
|
HA
|
F:THR137
|
4.6
|
23.3
|
1.0
|
HB3
|
F:HIS71
|
4.6
|
15.5
|
1.0
|
HB3
|
F:ASP83
|
4.6
|
12.8
|
1.0
|
N
|
F:HIS80
|
4.7
|
13.0
|
1.0
|
CA
|
F:ASP83
|
4.7
|
12.4
|
1.0
|
CA
|
F:HIS80
|
4.7
|
12.3
|
1.0
|
N
|
F:GLY72
|
4.7
|
15.4
|
1.0
|
HB2
|
F:ASP83
|
4.8
|
12.8
|
1.0
|
HE2
|
F:HIS80
|
4.8
|
30.0
|
0.0
|
C
|
F:HIS71
|
4.9
|
16.9
|
1.0
|
HE2
|
F:HIS71
|
4.9
|
30.0
|
0.0
|
N
|
F:HIS71
|
4.9
|
16.1
|
1.0
|
HE2
|
F:HIS63
|
4.9
|
30.0
|
0.0
|
CA
|
F:HIS63
|
4.9
|
13.6
|
1.0
|
O
|
F:HOH392
|
4.9
|
24.9
|
1.0
|
C
|
F:LYS136
|
5.0
|
23.6
|
1.0
|
N
|
F:ASP83
|
5.0
|
12.2
|
1.0
|
HD2
|
F:HIS80
|
5.0
|
14.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 7t8e
Go back to
Zinc Binding Sites List in 7t8e
Zinc binding site 4 out
of 4 in the G93A Mutant of Human SOD1 in P21 Space Group
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of G93A Mutant of Human SOD1 in P21 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn202
b:14.7
occ:0.40
|
NE2
|
F:HIS120
|
1.8
|
16.0
|
1.0
|
O2
|
F:SO4203
|
2.1
|
35.9
|
1.0
|
NE2
|
F:HIS48
|
2.1
|
13.7
|
1.0
|
ND1
|
F:HIS46
|
2.4
|
17.5
|
1.0
|
HE2
|
F:HIS63
|
2.4
|
30.0
|
0.0
|
CE1
|
F:HIS120
|
2.4
|
16.3
|
1.0
|
HE1
|
F:HIS120
|
2.6
|
16.4
|
1.0
|
HE1
|
F:HIS48
|
2.7
|
13.8
|
1.0
|
CE1
|
F:HIS48
|
2.8
|
14.1
|
1.0
|
O
|
F:HOH301
|
2.9
|
21.8
|
1.0
|
CD2
|
F:HIS120
|
2.9
|
15.6
|
1.0
|
NE2
|
F:HIS63
|
3.1
|
18.5
|
1.0
|
HB2
|
F:HIS46
|
3.1
|
13.3
|
1.0
|
HD2
|
F:HIS120
|
3.3
|
15.8
|
1.0
|
CE1
|
F:HIS46
|
3.3
|
17.8
|
1.0
|
CD2
|
F:HIS48
|
3.4
|
13.4
|
1.0
|
S
|
F:SO4203
|
3.4
|
35.0
|
1.0
|
HD2
|
F:HIS63
|
3.4
|
17.1
|
1.0
|
HE1
|
F:HIS46
|
3.4
|
17.5
|
1.0
|
CG
|
F:HIS46
|
3.5
|
14.5
|
1.0
|
ND1
|
F:HIS120
|
3.5
|
16.6
|
1.0
|
CD2
|
F:HIS63
|
3.6
|
17.2
|
1.0
|
O4
|
F:SO4203
|
3.7
|
37.6
|
1.0
|
HD2
|
F:HIS48
|
3.7
|
13.1
|
1.0
|
CB
|
F:HIS46
|
3.8
|
13.6
|
1.0
|
CG
|
F:HIS120
|
3.8
|
16.1
|
1.0
|
HB
|
F:VAL118
|
3.9
|
11.3
|
1.0
|
ND1
|
F:HIS48
|
4.0
|
13.0
|
1.0
|
HG11
|
F:VAL118
|
4.1
|
11.7
|
1.0
|
O1
|
F:SO4203
|
4.1
|
37.7
|
1.0
|
HB3
|
F:HIS46
|
4.2
|
13.3
|
1.0
|
HD1
|
F:HIS120
|
4.2
|
30.0
|
0.0
|
CE1
|
F:HIS63
|
4.2
|
16.4
|
1.0
|
CG
|
F:HIS48
|
4.3
|
12.1
|
1.0
|
O3
|
F:SO4203
|
4.3
|
41.2
|
1.0
|
HG12
|
F:VAL118
|
4.4
|
11.7
|
1.0
|
HG2
|
F:ARG143
|
4.4
|
16.5
|
1.0
|
NE2
|
F:HIS46
|
4.5
|
17.2
|
1.0
|
CG1
|
F:VAL118
|
4.6
|
11.9
|
1.0
|
CD2
|
F:HIS46
|
4.6
|
15.7
|
1.0
|
HE1
|
F:HIS63
|
4.6
|
16.5
|
1.0
|
HE
|
F:ARG143
|
4.6
|
16.4
|
1.0
|
CB
|
F:VAL118
|
4.7
|
11.3
|
1.0
|
HD1
|
F:HIS48
|
4.7
|
30.0
|
0.0
|
HB3
|
F:ALA140
|
4.7
|
19.3
|
1.0
|
CG
|
F:HIS63
|
4.8
|
15.7
|
1.0
|
NE
|
F:ARG143
|
4.9
|
16.4
|
1.0
|
HH21
|
F:ARG143
|
4.9
|
16.1
|
1.0
|
HG22
|
F:VAL118
|
4.9
|
11.1
|
1.0
|
|
Reference:
K.Amporndanai,
S.Watanabe,
R.Awais,
C.Latham,
P.M.O Neill,
K.Yamanaka,
S.S.Hasnain.
Disease Onset and Its Course Are Delayed By on-Target Cellular SOD1 Engagement of Organo-Selenium Drug Compounds For Amyotrophic Lateral Sclerosis To Be Published.
Page generated: Wed Oct 30 11:33:00 2024
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