Zinc in PDB 8yat: SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex
Enzymatic activity of SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex
All present enzymatic activity of SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex:
1.15.1.1;
Protein crystallography data
The structure of SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex, PDB code: 8yat
was solved by
S.Cheng,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
80.82 /
3.94
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
377.129,
46.672,
156.949,
90,
90,
90
|
R / Rfree (%)
|
30.3 /
36.8
|
Zinc Binding Sites:
The binding sites of Zinc atom in the SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex
(pdb code 8yat). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex, PDB code: 8yat:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8yat
Go back to
Zinc Binding Sites List in 8yat
Zinc binding site 1 out
of 4 in the SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn201
b:44.0
occ:1.00
|
OD1
|
A:ASP83
|
2.1
|
50.7
|
1.0
|
ND1
|
A:HIS71
|
2.3
|
58.3
|
1.0
|
ND1
|
A:HIS80
|
2.3
|
59.5
|
1.0
|
ND1
|
A:HIS63
|
2.3
|
51.3
|
1.0
|
OD2
|
A:ASP83
|
2.6
|
55.8
|
1.0
|
CG
|
A:ASP83
|
2.7
|
53.8
|
1.0
|
CG
|
A:HIS80
|
2.9
|
64.8
|
1.0
|
CE1
|
A:HIS71
|
2.9
|
57.7
|
1.0
|
CE1
|
A:HIS80
|
3.1
|
58.4
|
1.0
|
CG
|
A:HIS63
|
3.2
|
52.0
|
1.0
|
CB
|
A:HIS80
|
3.3
|
63.7
|
1.0
|
CE1
|
A:HIS63
|
3.3
|
44.9
|
1.0
|
CB
|
A:HIS63
|
3.4
|
54.3
|
1.0
|
CG
|
A:HIS71
|
3.5
|
54.5
|
1.0
|
O
|
A:LYS136
|
3.7
|
60.4
|
1.0
|
CD2
|
A:HIS80
|
3.8
|
68.0
|
1.0
|
NE2
|
A:HIS80
|
3.9
|
60.8
|
1.0
|
CB
|
A:ASP83
|
4.1
|
54.5
|
1.0
|
CB
|
A:HIS71
|
4.1
|
53.7
|
1.0
|
NE2
|
A:HIS71
|
4.2
|
54.9
|
1.0
|
CD2
|
A:HIS63
|
4.4
|
51.4
|
1.0
|
NE2
|
A:HIS63
|
4.4
|
44.8
|
1.0
|
N
|
A:HIS80
|
4.4
|
66.2
|
1.0
|
CA
|
A:HIS71
|
4.5
|
56.5
|
1.0
|
CA
|
A:HIS80
|
4.5
|
64.1
|
1.0
|
CD2
|
A:HIS71
|
4.5
|
52.4
|
1.0
|
CD2
|
A:HIS46
|
4.6
|
50.9
|
1.0
|
CA
|
A:ASP83
|
4.7
|
55.9
|
1.0
|
O
|
A:THR137
|
4.9
|
53.0
|
1.0
|
C
|
A:LYS136
|
4.9
|
60.3
|
1.0
|
N
|
A:ASP83
|
4.9
|
60.7
|
1.0
|
CA
|
A:HIS63
|
5.0
|
53.9
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8yat
Go back to
Zinc Binding Sites List in 8yat
Zinc binding site 2 out
of 4 in the SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn201
b:65.2
occ:1.00
|
ND1
|
E:HIS80
|
2.3
|
54.8
|
1.0
|
ND1
|
E:HIS71
|
2.3
|
53.1
|
1.0
|
ND1
|
E:HIS63
|
2.3
|
50.5
|
1.0
|
OD1
|
E:ASP83
|
2.4
|
51.0
|
1.0
|
CE1
|
E:HIS80
|
2.9
|
56.0
|
1.0
|
CG
|
E:ASP83
|
3.1
|
52.0
|
1.0
|
CG
|
E:HIS80
|
3.1
|
51.1
|
1.0
|
OD2
|
E:ASP83
|
3.2
|
56.9
|
1.0
|
CE1
|
E:HIS71
|
3.2
|
49.2
|
1.0
|
CE1
|
E:HIS63
|
3.2
|
51.5
|
1.0
|
CG
|
E:HIS63
|
3.3
|
47.5
|
1.0
|
CG
|
E:HIS71
|
3.4
|
56.8
|
1.0
|
O
|
E:LYS136
|
3.5
|
61.7
|
1.0
|
CB
|
E:HIS63
|
3.6
|
45.7
|
1.0
|
CB
|
E:HIS80
|
3.7
|
51.0
|
1.0
|
CB
|
E:HIS71
|
3.7
|
59.7
|
1.0
|
NE2
|
E:HIS80
|
3.9
|
59.5
|
1.0
|
CD2
|
E:HIS80
|
4.0
|
56.8
|
1.0
|
CA
|
E:HIS71
|
4.1
|
61.1
|
1.0
|
NE2
|
E:HIS71
|
4.3
|
53.6
|
1.0
|
NE2
|
E:HIS63
|
4.3
|
48.7
|
1.0
|
CD2
|
E:HIS63
|
4.4
|
48.2
|
1.0
|
CD2
|
E:HIS71
|
4.5
|
55.4
|
1.0
|
CB
|
E:ASP83
|
4.6
|
47.2
|
1.0
|
N
|
E:HIS80
|
4.7
|
58.3
|
1.0
|
C
|
E:LYS136
|
4.8
|
58.5
|
1.0
|
CA
|
E:HIS80
|
4.8
|
55.3
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8yat
Go back to
Zinc Binding Sites List in 8yat
Zinc binding site 3 out
of 4 in the SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn201
b:77.9
occ:1.00
|
CG
|
I:HIS80
|
2.0
|
96.0
|
1.0
|
CD2
|
I:HIS80
|
2.2
|
93.2
|
1.0
|
ND1
|
I:HIS71
|
2.3
|
71.9
|
1.0
|
ND1
|
I:HIS63
|
2.4
|
64.5
|
1.0
|
ND1
|
I:HIS80
|
2.4
|
98.2
|
1.0
|
NE2
|
I:HIS80
|
2.6
|
96.2
|
1.0
|
CE1
|
I:HIS80
|
2.7
|
95.4
|
1.0
|
CB
|
I:HIS80
|
2.8
|
87.6
|
1.0
|
CE1
|
I:HIS71
|
2.8
|
73.8
|
1.0
|
OD1
|
I:ASP83
|
2.9
|
73.0
|
1.0
|
OD2
|
I:ASP83
|
3.1
|
74.5
|
1.0
|
CG
|
I:HIS63
|
3.2
|
77.1
|
1.0
|
CG
|
I:ASP83
|
3.2
|
74.2
|
1.0
|
CB
|
I:HIS63
|
3.3
|
81.0
|
1.0
|
CE1
|
I:HIS63
|
3.4
|
61.8
|
1.0
|
CG
|
I:HIS71
|
3.6
|
72.6
|
1.0
|
O
|
I:LYS136
|
3.8
|
82.0
|
1.0
|
NE2
|
I:HIS71
|
4.1
|
74.3
|
1.0
|
CA
|
I:HIS80
|
4.2
|
85.6
|
1.0
|
CB
|
I:HIS71
|
4.2
|
76.2
|
1.0
|
CD2
|
I:HIS63
|
4.4
|
77.6
|
1.0
|
CD2
|
I:HIS71
|
4.5
|
74.2
|
1.0
|
NE2
|
I:HIS63
|
4.5
|
61.2
|
1.0
|
N
|
I:HIS80
|
4.5
|
85.4
|
1.0
|
CB
|
I:ASP83
|
4.5
|
78.4
|
1.0
|
CA
|
I:HIS71
|
4.6
|
78.3
|
1.0
|
CA
|
I:HIS63
|
4.8
|
71.3
|
1.0
|
CD2
|
I:HIS46
|
5.0
|
74.1
|
1.0
|
C
|
I:LYS136
|
5.0
|
73.8
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8yat
Go back to
Zinc Binding Sites List in 8yat
Zinc binding site 4 out
of 4 in the SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Zn201
b:88.9
occ:1.00
|
OD1
|
M:ASP83
|
2.3
|
73.0
|
1.0
|
ND1
|
M:HIS71
|
2.3
|
73.0
|
1.0
|
ND1
|
M:HIS63
|
2.3
|
75.5
|
1.0
|
ND1
|
M:HIS80
|
2.3
|
75.7
|
1.0
|
OD2
|
M:ASP83
|
2.8
|
77.8
|
1.0
|
CE1
|
M:HIS71
|
2.8
|
71.7
|
1.0
|
CG
|
M:ASP83
|
2.9
|
73.2
|
1.0
|
CG
|
M:HIS80
|
3.0
|
72.5
|
1.0
|
CE1
|
M:HIS80
|
3.1
|
74.7
|
1.0
|
CG
|
M:HIS63
|
3.2
|
70.5
|
1.0
|
CE1
|
M:HIS63
|
3.3
|
73.3
|
1.0
|
CB
|
M:HIS80
|
3.4
|
69.5
|
1.0
|
CB
|
M:HIS63
|
3.5
|
68.2
|
1.0
|
CG
|
M:HIS71
|
3.6
|
79.9
|
1.0
|
O
|
M:LYS136
|
3.8
|
78.3
|
1.0
|
CD2
|
M:HIS80
|
3.9
|
73.4
|
1.0
|
NE2
|
M:HIS80
|
3.9
|
74.2
|
1.0
|
NE2
|
M:HIS71
|
4.1
|
79.6
|
1.0
|
CB
|
M:HIS71
|
4.2
|
81.6
|
1.0
|
NE2
|
M:HIS63
|
4.3
|
69.9
|
1.0
|
CD2
|
M:HIS63
|
4.3
|
71.6
|
1.0
|
CB
|
M:ASP83
|
4.4
|
67.3
|
1.0
|
CD2
|
M:HIS71
|
4.5
|
81.4
|
1.0
|
CA
|
M:HIS71
|
4.5
|
78.4
|
1.0
|
CA
|
M:HIS80
|
4.6
|
69.8
|
1.0
|
N
|
M:HIS80
|
4.6
|
80.1
|
1.0
|
CD2
|
M:HIS46
|
4.6
|
75.6
|
1.0
|
CA
|
M:ASP83
|
4.9
|
63.0
|
1.0
|
C
|
M:LYS136
|
5.0
|
82.7
|
1.0
|
|
Reference:
S.Cheng,
S.Cheng.
N/A N/A.
Page generated: Tue Feb 25 12:11:58 2025
|