Zinc in PDB 8gv3: The Cryo-Em Structure of Gsnor with NYY001
Enzymatic activity of The Cryo-Em Structure of Gsnor with NYY001
All present enzymatic activity of The Cryo-Em Structure of Gsnor with NYY001:
1.1.1.1;
1.1.1.284;
Zinc Binding Sites:
The binding sites of Zinc atom in the The Cryo-Em Structure of Gsnor with NYY001
(pdb code 8gv3). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
The Cryo-Em Structure of Gsnor with NYY001, PDB code: 8gv3:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8gv3
Go back to
Zinc Binding Sites List in 8gv3
Zinc binding site 1 out
of 4 in the The Cryo-Em Structure of Gsnor with NYY001
![](/pictures/ZN/pdb/gv/8gv3-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/gv/8gv3-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of The Cryo-Em Structure of Gsnor with NYY001 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:103.9
occ:1.00
|
SG
|
A:CYS110
|
2.3
|
48.0
|
1.0
|
SG
|
A:CYS102
|
2.3
|
49.3
|
1.0
|
SG
|
A:CYS99
|
2.3
|
59.5
|
1.0
|
SG
|
A:CYS96
|
2.3
|
53.4
|
1.0
|
CB
|
A:CYS102
|
3.4
|
49.3
|
1.0
|
CB
|
A:CYS110
|
3.6
|
48.0
|
1.0
|
CB
|
A:CYS99
|
3.6
|
59.5
|
1.0
|
CB
|
A:CYS96
|
3.6
|
53.4
|
1.0
|
N
|
A:GLY97
|
3.8
|
59.9
|
1.0
|
N
|
A:CYS96
|
3.8
|
53.4
|
1.0
|
N
|
A:CYS99
|
3.9
|
59.5
|
1.0
|
CA
|
A:CYS110
|
4.1
|
48.0
|
1.0
|
CA
|
A:CYS96
|
4.2
|
53.4
|
1.0
|
N
|
A:GLU98
|
4.3
|
66.3
|
1.0
|
CA
|
A:CYS99
|
4.3
|
59.5
|
1.0
|
N
|
A:CYS102
|
4.4
|
49.3
|
1.0
|
CA
|
A:CYS102
|
4.4
|
49.3
|
1.0
|
C
|
A:CYS96
|
4.5
|
53.4
|
1.0
|
N
|
A:GLN111
|
4.7
|
47.7
|
1.0
|
CA
|
A:GLY97
|
4.7
|
59.9
|
1.0
|
C
|
A:GLN95
|
4.9
|
40.2
|
1.0
|
C
|
A:CYS110
|
4.9
|
48.0
|
1.0
|
C
|
A:GLY97
|
5.0
|
59.9
|
1.0
|
CB
|
A:LYS112
|
5.0
|
46.4
|
1.0
|
C
|
A:CYS99
|
5.0
|
59.5
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8gv3
Go back to
Zinc Binding Sites List in 8gv3
Zinc binding site 2 out
of 4 in the The Cryo-Em Structure of Gsnor with NYY001
![](/pictures/ZN/pdb/gv/8gv3-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/gv/8gv3-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of The Cryo-Em Structure of Gsnor with NYY001 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:100.4
occ:1.00
|
SG
|
A:CYS173
|
2.3
|
47.8
|
1.0
|
SG
|
A:CYS44
|
2.3
|
59.7
|
1.0
|
NE2
|
A:HIS66
|
2.3
|
46.9
|
1.0
|
N25
|
A:WKZ404
|
2.7
|
68.5
|
1.0
|
CE1
|
A:HIS66
|
3.0
|
46.9
|
1.0
|
CB
|
A:CYS173
|
3.1
|
47.8
|
1.0
|
CB
|
A:CYS44
|
3.1
|
59.7
|
1.0
|
CD2
|
A:HIS66
|
3.5
|
46.9
|
1.0
|
C24
|
A:WKZ404
|
3.6
|
68.5
|
1.0
|
C26
|
A:WKZ404
|
3.7
|
68.5
|
1.0
|
CG2
|
A:THR46
|
4.2
|
60.1
|
1.0
|
ND1
|
A:HIS66
|
4.2
|
46.9
|
1.0
|
CG
|
A:HIS66
|
4.5
|
46.9
|
1.0
|
OE1
|
A:GLU67
|
4.5
|
45.8
|
1.0
|
CD
|
A:GLU67
|
4.5
|
45.8
|
1.0
|
C5N
|
A:NAD403
|
4.6
|
62.5
|
1.0
|
CA
|
A:CYS173
|
4.6
|
47.8
|
1.0
|
CA
|
A:CYS44
|
4.6
|
59.7
|
1.0
|
OE2
|
A:GLU67
|
4.7
|
45.8
|
1.0
|
C23
|
A:WKZ404
|
4.8
|
68.5
|
1.0
|
N22
|
A:WKZ404
|
4.8
|
68.5
|
1.0
|
CG
|
A:GLU67
|
5.0
|
45.8
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8gv3
Go back to
Zinc Binding Sites List in 8gv3
Zinc binding site 3 out
of 4 in the The Cryo-Em Structure of Gsnor with NYY001
![](/pictures/ZN/pdb/gv/8gv3-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/gv/8gv3-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of The Cryo-Em Structure of Gsnor with NYY001 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:104.3
occ:1.00
|
SG
|
B:CYS110
|
2.3
|
48.6
|
1.0
|
SG
|
B:CYS102
|
2.3
|
50.9
|
1.0
|
SG
|
B:CYS99
|
2.3
|
60.8
|
1.0
|
SG
|
B:CYS96
|
2.3
|
53.5
|
1.0
|
CB
|
B:CYS102
|
3.4
|
50.9
|
1.0
|
CB
|
B:CYS110
|
3.6
|
48.6
|
1.0
|
CB
|
B:CYS99
|
3.6
|
60.8
|
1.0
|
CB
|
B:CYS96
|
3.6
|
53.5
|
1.0
|
N
|
B:GLY97
|
3.8
|
61.4
|
1.0
|
N
|
B:CYS96
|
3.8
|
53.5
|
1.0
|
N
|
B:CYS99
|
3.9
|
60.8
|
1.0
|
CA
|
B:CYS110
|
4.1
|
48.6
|
1.0
|
CA
|
B:CYS96
|
4.2
|
53.5
|
1.0
|
N
|
B:GLU98
|
4.3
|
67.4
|
1.0
|
CA
|
B:CYS99
|
4.3
|
60.8
|
1.0
|
N
|
B:CYS102
|
4.4
|
50.9
|
1.0
|
CA
|
B:CYS102
|
4.4
|
50.9
|
1.0
|
C
|
B:CYS96
|
4.5
|
53.5
|
1.0
|
N
|
B:GLN111
|
4.7
|
48.4
|
1.0
|
CA
|
B:GLY97
|
4.7
|
61.4
|
1.0
|
C
|
B:GLN95
|
4.8
|
40.4
|
1.0
|
C
|
B:CYS110
|
4.9
|
48.6
|
1.0
|
C
|
B:GLY97
|
5.0
|
61.4
|
1.0
|
CB
|
B:LYS112
|
5.0
|
46.9
|
1.0
|
C
|
B:CYS99
|
5.0
|
60.8
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8gv3
Go back to
Zinc Binding Sites List in 8gv3
Zinc binding site 4 out
of 4 in the The Cryo-Em Structure of Gsnor with NYY001
![](/pictures/ZN/pdb/gv/8gv3-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/gv/8gv3-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of The Cryo-Em Structure of Gsnor with NYY001 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:99.6
occ:1.00
|
SG
|
B:CYS173
|
2.3
|
47.6
|
1.0
|
SG
|
B:CYS44
|
2.3
|
60.5
|
1.0
|
NE2
|
B:HIS66
|
2.3
|
47.1
|
1.0
|
N25
|
B:WKZ404
|
2.7
|
68.8
|
1.0
|
CE1
|
B:HIS66
|
3.0
|
47.1
|
1.0
|
CB
|
B:CYS173
|
3.1
|
47.6
|
1.0
|
CB
|
B:CYS44
|
3.1
|
60.5
|
1.0
|
CD2
|
B:HIS66
|
3.5
|
47.1
|
1.0
|
C24
|
B:WKZ404
|
3.6
|
68.8
|
1.0
|
C26
|
B:WKZ404
|
3.7
|
68.8
|
1.0
|
CG2
|
B:THR46
|
4.2
|
60.1
|
1.0
|
ND1
|
B:HIS66
|
4.2
|
47.1
|
1.0
|
CG
|
B:HIS66
|
4.5
|
47.1
|
1.0
|
OE1
|
B:GLU67
|
4.5
|
46.1
|
1.0
|
CD
|
B:GLU67
|
4.5
|
46.1
|
1.0
|
C5N
|
B:NAD403
|
4.6
|
62.0
|
1.0
|
CA
|
B:CYS173
|
4.6
|
47.6
|
1.0
|
CA
|
B:CYS44
|
4.6
|
60.5
|
1.0
|
OE2
|
B:GLU67
|
4.7
|
46.1
|
1.0
|
C23
|
B:WKZ404
|
4.8
|
68.8
|
1.0
|
N22
|
B:WKZ404
|
4.8
|
68.8
|
1.0
|
CG
|
B:GLU67
|
5.0
|
46.1
|
1.0
|
|
Reference:
Y.Cao,
Y.Xia.
The Cryo-Em Structure of Gsnor with NYY001 To Be Published.
Page generated: Thu Dec 28 13:05:39 2023
|