Zinc in PDB 8dpc: Crystal Structure of Carbonic Anhydrase From Neisseria Gonorrhoeae
Enzymatic activity of Crystal Structure of Carbonic Anhydrase From Neisseria Gonorrhoeae
All present enzymatic activity of Crystal Structure of Carbonic Anhydrase From Neisseria Gonorrhoeae:
4.2.1.1;
Protein crystallography data
The structure of Crystal Structure of Carbonic Anhydrase From Neisseria Gonorrhoeae, PDB code: 8dpc
was solved by
A.K.Marapaka,
C.Das,
D.P.Flaherty,
R.Yadav,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.12 /
2.41
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
71.158,
122.76,
78.67,
90,
116.87,
90
|
R / Rfree (%)
|
19 /
24.6
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Carbonic Anhydrase From Neisseria Gonorrhoeae
(pdb code 8dpc). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Carbonic Anhydrase From Neisseria Gonorrhoeae, PDB code: 8dpc:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8dpc
Go back to
Zinc Binding Sites List in 8dpc
Zinc binding site 1 out
of 4 in the Crystal Structure of Carbonic Anhydrase From Neisseria Gonorrhoeae
![](/pictures/ZN/pdb/dp/8dpc-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/dp/8dpc-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 Crystal Structure of Carbonic Anhydrase From Neisseria Gonorrhoeae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:48.0
occ:1.00
|
NE2
|
A:HIS92
|
2.3
|
23.6
|
1.0
|
ND1
|
A:HIS111
|
2.4
|
25.0
|
1.0
|
NE2
|
A:HIS94
|
2.4
|
26.4
|
1.0
|
O
|
A:HOH433
|
2.7
|
15.2
|
1.0
|
CD2
|
A:HIS92
|
3.2
|
20.6
|
1.0
|
CE1
|
A:HIS111
|
3.3
|
25.5
|
1.0
|
CE1
|
A:HIS92
|
3.3
|
22.6
|
1.0
|
CD2
|
A:HIS94
|
3.3
|
24.2
|
1.0
|
CG
|
A:HIS111
|
3.3
|
22.1
|
1.0
|
CE1
|
A:HIS94
|
3.4
|
25.3
|
1.0
|
OG1
|
A:THR177
|
3.7
|
17.4
|
1.0
|
CB
|
A:HIS111
|
3.7
|
19.4
|
1.0
|
OE1
|
A:GLU98
|
4.1
|
26.0
|
1.0
|
CG
|
A:HIS92
|
4.4
|
18.8
|
1.0
|
ND1
|
A:HIS92
|
4.4
|
20.3
|
1.0
|
NE2
|
A:HIS111
|
4.4
|
22.1
|
1.0
|
CD2
|
A:HIS111
|
4.5
|
23.5
|
1.0
|
CG
|
A:HIS94
|
4.5
|
20.6
|
1.0
|
ND1
|
A:HIS94
|
4.5
|
23.4
|
1.0
|
CB
|
A:THR177
|
4.9
|
16.8
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8dpc
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Zinc Binding Sites List in 8dpc
Zinc binding site 2 out
of 4 in the Crystal Structure of Carbonic Anhydrase From Neisseria Gonorrhoeae
![](/pictures/ZN/pdb/dp/8dpc-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/dp/8dpc-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 Crystal Structure of Carbonic Anhydrase From Neisseria Gonorrhoeae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:59.9
occ:1.00
|
NE2
|
C:HIS92
|
2.1
|
27.0
|
1.0
|
NE2
|
C:HIS94
|
2.3
|
29.2
|
1.0
|
ND1
|
C:HIS111
|
2.4
|
25.8
|
1.0
|
O
|
C:HOH428
|
2.7
|
22.6
|
1.0
|
CE1
|
C:HIS92
|
3.1
|
24.9
|
1.0
|
CD2
|
C:HIS92
|
3.2
|
24.4
|
1.0
|
CD2
|
C:HIS94
|
3.3
|
29.8
|
1.0
|
CE1
|
C:HIS111
|
3.3
|
25.7
|
1.0
|
CE1
|
C:HIS94
|
3.3
|
27.9
|
1.0
|
OG1
|
C:THR177
|
3.4
|
19.0
|
1.0
|
CG
|
C:HIS111
|
3.4
|
24.4
|
1.0
|
CB
|
C:HIS111
|
3.8
|
21.7
|
1.0
|
OE1
|
C:GLU98
|
4.0
|
23.5
|
1.0
|
ND1
|
C:HIS92
|
4.2
|
23.4
|
1.0
|
CG
|
C:HIS92
|
4.3
|
22.6
|
1.0
|
CG
|
C:HIS94
|
4.4
|
25.8
|
1.0
|
ND1
|
C:HIS94
|
4.4
|
27.8
|
1.0
|
NE2
|
C:HIS111
|
4.5
|
22.3
|
1.0
|
CD2
|
C:HIS111
|
4.5
|
22.9
|
1.0
|
CB
|
C:THR177
|
4.7
|
18.5
|
1.0
|
CG2
|
C:THR177
|
5.0
|
17.3
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8dpc
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Zinc Binding Sites List in 8dpc
Zinc binding site 3 out
of 4 in the Crystal Structure of Carbonic Anhydrase From Neisseria Gonorrhoeae
![](/pictures/ZN/pdb/dp/8dpc-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/dp/8dpc-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 Crystal Structure of Carbonic Anhydrase From Neisseria Gonorrhoeae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn301
b:68.5
occ:1.00
|
NE2
|
E:HIS92
|
2.3
|
33.5
|
1.0
|
ND1
|
E:HIS111
|
2.3
|
30.4
|
1.0
|
NE2
|
E:HIS94
|
2.5
|
33.6
|
1.0
|
O
|
E:HOH434
|
3.1
|
23.7
|
1.0
|
CD2
|
E:HIS92
|
3.2
|
31.4
|
1.0
|
CE1
|
E:HIS111
|
3.2
|
28.4
|
1.0
|
CE1
|
E:HIS92
|
3.2
|
31.1
|
1.0
|
CG
|
E:HIS111
|
3.3
|
26.8
|
1.0
|
CD2
|
E:HIS94
|
3.4
|
30.3
|
1.0
|
CE1
|
E:HIS94
|
3.5
|
29.0
|
1.0
|
CB
|
E:HIS111
|
3.7
|
21.1
|
1.0
|
OG1
|
E:THR177
|
3.7
|
19.5
|
1.0
|
OE1
|
E:GLU98
|
4.0
|
27.8
|
1.0
|
ND1
|
E:HIS92
|
4.3
|
29.5
|
1.0
|
CG
|
E:HIS92
|
4.3
|
28.6
|
1.0
|
NE2
|
E:HIS111
|
4.4
|
27.3
|
1.0
|
CD2
|
E:HIS111
|
4.4
|
27.6
|
1.0
|
CG
|
E:HIS94
|
4.6
|
26.5
|
1.0
|
ND1
|
E:HIS94
|
4.6
|
24.6
|
1.0
|
CB
|
E:THR177
|
4.9
|
20.1
|
1.0
|
CG2
|
E:THR177
|
5.0
|
20.5
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8dpc
Go back to
Zinc Binding Sites List in 8dpc
Zinc binding site 4 out
of 4 in the Crystal Structure of Carbonic Anhydrase From Neisseria Gonorrhoeae
![](/pictures/ZN/pdb/dp/8dpc-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/dp/8dpc-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 Crystal Structure of Carbonic Anhydrase From Neisseria Gonorrhoeae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn301
b:76.7
occ:1.00
|
NE2
|
G:HIS92
|
2.4
|
42.5
|
1.0
|
O
|
G:HOH437
|
2.5
|
28.0
|
1.0
|
NE2
|
G:HIS94
|
2.6
|
45.2
|
1.0
|
ND1
|
G:HIS111
|
2.6
|
36.9
|
1.0
|
OG1
|
G:THR177
|
3.3
|
36.4
|
1.0
|
CE1
|
G:HIS92
|
3.3
|
42.4
|
1.0
|
CD2
|
G:HIS92
|
3.5
|
38.7
|
1.0
|
CE1
|
G:HIS111
|
3.5
|
35.6
|
1.0
|
CD2
|
G:HIS94
|
3.5
|
42.3
|
1.0
|
CE1
|
G:HIS94
|
3.6
|
43.8
|
1.0
|
CG
|
G:HIS111
|
3.7
|
33.8
|
1.0
|
OE1
|
G:GLU98
|
3.9
|
44.0
|
1.0
|
CB
|
G:HIS111
|
4.1
|
28.7
|
1.0
|
ND1
|
G:HIS92
|
4.5
|
40.1
|
1.0
|
CB
|
G:THR177
|
4.6
|
35.3
|
1.0
|
CG
|
G:HIS92
|
4.6
|
37.2
|
1.0
|
NE2
|
G:HIS111
|
4.7
|
30.6
|
1.0
|
ND1
|
G:HIS94
|
4.7
|
40.5
|
1.0
|
CG
|
G:HIS94
|
4.7
|
37.8
|
1.0
|
CG2
|
G:THR177
|
4.8
|
33.8
|
1.0
|
CD2
|
G:HIS111
|
4.8
|
32.5
|
1.0
|
CG2
|
G:THR178
|
5.0
|
37.8
|
1.0
|
|
Reference:
A.K.Marapaka,
A.Nocentini,
M.S.Youse,
W.An,
K.J.Holly,
C.Das,
R.Yadav,
M.N.Seleem,
C.T.Supuran,
D.P.Flaherty.
Structural Characterization of Thiadiazolesulfonamide Inhibitors Bound to Neisseria Gonorrhoeae Alpha-Carbonic Anhydrase Acs Med.Chem.Lett. 2022.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.2C00471
Page generated: Sat Apr 8 08:15:53 2023
|