Zinc in PDB 8dqf: Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with N- (5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Cyclohexanecarboxamide

Enzymatic activity of Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with N- (5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Cyclohexanecarboxamide

All present enzymatic activity of Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with N- (5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Cyclohexanecarboxamide:
4.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with N- (5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Cyclohexanecarboxamide, PDB code: 8dqf 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) 46.11 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.91, 122.818, 78.53, 90, 117.26, 90
R / Rfree (%) 18.7 / 25.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with N- (5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Cyclohexanecarboxamide (pdb code 8dqf). 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 Neisseria Gonorrhoeae Carbonic Anhydrase with N- (5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Cyclohexanecarboxamide, PDB code: 8dqf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8dqf

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Zinc binding site 1 out of 4 in the Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with N- (5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Cyclohexanecarboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with N- (5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Cyclohexanecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:22.2
occ:1.00
 NE2 A:HIS94 2.0 19.8 1.0
NE2 A:HIS92 2.0 20.9 1.0
N04 A:VGV301 2.1 27.3 1.0
ND1 A:HIS111 2.2 18.3 1.0
S01 A:VGV301 2.6 27.4 1.0
O03 A:VGV301 2.7 28.5 1.0
CD2 A:HIS94 2.9 20.8 1.0
CD2 A:HIS92 3.0 22.2 1.0
CE1 A:HIS94 3.1 20.4 1.0
CE1 A:HIS92 3.1 22.9 1.0
CE1 A:HIS111 3.1 19.0 1.0
CG A:HIS111 3.2 19.2 1.0
CB A:HIS111 3.6 20.0 1.0
O02 A:VGV301 3.8 28.2 1.0
OE1 A:GLU98 3.8 32.0 1.0
C05 A:VGV301 3.9 31.9 1.0
OG1 A:THR177 4.0 19.3 1.0
CG A:HIS94 4.1 20.9 1.0
ND1 A:HIS94 4.2 20.8 1.0
CG A:HIS92 4.2 21.6 1.0
ND1 A:HIS92 4.2 21.8 1.0
NE2 A:HIS111 4.3 18.8 1.0
CD2 A:HIS111 4.3 19.1 1.0
N06 A:VGV301 4.5 32.4 1.0
CD A:GLU98 4.7 30.6 1.0

Zinc binding site 2 out of 4 in 8dqf

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Zinc binding site 2 out of 4 in the Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with N- (5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Cyclohexanecarboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with N- (5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Cyclohexanecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:20.0
occ:1.00
 NE2 C:HIS94 2.0 16.3 1.0
NE2 C:HIS92 2.0 16.1 1.0
N04 C:VGV301 2.1 26.1 1.0
O03 C:VGV301 2.1 24.9 1.0
ND1 C:HIS111 2.1 18.7 1.0
S01 C:VGV301 2.6 23.4 1.0
CD2 C:HIS94 3.0 15.7 1.0
CE1 C:HIS92 3.0 17.2 1.0
CE1 C:HIS94 3.0 15.5 1.0
CE1 C:HIS111 3.0 20.6 1.0
CD2 C:HIS92 3.1 16.2 1.0
CG C:HIS111 3.1 20.3 1.0
CB C:HIS111 3.6 21.0 1.0
OG1 C:THR177 3.6 17.2 1.0
O02 C:VGV301 3.7 20.6 1.0
C05 C:VGV301 4.0 28.1 1.0
ND1 C:HIS94 4.1 14.6 1.0
CG C:HIS94 4.1 14.9 1.0
OE1 C:GLU98 4.1 20.6 1.0
ND1 C:HIS92 4.2 16.6 1.0
CG C:HIS92 4.2 17.0 1.0
NE2 C:HIS111 4.2 19.9 1.0
CD2 C:HIS111 4.3 20.9 1.0
N06 C:VGV301 4.6 30.1 1.0
CB C:THR177 5.0 19.1 1.0

Zinc binding site 3 out of 4 in 8dqf

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Zinc binding site 3 out of 4 in the Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with N- (5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Cyclohexanecarboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with N- (5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Cyclohexanecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn302

b:19.9
occ:1.00
 NE2 E:HIS94 1.9 20.6 1.0
NE2 E:HIS92 2.0 15.4 1.0
N04 E:VGV301 2.1 26.3 1.0
ND1 E:HIS111 2.2 19.6 1.0
S01 E:VGV301 2.6 25.9 1.0
O03 E:VGV301 2.7 28.3 1.0
CE1 E:HIS94 2.9 20.6 1.0
CE1 E:HIS92 2.9 16.7 1.0
CD2 E:HIS94 3.0 20.6 1.0
CD2 E:HIS92 3.0 16.3 1.0
CE1 E:HIS111 3.1 20.3 1.0
CG E:HIS111 3.2 22.1 1.0
CB E:HIS111 3.6 22.6 1.0
O02 E:VGV301 3.8 26.4 1.0
OG1 E:THR177 3.8 18.1 1.0
OE1 E:GLU98 3.9 21.6 1.0
C05 E:VGV301 3.9 28.9 1.0
ND1 E:HIS94 4.0 21.3 1.0
ND1 E:HIS92 4.1 16.8 1.0
CG E:HIS94 4.1 21.3 1.0
CG E:HIS92 4.1 16.7 1.0
NE2 E:HIS111 4.3 20.9 1.0
CD2 E:HIS111 4.3 21.9 1.0
N06 E:VGV301 4.7 29.7 1.0
CA E:HIS111 5.0 23.2 1.0

Zinc binding site 4 out of 4 in 8dqf

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Zinc binding site 4 out of 4 in the Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with N- (5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Cyclohexanecarboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with N- (5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Cyclohexanecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn302

b:25.1
occ:1.00
 NE2 G:HIS92 2.0 25.3 1.0
N04 G:VGV301 2.1 33.0 1.0
NE2 G:HIS94 2.1 25.2 1.0
ND1 G:HIS111 2.2 21.5 1.0
S01 G:VGV301 2.6 30.9 1.0
O03 G:VGV301 2.7 35.3 1.0
CE1 G:HIS92 3.0 26.9 1.0
CD2 G:HIS92 3.0 25.6 1.0
CE1 G:HIS94 3.0 26.2 1.0
CD2 G:HIS94 3.1 24.5 1.0
CE1 G:HIS111 3.1 22.5 1.0
CG G:HIS111 3.2 22.6 1.0
CB G:HIS111 3.5 24.2 1.0
OG1 G:THR177 3.9 18.2 1.0
C05 G:VGV301 3.9 33.6 1.0
O02 G:VGV301 3.9 28.2 1.0
OE1 G:GLU98 3.9 22.7 1.0
ND1 G:HIS92 4.2 26.8 1.0
CG G:HIS92 4.2 26.3 1.0
ND1 G:HIS94 4.2 26.4 1.0
CG G:HIS94 4.2 24.5 1.0
NE2 G:HIS111 4.3 21.3 1.0
CD2 G:HIS111 4.3 21.7 1.0
N06 G:VGV301 4.4 33.5 1.0
CD G:GLU98 4.9 23.4 1.0
CA G:HIS111 5.0 23.8 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 08:16:03 2023

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