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Zinc in PDB 8dr2: Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with 2- Cyclohexyl-N-(5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Acetamide

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

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

Protein crystallography data

The structure of Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with 2- Cyclohexyl-N-(5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Acetamide, PDB code: 8dr2 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) 46.20 / 2.81
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.673, 120.583, 80.423, 90, 116.62, 90
R / Rfree (%) 19.2 / 26.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with 2- Cyclohexyl-N-(5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Acetamide (pdb code 8dr2). 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 2- Cyclohexyl-N-(5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Acetamide, PDB code: 8dr2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8dr2

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


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 2- Cyclohexyl-N-(5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:34.1
occ:1.00
 ND1 A:HIS111 2.1 35.8 1.0
N01 A:TE3301 2.1 36.0 1.0
O04 A:TE3301 2.1 39.4 1.0
NE2 A:HIS94 2.1 36.8 1.0
NE2 A:HIS92 2.1 34.5 1.0
S02 A:TE3301 2.6 34.1 1.0
CE1 A:HIS111 3.0 41.8 1.0
CD2 A:HIS94 3.1 37.5 1.0
CE1 A:HIS94 3.1 36.2 1.0
CG A:HIS111 3.1 36.6 1.0
CD2 A:HIS92 3.1 32.9 1.0
CE1 A:HIS92 3.2 36.4 1.0
CB A:HIS111 3.5 33.5 1.0
O03 A:TE3301 3.6 28.2 1.0
OE1 A:GLU98 3.8 34.0 1.0
OG1 A:THR177 3.8 29.6 1.0
C05 A:TE3301 4.0 34.3 1.0
NE2 A:HIS111 4.2 42.0 1.0
ND1 A:HIS94 4.2 34.9 1.0
CD2 A:HIS111 4.2 38.9 1.0
CG A:HIS94 4.2 36.1 1.0
ND1 A:HIS92 4.3 34.7 1.0
CG A:HIS92 4.3 32.5 1.0
N06 A:TE3301 4.6 33.6 1.0
CD A:GLU98 4.9 34.1 1.0
CA A:HIS111 5.0 30.6 1.0

Zinc binding site 2 out of 4 in 8dr2

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


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 2- Cyclohexyl-N-(5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:29.9
occ:1.00
 NE2 C:HIS94 2.0 31.3 1.0
ND1 C:HIS111 2.1 27.7 1.0
O04 C:TE3301 2.1 33.4 1.0
N01 C:TE3301 2.1 36.6 1.0
NE2 C:HIS92 2.1 25.1 1.0
S02 C:TE3301 2.6 34.2 1.0
CE1 C:HIS94 3.0 33.6 1.0
CD2 C:HIS94 3.0 32.0 1.0
CE1 C:HIS111 3.0 29.2 1.0
CE1 C:HIS92 3.1 26.5 1.0
CG C:HIS111 3.1 26.9 1.0
CD2 C:HIS92 3.1 26.6 1.0
CB C:HIS111 3.5 26.4 1.0
O03 C:TE3301 3.7 30.0 1.0
OG1 C:THR177 3.9 21.9 1.0
OE1 C:GLU98 3.9 25.4 1.0
C05 C:TE3301 4.0 32.8 1.0
ND1 C:HIS94 4.1 34.0 1.0
CG C:HIS94 4.1 34.6 1.0
NE2 C:HIS111 4.2 28.2 1.0
ND1 C:HIS92 4.2 24.2 1.0
CD2 C:HIS111 4.2 28.7 1.0
CG C:HIS92 4.2 26.7 1.0
N06 C:TE3301 4.6 31.6 1.0
CD C:GLU98 4.9 26.9 1.0
CA C:HIS111 4.9 28.8 1.0

Zinc binding site 3 out of 4 in 8dr2

Go back to Zinc Binding Sites List in 8dr2
Zinc binding site 3 out of 4 in the Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with 2- Cyclohexyl-N-(5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Acetamide


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 2- Cyclohexyl-N-(5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn302

b:30.5
occ:1.00
 NE2 E:HIS92 2.0 30.2 1.0
NE2 E:HIS94 2.0 30.1 1.0
ND1 E:HIS111 2.1 25.4 1.0
O04 E:TE3301 2.1 38.1 1.0
N01 E:TE3301 2.1 36.4 1.0
S02 E:TE3301 2.6 34.2 1.0
CE1 E:HIS111 3.0 26.7 1.0
CD2 E:HIS92 3.0 31.2 1.0
CD2 E:HIS94 3.0 30.3 1.0
CE1 E:HIS94 3.0 30.4 1.0
CE1 E:HIS92 3.0 31.4 1.0
CG E:HIS111 3.1 25.9 1.0
CB E:HIS111 3.5 27.3 1.0
O03 E:TE3301 3.6 35.1 1.0
OG1 E:THR177 3.8 29.0 1.0
C05 E:TE3301 3.9 36.5 1.0
OE1 E:GLU98 3.9 31.3 1.0
ND1 E:HIS94 4.1 29.3 1.0
CG E:HIS94 4.1 31.3 1.0
ND1 E:HIS92 4.1 32.2 1.0
CG E:HIS92 4.1 32.0 1.0
NE2 E:HIS111 4.2 26.0 1.0
CD2 E:HIS111 4.2 25.7 1.0
N06 E:TE3301 4.4 37.2 1.0
CD E:GLU98 4.9 32.4 1.0
CA E:HIS111 5.0 28.4 1.0

Zinc binding site 4 out of 4 in 8dr2

Go back to Zinc Binding Sites List in 8dr2
Zinc binding site 4 out of 4 in the Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with 2- Cyclohexyl-N-(5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Acetamide


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 2- Cyclohexyl-N-(5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn302

b:30.2
occ:1.00
 NE2 G:HIS92 1.9 28.6 1.0
NE2 G:HIS94 2.0 32.4 1.0
N01 G:TE3301 2.1 35.5 1.0
ND1 G:HIS111 2.1 31.4 1.0
S02 G:TE3301 2.6 32.7 1.0
O04 G:TE3301 2.7 33.1 1.0
CE1 G:HIS92 2.9 30.5 1.0
CD2 G:HIS92 3.0 29.5 1.0
CD2 G:HIS94 3.0 34.7 1.0
CE1 G:HIS111 3.1 35.1 1.0
CG G:HIS111 3.1 33.8 1.0
CE1 G:HIS94 3.1 31.3 1.0
CB G:HIS111 3.5 35.3 1.0
OG1 G:THR177 3.6 23.5 1.0
O03 G:TE3301 3.7 29.3 1.0
OE1 G:GLU98 3.9 31.7 1.0
C05 G:TE3301 4.0 31.6 1.0
ND1 G:HIS92 4.0 31.6 1.0
CG G:HIS92 4.1 30.7 1.0
CG G:HIS94 4.2 35.6 1.0
ND1 G:HIS94 4.2 34.2 1.0
NE2 G:HIS111 4.2 33.2 1.0
CD2 G:HIS111 4.2 34.3 1.0
N06 G:TE3301 4.6 31.1 1.0
CD G:GLU98 4.9 35.2 1.0
CA G:HIS111 4.9 34.7 1.0
CB G:THR177 4.9 27.1 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: Wed Oct 30 19:16:52 2024

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