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

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

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

Protein crystallography data

The structure of Crystal Structure of Neisseria Gonorrhoeae Carbonic Anhydrase with 3- Phenyl-N-(5-Sulfamoyl-1,3,4-Thiadiazol-2-Yl)Propanamide, PDB code: 8drb 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) 46.03 / 2.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.705, 121.89, 78.516, 90, 116.59, 90
R / Rfree (%) 19.1 / 25.3

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 8drb

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


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

b:39.8
occ:1.00
 N01 A:TBW301 2.1 45.4 1.0
O03 A:TBW301 2.1 46.4 1.0
NE2 A:HIS92 2.1 26.8 1.0
NE2 A:HIS94 2.2 38.2 1.0
ND1 A:HIS111 2.2 28.0 1.0
S02 A:TBW301 2.6 40.4 1.0
CD2 A:HIS94 3.1 35.8 1.0
CD2 A:HIS92 3.1 29.4 1.0
CE1 A:HIS111 3.1 30.6 1.0
CE1 A:HIS92 3.1 27.0 1.0
CG A:HIS111 3.2 32.8 1.0
CE1 A:HIS94 3.2 38.5 1.0
CB A:HIS111 3.6 33.4 1.0
O04 A:TBW301 3.7 41.4 1.0
OG1 A:THR177 3.9 30.5 1.0
C05 A:TBW301 3.9 45.5 1.0
OE1 A:GLU98 4.2 32.5 1.0
CG A:HIS94 4.2 34.1 1.0
CG A:HIS92 4.2 27.7 1.0
ND1 A:HIS92 4.2 26.0 1.0
ND1 A:HIS94 4.3 35.5 1.0
NE2 A:HIS111 4.3 28.2 1.0
CD2 A:HIS111 4.3 33.4 1.0
N06 A:TBW301 4.6 41.5 1.0

Zinc binding site 2 out of 4 in 8drb

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


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

b:50.0
occ:1.00
 O03 C:TBW301 2.1 66.3 1.0
NE2 C:HIS92 2.1 28.4 1.0
N01 C:TBW301 2.1 57.0 1.0
NE2 C:HIS94 2.3 37.0 1.0
ND1 C:HIS111 2.3 33.1 1.0
S02 C:TBW301 2.5 56.4 1.0
CE1 C:HIS92 3.0 30.8 1.0
CD2 C:HIS92 3.1 31.4 1.0
CD2 C:HIS94 3.2 37.6 1.0
CE1 C:HIS111 3.2 35.6 1.0
CE1 C:HIS94 3.3 40.2 1.0
CG C:HIS111 3.3 35.3 1.0
CB C:HIS111 3.6 33.3 1.0
O04 C:TBW301 3.7 44.4 1.0
C05 C:TBW301 3.9 60.0 1.0
OE1 C:GLU98 4.0 37.4 1.0
OG1 C:THR177 4.0 32.0 1.0
ND1 C:HIS92 4.2 31.0 1.0
CG C:HIS92 4.2 33.2 1.0
CG C:HIS94 4.3 37.3 1.0
ND1 C:HIS94 4.3 38.0 1.0
NE2 C:HIS111 4.4 32.5 1.0
CD2 C:HIS111 4.4 35.8 1.0
N06 C:TBW301 4.6 54.5 1.0
CG2 C:THR177 5.0 31.7 1.0

Zinc binding site 3 out of 4 in 8drb

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


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

b:57.0
occ:1.00
 O03 E:TBW301 2.1 65.0 1.0
N01 E:TBW301 2.1 64.7 1.0
ND1 E:HIS111 2.2 34.3 1.0
NE2 E:HIS94 2.3 44.4 1.0
NE2 E:HIS92 2.3 44.8 1.0
S02 E:TBW301 2.6 58.8 1.0
CE1 E:HIS111 3.1 37.1 1.0
CD2 E:HIS94 3.2 41.1 1.0
CG E:HIS111 3.2 34.6 1.0
CD2 E:HIS92 3.2 45.2 1.0
CE1 E:HIS92 3.3 45.9 1.0
CE1 E:HIS94 3.3 37.0 1.0
CB E:HIS111 3.6 34.3 1.0
O04 E:TBW301 3.7 52.0 1.0
OG1 E:THR177 3.8 40.8 1.0
C05 E:TBW301 4.0 59.8 1.0
OE1 E:GLU98 4.1 34.6 1.0
NE2 E:HIS111 4.3 37.9 1.0
CD2 E:HIS111 4.4 34.6 1.0
CG E:HIS94 4.4 38.1 1.0
CG E:HIS92 4.4 43.1 1.0
ND1 E:HIS92 4.4 43.6 1.0
ND1 E:HIS94 4.4 36.2 1.0
N06 E:TBW301 4.7 55.0 1.0
CG2 E:THR177 4.9 35.3 1.0
CB E:THR177 4.9 34.4 1.0

Zinc binding site 4 out of 4 in 8drb

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


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

b:61.8
occ:1.00
 N01 G:TBW301 2.1 62.8 1.0
NE2 G:HIS92 2.1 44.5 1.0
NE2 G:HIS94 2.3 57.2 1.0
ND1 G:HIS111 2.4 38.8 1.0
S02 G:TBW301 2.6 60.3 1.0
O03 G:TBW301 2.7 58.7 1.0
CE1 G:HIS92 3.1 50.6 1.0
CD2 G:HIS92 3.1 47.3 1.0
CD2 G:HIS94 3.3 52.2 1.0
CE1 G:HIS111 3.3 42.4 1.0
CE1 G:HIS94 3.4 49.1 1.0
CG G:HIS111 3.4 37.5 1.0
CB G:HIS111 3.7 35.7 1.0
C05 G:TBW301 3.8 61.8 1.0
O04 G:TBW301 3.8 56.9 1.0
OG1 G:THR177 3.9 42.6 1.0
OE1 G:GLU98 4.0 38.7 1.0
ND1 G:HIS92 4.2 47.4 1.0
CG G:HIS92 4.3 44.3 1.0
N06 G:TBW301 4.3 53.4 1.0
CG G:HIS94 4.4 51.5 1.0
ND1 G:HIS94 4.5 53.5 1.0
NE2 G:HIS111 4.5 38.4 1.0
CD2 G:HIS111 4.6 38.4 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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