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Zinc in PDB 5tv3: Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide

Enzymatic activity of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide

All present enzymatic activity of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide:
4.2.1.1;

Protein crystallography data

The structure of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide, PDB code: 5tv3 was solved by J.K.Modak, A.Roujeinikova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.94 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.560, 133.890, 166.600, 90.00, 90.30, 90.00
R / Rfree (%) 18.7 / 24.3

Other elements in 5tv3:

The structure of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide (pdb code 5tv3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide, PDB code: 5tv3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5tv3

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Zinc binding site 1 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide


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 the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:30.3
occ:0.87
 NAI A:7L3302 1.8 32.6 1.0
NE2 A:HIS112 1.8 43.8 1.0
ND1 A:HIS129 2.3 45.5 1.0
NE2 A:HIS110 2.4 47.2 1.0
CD2 A:HIS112 2.6 45.4 1.0
CE1 A:HIS112 2.8 43.6 1.0
CE1 A:HIS129 2.9 45.1 1.0
CD2 A:HIS110 2.9 42.6 1.0
SAF A:7L3302 3.1 32.6 1.0
OAG A:7L3302 3.2 35.1 1.0
CG A:HIS129 3.6 38.5 1.0
OG1 A:THR191 3.6 28.4 1.0
CG A:HIS112 3.7 43.5 1.0
CE1 A:HIS110 3.7 50.9 1.0
ND1 A:HIS112 3.7 44.8 1.0
CAE A:7L3302 4.0 32.6 1.0
NE2 A:HIS129 4.1 47.0 1.0
OE1 A:GLU116 4.1 46.6 1.0
CB A:HIS129 4.2 38.2 1.0
OAH A:7L3302 4.2 32.6 1.0
CG A:HIS110 4.2 44.0 1.0
CD2 A:HIS129 4.5 43.2 1.0
ND1 A:HIS110 4.5 48.6 1.0
SAA A:7L3302 4.9 32.7 1.0
NAD A:7L3302 4.9 32.6 1.0

Zinc binding site 2 out of 8 in 5tv3

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Zinc binding site 2 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide


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 the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:33.6
occ:1.00
 NE2 B:HIS112 1.8 28.9 1.0
NE2 B:HIS110 2.0 27.1 1.0
NAI B:7L3302 2.0 32.6 0.8
ND1 B:HIS129 2.0 29.6 1.0
CD2 B:HIS110 2.5 22.0 1.0
CE1 B:HIS112 2.8 42.8 1.0
CD2 B:HIS112 2.9 30.8 1.0
CE1 B:HIS129 2.9 33.2 1.0
CG B:HIS129 3.1 27.4 1.0
SAF B:7L3302 3.1 32.6 0.8
OAG B:7L3302 3.2 38.3 0.8
CE1 B:HIS110 3.2 38.3 1.0
CB B:HIS129 3.5 26.3 1.0
CG B:HIS110 3.8 24.2 1.0
ND1 B:HIS112 3.9 38.0 1.0
CG B:HIS112 4.0 33.8 1.0
CAE B:7L3302 4.0 33.0 0.8
OG1 B:THR191 4.0 30.8 1.0
NE2 B:HIS129 4.1 31.5 1.0
ND1 B:HIS110 4.1 32.4 1.0
CD2 B:HIS129 4.2 31.4 1.0
OE1 B:GLU116 4.2 33.6 1.0
OAH B:7L3302 4.4 32.6 0.8
NAD B:7L3302 4.7 41.8 0.8
CA B:HIS129 4.9 23.7 1.0
SAA B:7L3302 5.0 32.6 0.8

Zinc binding site 3 out of 8 in 5tv3

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Zinc binding site 3 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide


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 the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:31.0
occ:1.00
 NE2 C:HIS112 1.8 31.4 1.0
NAI C:7L3303 2.0 32.6 0.9
ND1 C:HIS129 2.1 30.4 1.0
NE2 C:HIS110 2.3 23.8 1.0
CE1 C:HIS112 2.5 26.1 1.0
CE1 C:HIS129 2.5 26.3 1.0
CD2 C:HIS112 2.7 26.7 1.0
CD2 C:HIS110 2.8 31.2 1.0
OG1 C:THR191 3.1 23.9 1.0
CG C:HIS129 3.4 24.2 1.0
SAF C:7L3303 3.4 32.6 0.9
ND1 C:HIS112 3.5 30.6 1.0
CE1 C:HIS110 3.6 30.4 1.0
CG C:HIS112 3.6 31.7 1.0
OAG C:7L3303 3.7 32.6 0.9
OE1 C:GLU116 3.8 48.6 1.0
NE2 C:HIS129 3.8 29.7 1.0
CB C:HIS129 4.1 27.1 1.0
CG C:HIS110 4.1 27.3 1.0
CD2 C:HIS129 4.2 28.1 1.0
OAH C:7L3303 4.4 32.6 0.9
C1 C:GOL302 4.4 43.1 1.0
CB C:THR191 4.5 28.0 1.0
ND1 C:HIS110 4.5 25.2 1.0
CAE C:7L3303 4.5 32.6 0.9
CD C:GLU116 4.9 41.7 1.0
CB C:HIS112 5.0 31.0 1.0

Zinc binding site 4 out of 8 in 5tv3

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Zinc binding site 4 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide


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 the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:51.0
occ:1.00
 NE2 D:HIS112 1.9 36.4 1.0
NAI D:7L3303 2.0 32.6 0.9
ND1 D:HIS129 2.1 38.9 1.0
CD2 D:HIS112 2.5 34.9 1.0
NE2 D:HIS110 2.6 35.5 1.0
CE1 D:HIS129 2.8 36.9 1.0
CE1 D:HIS112 2.8 34.3 1.0
CD2 D:HIS110 3.1 37.1 1.0
CG D:HIS129 3.3 38.2 1.0
OG1 D:THR191 3.3 42.6 1.0
SAF D:7L3303 3.4 32.6 0.9
CG D:HIS112 3.5 33.3 1.0
OAG D:7L3303 3.6 36.0 0.9
ND1 D:HIS112 3.6 39.7 1.0
CE1 D:HIS110 3.8 32.0 1.0
CB D:HIS129 3.9 33.9 1.0
NE2 D:HIS129 3.9 31.6 1.0
OE2 D:GLU116 4.1 36.6 1.0
CD2 D:HIS129 4.2 37.1 1.0
OAH D:7L3303 4.3 40.2 0.9
CG D:HIS110 4.4 36.3 1.0
CAE D:7L3303 4.5 42.3 0.9
CB D:THR191 4.6 40.1 1.0
ND1 D:HIS110 4.7 33.0 1.0
CD D:GLU116 4.7 46.4 1.0
CB D:HIS112 4.8 39.2 1.0
OE1 D:GLU116 4.8 52.2 1.0

Zinc binding site 5 out of 8 in 5tv3

Go back to Zinc Binding Sites List in 5tv3
Zinc binding site 5 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:32.6
occ:1.00
 NE2 E:HIS110 1.9 21.3 1.0
NE2 E:HIS112 1.9 25.5 1.0
NAI E:7L3302 2.0 21.6 1.0
ND1 E:HIS129 2.3 29.8 1.0
CD2 E:HIS112 2.5 26.0 1.0
CD2 E:HIS110 2.7 21.0 1.0
CE1 E:HIS110 3.0 22.1 1.0
CE1 E:HIS112 3.1 36.3 1.0
CG E:HIS129 3.2 20.5 1.0
SAF E:7L3302 3.3 21.8 1.0
CE1 E:HIS129 3.3 23.7 1.0
CB E:HIS129 3.4 18.4 1.0
OG1 E:THR191 3.4 24.4 1.0
OAG E:7L3302 3.4 33.4 1.0
CG E:HIS112 3.7 25.8 1.0
OE1 E:GLU116 3.9 28.6 1.0
CG E:HIS110 3.9 20.9 1.0
ND1 E:HIS112 3.9 32.2 1.0
ND1 E:HIS110 4.0 20.2 1.0
CAE E:7L3302 4.3 23.0 1.0
CD2 E:HIS129 4.3 19.6 1.0
OAH E:7L3302 4.4 31.9 1.0
NE2 E:HIS129 4.4 19.3 1.0
CB E:THR191 4.7 25.5 1.0
CA E:HIS129 4.8 25.7 1.0
CD E:GLU116 4.8 30.1 1.0
O E:PHE111 4.8 40.2 1.0
CB E:HIS112 5.0 27.9 1.0

Zinc binding site 6 out of 8 in 5tv3

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Zinc binding site 6 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:33.4
occ:0.89
 NE2 F:HIS112 1.7 45.7 1.0
NAI F:7L3302 1.9 32.6 0.9
ND1 F:HIS129 1.9 35.2 1.0
NE2 F:HIS110 2.2 38.2 1.0
CD2 F:HIS110 2.6 37.7 1.0
CD2 F:HIS112 2.6 44.6 1.0
CE1 F:HIS129 2.7 33.4 1.0
CE1 F:HIS112 2.8 52.1 1.0
CG F:HIS129 3.0 40.6 1.0
SAF F:7L3302 3.1 32.6 0.9
OAG F:7L3302 3.3 41.0 0.9
OG1 F:THR191 3.4 35.1 1.0
CE1 F:HIS110 3.5 32.1 1.0
CB F:HIS129 3.6 39.9 1.0
OE1 F:GLU116 3.6 34.3 1.0
CG F:HIS112 3.8 45.4 1.0
ND1 F:HIS112 3.8 49.9 1.0
NE2 F:HIS129 3.8 34.0 1.0
CG F:HIS110 3.9 34.8 1.0
CD2 F:HIS129 4.0 38.1 1.0
CAE F:7L3302 4.1 39.4 0.9
OAH F:7L3302 4.3 32.6 0.9
ND1 F:HIS110 4.3 33.2 1.0
CD F:GLU116 4.5 43.6 1.0
CB F:THR191 4.8 34.0 1.0
NAD F:7L3302 4.9 40.9 0.9
OE2 F:GLU116 4.9 52.9 1.0
CA F:HIS129 4.9 33.1 1.0

Zinc binding site 7 out of 8 in 5tv3

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Zinc binding site 7 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:32.6
occ:1.00
 NE2 G:HIS110 1.9 30.4 1.0
ND1 G:HIS129 2.0 34.7 1.0
NAI G:7L3303 2.0 32.6 0.9
NE2 G:HIS112 2.1 31.8 1.0
CD2 G:HIS110 2.5 26.3 1.0
CE1 G:HIS129 2.8 29.9 1.0
CG G:HIS129 3.0 36.5 1.0
CE1 G:HIS112 3.0 34.4 1.0
CD2 G:HIS112 3.1 34.1 1.0
CE1 G:HIS110 3.1 28.1 1.0
SAF G:7L3303 3.2 32.6 0.9
OAG G:7L3303 3.2 32.6 0.9
CB G:HIS129 3.4 38.3 1.0
OG1 G:THR191 3.6 33.1 1.0
CG G:HIS110 3.8 25.5 1.0
NE2 G:HIS129 3.9 29.9 1.0
CD2 G:HIS129 4.0 32.0 1.0
ND1 G:HIS110 4.0 25.1 1.0
ND1 G:HIS112 4.1 36.3 1.0
CAE G:7L3303 4.2 32.6 0.9
CG G:HIS112 4.2 36.6 1.0
OAH G:7L3303 4.3 32.6 0.9
OE1 G:GLU116 4.3 38.0 1.0
CH2 G:TRP201 4.8 29.5 1.0
CA G:HIS129 4.9 34.6 1.0
NAD G:7L3303 4.9 37.3 0.9

Zinc binding site 8 out of 8 in 5tv3

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Zinc binding site 8 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with (E)-5-(((4-(Tert-Butyl)Phenyl)Sulfonyl)Imino)-4- Methyl-4,5-Dihydro-1,3,4-Thiadiazole-2-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:32.6
occ:1.00
 NE2 H:HIS112 1.8 26.4 1.0
NAI H:7L3302 2.0 32.6 1.0
NE2 H:HIS110 2.0 31.1 1.0
ND1 H:HIS129 2.1 27.0 1.0
CD2 H:HIS110 2.6 23.9 1.0
CE1 H:HIS112 2.7 27.8 1.0
CD2 H:HIS112 2.8 27.9 1.0
CE1 H:HIS129 3.0 26.4 1.0
CG H:HIS129 3.2 23.8 1.0
SAF H:7L3302 3.2 32.6 1.0
CE1 H:HIS110 3.2 41.1 1.0
OAG H:7L3302 3.3 32.6 1.0
CB H:HIS129 3.5 24.0 1.0
ND1 H:HIS112 3.8 30.3 1.0
OG1 H:THR191 3.8 24.7 1.0
CG H:HIS110 3.8 26.0 1.0
CG H:HIS112 3.9 30.2 1.0
OE1 H:GLU116 4.0 33.5 1.0
ND1 H:HIS110 4.1 41.7 1.0
NE2 H:HIS129 4.2 29.4 1.0
CAE H:7L3302 4.2 32.6 1.0
CD2 H:HIS129 4.2 25.7 1.0
OAH H:7L3302 4.4 32.6 1.0
CD H:GLU116 4.9 32.1 1.0
SAA H:7L3302 4.9 44.6 1.0
CA H:HIS129 4.9 30.6 1.0

Reference:

J.K.Modak, Y.C.Liu, C.T.Supuran, A.Roujeinikova. Structure-Activity Relationship For Sulfonamide Inhibition of Helicobacter Pylori Alpha-Carbonic Anhydrase. J. Med. Chem. V. 59 11098 2016.
ISSN: ISSN 1520-4804
PubMed: 28002963
DOI: 10.1021/ACS.JMEDCHEM.6B01333
Page generated: Mon Oct 28 08:49:30 2024

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