Atomistry » Zinc » PDB 5tte-5u0e » 5tv3
Atomistry »
  Zinc »
    PDB 5tte-5u0e »
      5tv3 »

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

Go back to Zinc Binding Sites List in 5tv3
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

Go back to Zinc Binding Sites List in 5tv3
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

Go back to Zinc Binding Sites List in 5tv3
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

Go back to Zinc Binding Sites List in 5tv3
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

Go back to Zinc Binding Sites List in 5tv3
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

Go back to Zinc Binding Sites List in 5tv3
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

Go back to Zinc Binding Sites List in 5tv3
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

Last articles

Na in 3CCE
Na in 3CC7
Na in 3CC4
Na in 3CC9
Na in 3CBC
Na in 3CBT
Na in 3C9F
Na in 3CB8
Na in 3C7O
Na in 3C88
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy