Zinc in PDB 4ygf: Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Acetazolamide

The structure of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Acetazolamide, PDB code: 4ygf was solved by A.Roujeinikova, J.K.Modak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.57 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.780, 133.610, 166.540, 90.00, 90.16, 90.00
R / Rfree (%)	18.7 / 21.5

The structure of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Acetazolamide also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Zinc atom in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Acetazolamide (pdb code 4ygf). 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 Acetazolamide, PDB code: 4ygf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Acetazolamide


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 Acetazolamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:21.4 occ:1.00 N1 A:AZM303 2.0 15.0 1.0 ND1 A:HIS129 2.0 14.1 1.0 NE2 A:HIS110 2.1 22.6 1.0 NE2 A:HIS112 2.1 15.0 1.0 CE1 A:HIS129 2.9 15.0 1.0 CD2 A:HIS112 2.9 15.7 1.0 O2 A:AZM303 2.9 15.1 1.0 CD2 A:HIS110 3.0 19.6 1.0 S1 A:AZM303 3.0 16.4 1.0 CG A:HIS129 3.1 13.3 1.0 CE1 A:HIS110 3.2 18.5 1.0 CE1 A:HIS112 3.3 15.7 1.0 CB A:HIS129 3.5 16.1 1.0 OG1 A:THR191 4.0 18.9 1.0 NE2 A:HIS129 4.0 13.6 1.0 C1 A:AZM303 4.1 15.1 1.0 CD2 A:HIS129 4.1 15.8 1.0 CG A:HIS112 4.1 15.7 1.0 O1 A:AZM303 4.1 17.0 1.0 CG A:HIS110 4.2 19.3 1.0 ND1 A:HIS110 4.2 17.4 1.0 ND1 A:HIS112 4.3 14.1 1.0 O2 A:GOL304 4.3 23.8 1.0 OE1 A:GLU116 4.4 22.2 1.0 C3 A:GOL304 4.6 18.7 1.0 S2 A:AZM303 4.9 21.2 1.0 C2 A:GOL304 4.9 18.9 1.0 CA A:HIS129 5.0 21.6 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Acetazolamide


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 Acetazolamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:19.6 occ:1.00 CE1 B:HIS112 1.9 19.7 1.0 N1 B:AZM303 1.9 21.7 1.0 CD2 B:HIS129 2.1 15.9 1.0 NE2 B:HIS110 2.3 19.3 1.0 NE2 B:HIS112 2.4 21.4 1.0 O2 B:AZM303 2.9 16.4 0.9 NE2 B:HIS129 2.9 18.8 1.0 CD2 B:HIS110 3.0 19.2 1.0 S1 B:AZM303 3.0 14.8 1.0 CG B:HIS129 3.1 17.8 1.0 ND1 B:HIS112 3.1 22.1 1.0 CE1 B:HIS110 3.4 16.3 1.0 OE1 B:GLU116 3.7 18.8 1.0 CD2 B:HIS112 3.7 24.9 1.0 CB B:HIS129 3.7 17.9 1.0 OG1 B:THR191 3.8 16.5 1.0 CE1 B:HIS129 4.0 18.9 1.0 CG B:HIS112 4.0 23.0 1.0 ND1 B:HIS129 4.1 22.3 1.0 O1 B:AZM303 4.2 12.6 1.0 C1 B:AZM303 4.2 15.8 1.0 CG B:HIS110 4.3 19.5 1.0 ND1 B:HIS110 4.4 16.9 1.0 CD B:GLU116 4.6 23.3 1.0 O B:HOH404 5.0 21.8 1.0 S2 B:AZM303 5.0 21.1 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Acetazolamide


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 Acetazolamide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:15.0 occ:1.00 NE2 C:HIS110 1.8 9.4 1.0 N1 C:AZM303 2.0 14.2 1.0 ND1 C:HIS129 2.1 11.3 1.0 CE1 C:HIS112 2.1 13.9 1.0 CD2 C:HIS110 2.7 10.5 1.0 CE1 C:HIS110 2.9 10.2 1.0 CE1 C:HIS129 2.9 11.2 1.0 NE2 C:HIS112 3.0 15.7 1.0 ND1 C:HIS112 3.1 18.7 1.0 S1 C:AZM303 3.1 14.0 1.0 O2 C:AZM303 3.1 11.1 0.7 CG C:HIS129 3.2 10.3 1.0 CB C:HIS129 3.6 11.4 1.0 CG C:HIS110 3.9 12.9 1.0 OG1 C:THR191 3.9 16.2 1.0 ND1 C:HIS110 3.9 10.9 1.0 NE2 C:HIS129 4.1 12.1 1.0 CD2 C:HIS112 4.1 13.9 1.0 C1 C:AZM303 4.1 11.2 0.8 CG C:HIS112 4.2 13.9 1.0 O1 C:AZM303 4.2 11.7 0.6 CD2 C:HIS129 4.2 11.2 1.0 OE1 C:GLU116 4.3 17.2 1.0 C1 C:GOL304 4.5 17.1 1.0 S2 C:AZM303 4.8 19.9 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Acetazolamide


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 Acetazolamide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:32.3 occ:1.00 NE2 D:HIS112 1.8 23.7 1.0 N1 D:AZM303 1.9 21.8 0.7 NE2 D:HIS110 2.0 27.2 1.0 ND1 D:HIS129 2.3 25.0 1.0 CD2 D:HIS110 2.7 25.7 1.0 CE1 D:HIS112 2.8 26.9 1.0 CD2 D:HIS112 2.8 25.4 1.0 S1 D:AZM303 3.1 21.6 0.7 CE1 D:HIS129 3.1 26.2 1.0 O2 D:AZM303 3.2 21.8 0.7 CE1 D:HIS110 3.2 26.3 1.0 CG D:HIS129 3.4 23.5 1.0 OG1 D:THR191 3.7 22.0 1.0 CB D:HIS129 3.9 22.9 1.0 ND1 D:HIS112 3.9 28.8 1.0 CG D:HIS110 4.0 27.9 1.0 CG D:HIS112 4.0 25.3 1.0 OE1 D:GLU116 4.0 29.2 1.0 C1 D:AZM303 4.0 22.9 1.0 ND1 D:HIS110 4.2 29.4 1.0 O1 D:AZM303 4.3 19.8 0.7 NE2 D:HIS129 4.3 28.6 1.0 CD2 D:HIS129 4.5 26.3 1.0 CD D:GLU116 4.8 28.6 1.0 S2 D:AZM303 4.8 31.8 1.0 N3 D:AZM303 4.8 21.9 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Acetazolamide


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 Acetazolamide within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:14.5 occ:1.00 NE2 E:HIS112 1.8 9.1 1.0 NE2 E:HIS110 2.0 9.5 1.0 N1 E:AZM303 2.1 10.6 1.0 ND1 E:HIS129 2.3 10.5 1.0 O2 E:AZM303 2.7 10.0 0.7 CD2 E:HIS112 2.8 9.7 1.0 CD2 E:HIS110 2.8 10.6 1.0 CE1 E:HIS112 2.8 15.7 1.0 S1 E:AZM303 3.0 11.9 0.9 CE1 E:HIS110 3.1 9.7 1.0 CE1 E:HIS129 3.1 10.0 1.0 CG E:HIS129 3.2 8.4 1.0 CB E:HIS129 3.6 7.4 1.0 O3 E:GOL304 3.9 16.9 1.0 ND1 E:HIS112 3.9 11.4 1.0 CG E:HIS112 3.9 8.8 1.0 OG1 E:THR191 4.0 10.7 1.0 CG E:HIS110 4.0 11.2 1.0 C1 E:AZM303 4.0 10.9 0.8 OE1 E:GLU116 4.1 16.2 1.0 ND1 E:HIS110 4.1 9.6 1.0 O1 E:AZM303 4.1 11.2 0.7 NE2 E:HIS129 4.2 9.3 1.0 CD2 E:HIS129 4.3 8.2 1.0 C3 E:GOL304 4.6 14.7 1.0 S2 E:AZM303 4.8 19.3 0.9 O2 E:GOL304 5.0 19.9 1.0 CA E:HIS129 5.0 9.6 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Acetazolamide


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 Acetazolamide within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:31.1 occ:1.00 N1 F:AZM303 1.9 20.7 0.8 NE2 F:HIS110 2.0 23.7 1.0 ND1 F:HIS129 2.3 18.7 1.0 CE1 F:HIS112 2.3 29.7 1.0 CD2 F:HIS110 2.7 22.8 1.0 S1 F:AZM303 3.0 20.9 0.8 O2 F:AZM303 3.1 23.2 0.8 NE2 F:HIS112 3.1 35.0 1.0 CE1 F:HIS129 3.1 22.0 1.0 CE1 F:HIS110 3.2 25.0 1.0 ND1 F:HIS112 3.2 31.1 1.0 CG F:HIS129 3.4 21.6 1.0 O F:HOH457 3.7 28.4 1.0 OG1 F:THR191 3.7 21.4 1.0 CB F:HIS129 3.8 22.5 1.0 CG F:HIS110 3.9 26.3 1.0 C1 F:AZM303 4.1 20.6 0.8 ND1 F:HIS110 4.1 24.7 1.0 O1 F:AZM303 4.2 22.8 0.8 CD2 F:HIS112 4.2 32.9 1.0 CG F:HIS112 4.2 30.2 1.0 NE2 F:HIS129 4.3 18.9 1.0 OE1 F:GLU116 4.3 29.5 1.0 CD2 F:HIS129 4.4 21.1 1.0 S2 F:AZM303 4.8 24.7 1.0 O F:HOH462 5.0 27.4 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Acetazolamide


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 Acetazolamide within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn301 b:24.6 occ:1.00 N1 G:AZM303 1.8 20.4 1.0 ND1 G:HIS129 2.1 23.1 1.0 NE2 G:HIS112 2.1 22.5 1.0 NE2 G:HIS110 2.1 27.4 1.0 CE1 G:HIS129 2.8 23.4 1.0 CE1 G:HIS112 2.9 28.7 1.0 CD2 G:HIS110 3.0 24.6 1.0 S1 G:AZM303 3.0 16.3 0.9 O2 G:AZM303 3.0 18.9 0.8 CD2 G:HIS112 3.1 29.6 1.0 CE1 G:HIS110 3.2 20.4 1.0 CG G:HIS129 3.3 20.9 1.0 OG1 G:THR191 3.8 22.4 1.0 CB G:HIS129 3.8 24.5 1.0 ND1 G:HIS112 4.0 33.2 1.0 NE2 G:HIS129 4.0 21.2 1.0 C1 G:AZM303 4.1 21.6 0.9 CG G:HIS112 4.1 26.1 1.0 O1 G:AZM303 4.1 18.4 1.0 CG G:HIS110 4.2 25.4 1.0 OE1 G:GLU116 4.2 26.0 1.0 ND1 G:HIS110 4.3 23.4 1.0 CD2 G:HIS129 4.3 19.6 1.0 O1 G:GOL304 4.7 26.5 1.0 S2 G:AZM303 4.9 22.4 0.8 N3 G:AZM303 5.0 21.9 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Acetazolamide


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 Acetazolamide within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:24.1 occ:1.00 NE2 H:HIS110 1.7 18.0 1.0 N1 H:AZM303 2.0 19.4 1.0 CD2 H:HIS129 2.4 16.8 1.0 CD2 H:HIS110 2.4 19.6 1.0 CE1 H:HIS112 2.7 19.8 1.0 CE1 H:HIS110 2.9 18.4 1.0 O2 H:AZM303 3.0 17.8 0.8 S1 H:AZM303 3.0 16.8 1.0 CG H:HIS129 3.2 16.4 1.0 NE2 H:HIS112 3.2 21.7 1.0 CB H:HIS129 3.5 20.4 1.0 NE2 H:HIS129 3.5 19.1 1.0 C3 H:GOL304 3.6 18.5 1.0 CG H:HIS110 3.7 19.7 1.0 ND1 H:HIS112 3.7 26.1 1.0 ND1 H:HIS110 3.9 15.7 1.0 C1 H:AZM303 3.9 18.0 1.0 OG1 H:THR191 4.2 19.4 1.0 O3 H:GOL304 4.2 27.1 1.0 O1 H:AZM303 4.3 14.6 0.8 CD2 H:HIS112 4.3 20.8 1.0 ND1 H:HIS129 4.4 20.1 1.0 CG H:HIS112 4.6 22.4 1.0 CE1 H:HIS129 4.6 17.3 1.0 S2 H:AZM303 4.6 22.7 1.0 N3 H:AZM303 4.7 16.7 1.0 OE1 H:GLU116 4.8 22.5 1.0 C2 H:GOL304 4.9 20.5 1.0 CA H:HIS129 4.9 17.6 1.0 CB H:HIS110 5.0 19.0 1.0

J.K.Modakh, Y.C.Liu, M.A.Machuca, C.T.Supuran, A.Roujeinikova. Structural Basis For the Inhibition of Helicobacter Pylori Alpha-Carbonic Anhydrase By Sulfonamides. Plos One V. 10 27149 2015.
ISSN: ESSN 1932-6203
PubMed: 26010545
DOI: 10.1371/JOURNAL.PONE.0127149