Zinc in PDB 5ogn: Metalacarborane Inhibitors of Carbonic Anhydrase IX

All present enzymatic activity of Metalacarborane Inhibitors of Carbonic Anhydrase IX:
4.2.1.1;

The structure of Metalacarborane Inhibitors of Carbonic Anhydrase IX, PDB code: 5ogn was solved by J.Brynda, P.Rezacova, K.Pospisilova, M.Kugler, B.Gruner, V.Sicha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.46 / 1.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.568, 76.099, 143.335, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.2

The structure of Metalacarborane Inhibitors of Carbonic Anhydrase IX also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Zinc atom in the Metalacarborane Inhibitors of Carbonic Anhydrase IX (pdb code 5ogn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Metalacarborane Inhibitors of Carbonic Anhydrase IX, PDB code: 5ogn:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Metalacarborane Inhibitors of Carbonic Anhydrase IX


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Metalacarborane Inhibitors of Carbonic Anhydrase IX within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.2 occ:1.00 N2 A:B8B302 1.9 9.5 1.0 NE2 A:HIS94 2.0 9.1 1.0 ND1 A:HIS119 2.0 10.0 1.0 NE2 A:HIS96 2.1 8.7 1.0 CE1 A:HIS119 2.9 8.4 1.0 S A:B8B302 3.0 9.8 1.0 CD2 A:HIS94 3.0 9.4 1.0 CE1 A:HIS94 3.0 9.3 1.0 CD2 A:HIS96 3.1 10.1 1.0 CE1 A:HIS96 3.1 9.6 1.0 O1 A:B8B302 3.1 9.4 1.0 CG A:HIS119 3.1 9.0 1.0 CB A:HIS119 3.6 9.5 1.0 N1 A:B8B302 3.9 10.6 1.0 OG1 A:THR198 3.9 10.1 1.0 O A:HOH541 4.0 19.7 1.0 OE1 A:GLU106 4.1 10.4 1.0 NE2 A:HIS119 4.1 9.9 1.0 ND1 A:HIS94 4.1 10.0 1.0 CG A:HIS94 4.2 9.0 1.0 CD2 A:HIS119 4.2 9.8 1.0 ND1 A:HIS96 4.2 9.9 1.0 CG A:HIS96 4.2 9.8 1.0 O3 A:B8B302 4.3 10.4 1.0 CD A:GLU106 5.0 9.3 1.0

Zinc binding site 2 out of 3 in the Metalacarborane Inhibitors of Carbonic Anhydrase IX


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Metalacarborane Inhibitors of Carbonic Anhydrase IX within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:12.7 occ:1.00 NE2 B:HIS4 2.0 13.2 1.0 N A:HIS2 2.1 16.0 1.0 NE2 B:HIS64 2.1 11.5 1.0 O A:HIS2 2.2 12.2 1.0 O A:HOH498 2.2 7.5 0.5 C A:HIS2 2.9 13.2 1.0 CE1 B:HIS64 3.0 10.7 1.0 CA A:HIS2 3.0 14.2 1.0 CE1 B:HIS4 3.0 13.4 1.0 CD2 B:HIS4 3.0 12.9 1.0 CD2 B:HIS64 3.1 10.9 1.0 CB A:HIS2 3.7 15.9 1.0 O B:ASN62 4.1 10.7 1.0 ND1 B:HIS64 4.1 10.9 1.0 ND1 B:HIS4 4.1 14.1 1.0 CG B:HIS4 4.2 13.9 1.0 CG B:HIS64 4.2 10.2 1.0 N A:HIS3 4.2 13.8 1.0 OE2 B:GLU169 4.3 14.7 1.0 NE2 A:HIS3 4.3 20.4 1.0 O B:HOH467 4.5 13.1 1.0 CD2 A:HIS3 4.5 16.0 1.0 CE1 A:HIS3 4.5 17.9 1.0 CG A:HIS2 4.6 14.4 1.0 NE1 B:TRP5 4.8 13.5 1.0 ND1 A:HIS3 4.8 21.5 1.0 CG A:HIS3 4.9 16.5 1.0 B5 B:B8B302 4.9 16.6 1.0 CD B:GLU169 5.0 14.3 1.0

Zinc binding site 3 out of 3 in the Metalacarborane Inhibitors of Carbonic Anhydrase IX


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Metalacarborane Inhibitors of Carbonic Anhydrase IX within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:9.0 occ:1.00 N2 B:B8B302 1.9 11.1 1.0 NE2 B:HIS94 2.0 9.1 1.0 ND1 B:HIS119 2.0 9.2 1.0 NE2 B:HIS96 2.1 8.9 1.0 CE1 B:HIS119 2.9 8.3 1.0 CD2 B:HIS94 3.0 9.0 1.0 CE1 B:HIS96 3.0 8.7 1.0 S B:B8B302 3.0 10.4 1.0 CD2 B:HIS96 3.1 8.8 1.0 CE1 B:HIS94 3.1 8.5 1.0 O1 B:B8B302 3.1 10.3 1.0 CG B:HIS119 3.1 8.4 1.0 CB B:HIS119 3.6 8.7 1.0 N1 B:B8B302 3.9 11.6 1.0 OE1 B:GLU106 3.9 11.9 1.0 OG1 B:THR198 4.0 11.3 1.0 NE2 B:HIS119 4.1 9.2 1.0 O B:HOH530 4.1 14.4 1.0 CG B:HIS94 4.1 8.7 1.0 ND1 B:HIS94 4.1 8.7 1.0 ND1 B:HIS96 4.1 9.7 1.0 CG B:HIS96 4.2 9.1 1.0 CD2 B:HIS119 4.2 9.1 1.0 O3 B:B8B302 4.2 11.0 1.0 CD B:GLU106 4.9 10.9 1.0

B.Gruner, J.Brynda, V.Das, V.Sicha, J.Stepankova, J.Nekvinda, J.Holub, K.Pospisilova, M.Fabry, P.Pachl, V.Kral, M.Kugler, V.Masek, M.Medvedikova, S.Matejkova, A.Nova, B.Liskova, S.Gurska, P.Dzubak, M.Hajduch, P.Rezacova. Metallacarborane Sulfamides: Unconventional, Specific, and Highly Selective Inhibitors of Carbonic Anhydrase IX. J.Med.Chem. 2019.
ISSN: ISSN 0022-2623
PubMed: 31568723
DOI: 10.1021/ACS.JMEDCHEM.9B00945