Zinc in PDB 4yf6: Crystal Structure of Oxidised RV1284

All present enzymatic activity of Crystal Structure of Oxidised RV1284:
4.2.1.1;

The structure of Crystal Structure of Oxidised RV1284, PDB code: 4yf6 was solved by A.Hofmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.39 / 3.00
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	101.068, 153.947, 157.174, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 26

The structure of Crystal Structure of Oxidised RV1284 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Oxidised RV1284 (pdb code 4yf6). 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 Oxidised RV1284, PDB code: 4yf6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Oxidised RV1284


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 Oxidised RV1284 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn200 b:37.0 occ:0.59 NE2 A:HIS88 2.2 40.4 1.0 SG A:CYS91 2.3 37.8 1.0 SG A:CYS35 2.4 2.4 0.7 CD2 A:HIS88 3.1 40.4 1.0 CE1 A:HIS88 3.2 40.4 1.0 CB A:CYS35 3.6 2.4 0.7 CB A:CYS35 3.7 2.4 0.3 CB A:CYS91 3.7 37.8 1.0 CB A:ASP37 3.7 10.4 1.0 OD2 A:ASP37 3.7 10.4 1.0 N A:GLY92 3.8 69.0 1.0 CA A:CYS91 4.0 71.4 1.0 CG A:ASP37 4.2 10.4 1.0 SG A:CYS35 4.3 2.4 0.3 CG A:HIS88 4.3 40.4 1.0 ND1 A:HIS88 4.3 40.4 1.0 CA A:GLY60 4.3 5.5 1.0 N A:GLY60 4.3 5.5 1.0 C A:CYS91 4.4 71.4 1.0 N A:ASP37 4.5 20.7 1.0 CA A:ASP37 4.6 20.7 1.0 SG A:CYS61 4.8 5.4 0.3 CA A:GLY92 4.8 69.0 1.0 C A:GLY60 5.0 5.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Oxidised RV1284


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 Oxidised RV1284 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn200 b:37.0 occ:0.55 SG B:CYS91 2.2 52.1 1.0 SG B:CYS35 2.3 10.8 0.6 NE2 B:HIS88 2.4 25.9 1.0 CE1 B:HIS88 3.4 25.9 1.0 CD2 B:HIS88 3.4 25.9 1.0 CB B:ASP37 3.6 17.6 1.0 OD2 B:ASP37 3.6 17.6 1.0 CB B:CYS35 3.7 10.8 0.6 CB B:CYS35 3.7 10.8 0.4 CB B:CYS91 3.8 52.1 1.0 CG B:ASP37 4.1 17.6 1.0 N B:GLY60 4.1 37.1 1.0 N B:GLY92 4.2 64.4 1.0 N B:ASP37 4.2 3.9 1.0 CA B:CYS91 4.2 92.6 1.0 CA B:GLY60 4.2 37.1 1.0 CA B:ASP37 4.3 3.9 1.0 SG B:CYS35 4.5 10.8 0.4 ND1 B:HIS88 4.5 25.9 1.0 CG B:HIS88 4.6 25.9 1.0 C B:CYS91 4.7 92.6 1.0 N B:MET36 4.9 14.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Oxidised RV1284


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 Oxidised RV1284 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn200 b:37.0 occ:0.60 NE2 C:HIS88 2.1 44.3 1.0 SG C:CYS91 2.5 51.0 1.0 SG C:CYS35 2.5 5.4 0.6 CE1 C:HIS88 2.9 44.3 1.0 CD2 C:HIS88 3.2 44.3 1.0 CB C:CYS35 3.4 5.4 0.6 CB C:CYS35 3.5 5.4 0.4 CB C:ASP37 3.7 38.8 1.0 O C:HOH301 3.9 32.4 1.0 OD2 C:ASP37 4.0 38.8 1.0 CB C:CYS91 4.0 51.0 1.0 ND1 C:HIS88 4.1 44.3 1.0 CA C:GLY60 4.1 19.6 1.0 N C:GLY60 4.1 19.6 1.0 CG C:HIS88 4.2 44.3 1.0 SG C:CYS35 4.3 5.4 0.4 N C:GLY92 4.3 79.2 1.0 CG C:ASP37 4.3 38.8 1.0 CA C:CYS91 4.5 97.4 1.0 N C:ASP37 4.5 18.1 1.0 CA C:ASP37 4.5 18.1 1.0 SG C:CYS61 4.5 11.2 0.4 CG C:MET93 4.8 77.5 1.0 C C:GLY60 4.8 19.6 1.0 CA C:CYS35 4.8 23.8 0.4 CA C:CYS35 4.9 23.8 0.6 C C:CYS91 4.9 97.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Oxidised RV1284


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 Oxidised RV1284 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn200 b:37.0 occ:0.58 NE2 D:HIS88 2.2 36.4 1.0 SG D:CYS35 2.4 3.4 0.5 SG D:CYS91 2.6 58.7 1.0 CE1 D:HIS88 2.8 36.4 1.0 CD2 D:HIS88 3.4 36.4 1.0 N D:GLY92 3.5 82.9 1.0 CB D:CYS35 3.9 3.4 0.5 OD2 D:ASP37 3.9 32.8 1.0 CB D:CYS35 4.0 3.4 0.5 CB D:ASP37 4.0 32.8 1.0 CB D:CYS91 4.0 58.7 1.0 ND1 D:HIS88 4.1 36.4 1.0 N D:GLY60 4.1 18.7 1.0 CA D:GLY60 4.1 18.7 1.0 CA D:CYS91 4.2 66.4 1.0 CA D:GLY92 4.3 82.9 1.0 CG D:HIS88 4.3 36.4 1.0 C D:CYS91 4.4 66.4 1.0 CG D:ASP37 4.4 32.8 1.0 N D:ASP37 4.7 17.0 1.0 CA D:ASP37 4.7 17.0 1.0 SG D:CYS35 4.8 3.4 0.5 N D:MET93 5.0 52.0 1.0 CG D:MET93 5.0 37.3 1.0

L.Nienaber, E.Cave-Freeman, M.Cross, L.Mason, U.M.Bailey, P.Amani, R.Davis, P.Taylor, A.Hofmann. Chemical Probing Suggests Redox-Regulation of the Carbonic Anhydrase Activity of Mycobacterial RV1284. Febs J. 2015.
ISSN: ISSN 1742-464X
PubMed: 25929542
DOI: 10.1111/FEBS.13313