Zinc in PDB 7bf0: Zn-Bound Domain 3 of CDCA1 in Complex with Carbon Dioxide

The structure of Zn-Bound Domain 3 of CDCA1 in Complex with Carbon Dioxide, PDB code: 7bf0 was solved by V.Alterio, G.De Simone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.576, 62.712, 75.018, 90, 119.78, 90
R / Rfree (%)	21.5 / 24.6

The structure of Zn-Bound Domain 3 of CDCA1 in Complex with Carbon Dioxide also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Zn-Bound Domain 3 of CDCA1 in Complex with Carbon Dioxide (pdb code 7bf0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Zn-Bound Domain 3 of CDCA1 in Complex with Carbon Dioxide, PDB code: 7bf0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Zn-Bound Domain 3 of CDCA1 in Complex with Carbon Dioxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zn-Bound Domain 3 of CDCA1 in Complex with Carbon Dioxide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:20.5 occ:1.00 NE2 A:HIS499 2.0 17.6 1.0 CL A:CL702 2.3 25.4 1.0 SG A:CYS447 2.3 18.0 1.0 SG A:CYS509 2.3 19.1 1.0 CE1 A:HIS499 3.0 19.5 1.0 CD2 A:HIS499 3.0 18.7 1.0 CB A:CYS447 3.2 20.5 1.0 CB A:CYS509 3.2 19.8 1.0 CA A:CYS509 3.5 20.4 1.0 O1 A:CO2703 3.6 31.3 1.0 C A:CO2703 3.9 32.8 1.0 N A:GLY510 4.0 20.6 1.0 C A:CYS509 4.1 21.2 1.0 ND1 A:HIS499 4.1 19.2 1.0 CG A:HIS499 4.2 18.8 1.0 CB A:ASP449 4.3 22.6 1.0 CA A:GLY465 4.3 17.8 1.0 O A:HOH860 4.4 19.6 1.0 N A:GLY465 4.4 17.9 1.0 O2 A:CO2703 4.4 32.3 1.0 OD2 A:ASP449 4.5 27.9 1.0 N A:PHE511 4.5 21.9 1.0 CA A:CYS447 4.7 18.3 1.0 CB A:PHE511 4.8 20.6 1.0 N A:CYS509 4.8 20.4 1.0 CG A:ASP449 4.9 26.3 1.0 O A:CYS509 5.0 19.8 1.0 O A:GLY508 5.0 22.8 1.0

Zinc binding site 2 out of 2 in the Zn-Bound Domain 3 of CDCA1 in Complex with Carbon Dioxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zn-Bound Domain 3 of CDCA1 in Complex with Carbon Dioxide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:16.9 occ:1.00 NE2 B:HIS499 2.0 15.6 1.0 O B:HOH866 2.1 12.1 1.0 SG B:CYS509 2.3 16.4 1.0 SG B:CYS447 2.3 16.4 1.0 CD2 B:HIS499 3.0 15.6 1.0 CE1 B:HIS499 3.1 18.0 1.0 CB B:CYS447 3.2 18.7 1.0 CB B:CYS509 3.2 17.2 1.0 O2 B:CO2702 3.4 31.5 1.0 CA B:CYS509 3.4 18.1 1.0 C B:CO2702 3.8 32.9 1.0 N B:GLY510 4.0 18.7 1.0 C B:CYS509 4.0 17.7 1.0 CG B:HIS499 4.2 16.4 1.0 ND1 B:HIS499 4.2 16.5 1.0 OD2 B:ASP449 4.2 24.0 1.0 CA B:GLY465 4.3 18.4 1.0 N B:GLY465 4.3 17.0 1.0 CB B:ASP449 4.3 17.7 1.0 O1 B:CO2702 4.4 36.2 1.0 O B:HOH862 4.4 19.1 1.0 N B:PHE511 4.5 17.7 1.0 CA B:CYS447 4.6 17.2 1.0 CG B:ASP449 4.8 21.7 1.0 N B:CYS509 4.8 18.3 1.0 CB B:PHE511 4.8 17.6 1.0 O B:GLY508 4.9 21.6 1.0 O B:CYS509 4.9 18.6 1.0

V.Alterio, E.Langella, M.Buonanno, D.Esposito, A.Nocentini, E.Berrino, S.Bua, M.Polentarutti, C.T.Supuran, S.M.Monti, G.De Simone. Zeta-Carbonic Anhydrases Show Cs 2 Hydrolase Activity: A New Metabolic Carbon Acquisition Pathway in Diatoms? Comput Struct Biotechnol J V. 19 3427 2021.
ISSN: ESSN 2001-0370
PubMed: 34194668
DOI: 10.1016/J.CSBJ.2021.05.057