Zinc in PDB 6cpt: Crystal Structure of Yeast CAPDE2 in Complex with Ibmx

The structure of Crystal Structure of Yeast CAPDE2 in Complex with Ibmx, PDB code: 6cpt was solved by H.Ke, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.53 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.190, 73.639, 64.954, 90.00, 108.49, 90.00
R / Rfree (%)	19 / 21.3

The structure of Crystal Structure of Yeast CAPDE2 in Complex with Ibmx also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Yeast CAPDE2 in Complex with Ibmx (pdb code 6cpt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Yeast CAPDE2 in Complex with Ibmx, PDB code: 6cpt:

Zinc binding site 1 out of 1 in the Crystal Structure of Yeast CAPDE2 in Complex with Ibmx


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 Yeast CAPDE2 in Complex with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:32.7 occ:1.00 O A:HOH722 2.0 28.9 1.0 OD1 A:ASP462 2.1 25.1 1.0 OD2 A:ASP350 2.2 22.2 1.0 O A:HOH759 2.2 32.0 1.0 NE2 A:HIS349 2.3 23.1 1.0 NE2 A:HIS278 2.4 26.9 1.0 CG A:ASP462 3.1 27.9 1.0 CG A:ASP350 3.1 23.2 1.0 CD2 A:HIS349 3.1 23.5 1.0 CD2 A:HIS278 3.1 25.3 1.0 OD2 A:ASP462 3.3 30.2 1.0 CE1 A:HIS349 3.4 24.1 1.0 CE1 A:HIS278 3.4 25.8 1.0 OD1 A:ASP350 3.5 23.5 1.0 MG A:MG602 3.6 27.4 1.0 O A:HOH866 3.9 31.2 1.0 CD2 A:HIS274 4.1 24.2 1.0 CG A:HIS349 4.3 23.3 1.0 CB A:ASP350 4.3 22.3 1.0 CG A:HIS278 4.4 24.7 1.0 ND1 A:HIS349 4.4 23.3 1.0 CB A:ASP462 4.4 27.0 1.0 NE2 A:HIS274 4.5 25.0 1.0 ND1 A:HIS278 4.5 25.5 1.0 O A:HOH737 4.6 26.5 1.0 CG2 A:VAL282 4.7 24.8 1.0 O A:ASP462 4.8 27.3 1.0 CA A:ASP462 4.9 27.5 1.0 O A:HOH762 4.9 29.5 1.0

T.Yao, Y.Huang, M.Zhang, Y.Chen, H.Pei, J.Shi, H.Wang, Y.Wang, H.Ke. Crystal Structures of Candida Albicans Phosphodiesterase 2 and Implications For Its Biological Functions. Biochemistry V. 57 6070 2018.
ISSN: ISSN 0006-2960
PubMed: 30231198
DOI: 10.1021/ACS.BIOCHEM.8B00707