Zinc in PDB 8vlj: Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form)

All present enzymatic activity of Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form):
3.5.4.1;

The structure of Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form), PDB code: 8vlj was solved by M.-E.Picard, J.Grenier, P.C.Despres, A.K.Dube, C.R.Landry, R.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.55 / 1.39
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.108, 55.073, 66.867, 90, 90.5, 90
R / Rfree (%)	14.2 / 16.7

The structure of Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form) also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Arsenic	(As)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form) (pdb code 8vlj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form), PDB code: 8vlj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form)


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 Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:5.3 occ:1.00 O2 A:CAC201 2.0 7.7 1.0 ND1 A:HIS62 2.0 4.8 1.0 SG A:CYS94 2.3 5.8 1.0 SG A:CYS91 2.3 5.3 1.0 CE1 A:HIS62 2.9 5.8 1.0 CG A:HIS62 3.1 5.5 1.0 CB A:CYS94 3.2 4.7 1.0 AS A:CAC201 3.2 8.0 1.0 CB A:CYS91 3.3 6.0 1.0 CB A:HIS62 3.5 5.7 1.0 O1 A:CAC201 3.6 9.1 1.0 N A:CYS94 3.8 5.0 1.0 N A:CYS91 3.8 5.9 1.0 C2 A:CAC201 4.1 9.4 1.0 CA A:CYS91 4.1 5.7 1.0 NE2 A:HIS62 4.1 6.3 1.0 CA A:CYS94 4.1 4.8 1.0 CE A:MET93 4.2 9.3 1.0 CD2 A:HIS62 4.2 6.1 1.0 OE1 A:GLU64 4.2 8.6 1.0 OE2 A:GLU64 4.5 11.6 1.0 CD A:GLU64 4.5 8.9 1.0 C A:CYS91 4.6 5.1 1.0 CB A:MET93 4.7 6.5 1.0 O A:CYS91 4.8 5.9 1.0 C1 A:CAC201 4.9 8.6 1.0 C A:MET93 4.9 5.0 1.0 C A:PRO90 4.9 5.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form)


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 Cacodylate-Bound Yeast Cytosine Deaminase (Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:5.8 occ:1.00 O2 B:CAC201 2.0 8.6 1.0 ND1 B:HIS62 2.1 6.0 1.0 SG B:CYS94 2.3 6.4 1.0 SG B:CYS91 2.3 6.1 1.0 CE1 B:HIS62 3.0 6.9 1.0 CG B:HIS62 3.1 6.2 1.0 CB B:CYS94 3.2 5.8 1.0 AS B:CAC201 3.2 8.5 1.0 CB B:CYS91 3.3 5.4 1.0 CB B:HIS62 3.5 6.0 1.0 O1 B:CAC201 3.6 10.2 1.0 N B:CYS91 3.8 5.2 1.0 N B:CYS94 3.9 5.0 1.0 CA B:CYS91 4.1 5.2 1.0 C2 B:CAC201 4.1 9.6 1.0 NE2 B:HIS62 4.1 6.7 1.0 CA B:CYS94 4.2 5.4 1.0 OE1 B:GLU64 4.2 9.2 1.0 CD2 B:HIS62 4.2 6.3 1.0 CE B:MET93 4.2 8.4 1.0 OE2 B:GLU64 4.4 12.3 1.0 CD B:GLU64 4.5 9.7 1.0 C B:CYS91 4.6 5.1 1.0 O B:CYS91 4.8 5.4 1.0 CB B:MET93 4.8 6.3 1.0 C1 B:CAC201 4.9 8.9 1.0 C B:PRO90 4.9 5.4 1.0 C B:MET93 4.9 5.2 1.0

P.C.Despres, A.K.Dube, M.-E.Picard, J.Grenier, R.Shi, C.R.Landry. Compensatory Mutations Potentiate Constructive Neutral Evolution By Gene Duplication Science 2024.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ADO5719