Zinc in PDB 8vlk: Crystal Structure of the Yeast Cytosine Deaminase Containing Both Open and Closed Active Sites

All present enzymatic activity of Crystal Structure of the Yeast Cytosine Deaminase Containing Both Open and Closed Active Sites:
3.5.4.1;

The structure of Crystal Structure of the Yeast Cytosine Deaminase Containing Both Open and Closed Active Sites, PDB code: 8vlk 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)	52.74 / 1.76
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.865, 40.825, 97.728, 90, 104.79, 90
R / Rfree (%)	16.1 / 19.4

The binding sites of Zinc atom in the Crystal Structure of the Yeast Cytosine Deaminase Containing Both Open and Closed Active Sites (pdb code 8vlk). 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 the Yeast Cytosine Deaminase Containing Both Open and Closed Active Sites, PDB code: 8vlk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Yeast Cytosine Deaminase Containing Both Open and Closed Active Sites


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 Yeast Cytosine Deaminase Containing Both Open and Closed Active Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:20.9 occ:1.00 O A:HOH301 2.0 22.9 1.0 ND1 A:HIS62 2.0 17.2 1.0 SG A:CYS94 2.2 20.9 1.0 SG A:CYS91 2.3 18.3 1.0 CE1 A:HIS62 3.0 20.7 1.0 CG A:HIS62 3.1 18.3 1.0 CB A:CYS94 3.2 18.0 1.0 CB A:HIS62 3.4 17.4 1.0 CB A:CYS91 3.4 18.1 1.0 N A:CYS94 3.8 18.1 1.0 N A:CYS91 3.9 18.5 1.0 O1 A:EDO202 3.9 37.6 1.0 OE1 A:GLU64 4.1 21.9 1.0 CA A:CYS91 4.1 19.1 1.0 C1 A:EDO202 4.1 36.3 1.0 NE2 A:HIS62 4.1 20.2 1.0 CD2 A:HIS62 4.2 20.9 1.0 CA A:CYS94 4.2 18.6 1.0 CE A:MET93 4.2 22.7 1.0 OE2 A:GLU64 4.4 34.3 1.0 CD A:GLU64 4.4 24.3 1.0 O2 A:EDO202 4.5 28.5 1.0 C A:CYS91 4.7 19.8 1.0 O A:HOH318 4.7 24.6 1.0 CB A:MET93 4.7 19.3 1.0 O A:CYS91 4.8 15.9 1.0 C2 A:EDO202 4.9 34.9 1.0 CA A:HIS62 4.9 18.2 1.0 C A:MET93 4.9 18.9 1.0 O A:HOH302 4.9 37.3 1.0 C A:PRO90 5.0 18.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Yeast Cytosine Deaminase Containing Both Open and Closed Active Sites


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 Yeast Cytosine Deaminase Containing Both Open and Closed Active Sites within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:21.2 occ:1.00 ND1 B:HIS62 2.1 18.7 1.0 O2 B:EDO202 2.1 27.3 1.0 SG B:CYS94 2.2 20.9 1.0 SG B:CYS91 2.3 18.9 1.0 CE1 B:HIS62 3.0 19.7 1.0 C2 B:EDO202 3.1 33.4 1.0 CG B:HIS62 3.1 19.1 1.0 CB B:CYS94 3.2 19.4 1.0 CB B:CYS91 3.4 19.8 1.0 CB B:HIS62 3.4 18.3 1.0 N B:CYS91 3.8 19.4 1.0 N B:CYS94 3.9 17.6 1.0 OE2 B:GLU64 4.0 32.3 1.0 CA B:CYS91 4.1 18.5 1.0 OE1 B:GLU64 4.2 25.3 1.0 CA B:CYS94 4.2 17.4 1.0 NE2 B:HIS62 4.2 19.4 1.0 CD2 B:HIS62 4.2 21.3 1.0 CE B:MET93 4.3 23.9 1.0 CD B:GLU64 4.3 26.5 1.0 C1 B:EDO202 4.4 35.2 1.0 O1 B:EDO202 4.6 28.7 1.0 C B:CYS91 4.6 17.7 1.0 O B:CYS91 4.8 19.1 1.0 O B:HOH367 4.8 23.5 1.0 CB B:MET93 4.8 19.7 1.0 O B:HOH392 4.8 29.0 1.0 C B:MET93 4.9 19.0 1.0 C B:PRO90 4.9 17.7 1.0 CA B:HIS62 4.9 18.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Yeast Cytosine Deaminase Containing Both Open and Closed Active Sites


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 the Yeast Cytosine Deaminase Containing Both Open and Closed Active Sites within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:29.2 occ:1.00 O C:HOH336 2.0 32.3 1.0 ND1 C:HIS62 2.0 28.7 1.0 SG C:CYS94 2.2 26.4 1.0 SG C:CYS91 2.3 29.1 1.0 CE1 C:HIS62 3.0 30.9 1.0 CG C:HIS62 3.0 27.8 1.0 CB C:CYS94 3.3 25.6 1.0 CB C:CYS91 3.3 30.9 1.0 CB C:HIS62 3.4 26.6 1.0 N C:CYS91 3.8 28.2 1.0 N C:CYS94 3.9 24.4 1.0 CA C:CYS91 4.1 29.1 1.0 NE2 C:HIS62 4.1 31.9 1.0 OE1 C:GLU64 4.1 32.0 1.0 CD2 C:HIS62 4.2 31.8 1.0 CA C:CYS94 4.2 24.5 1.0 OE2 C:GLU64 4.3 41.0 1.0 CE C:MET93 4.3 28.3 1.0 O C:HOH365 4.3 52.6 1.0 CD C:GLU64 4.4 30.5 1.0 O C:HOH355 4.5 32.6 1.0 O C:HOH308 4.5 34.8 1.0 C C:CYS91 4.6 26.6 1.0 CB C:MET93 4.6 26.4 1.0 O C:CYS91 4.8 29.3 1.0 C C:MET93 4.9 23.7 1.0 CA C:HIS62 4.9 24.2 1.0 O C:HOH344 4.9 48.7 1.0 C C:PRO90 5.0 31.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Yeast Cytosine Deaminase Containing Both Open and Closed Active Sites


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 the Yeast Cytosine Deaminase Containing Both Open and Closed Active Sites within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn203 b:25.4 occ:1.00 O1 D:EDO202 2.1 29.1 1.0 ND1 D:HIS62 2.1 24.8 1.0 SG D:CYS94 2.2 24.8 1.0 SG D:CYS91 2.3 26.3 1.0 C1 D:EDO202 3.1 32.8 1.0 CE1 D:HIS62 3.1 25.4 1.0 CG D:HIS62 3.1 21.4 1.0 CB D:CYS94 3.2 21.6 1.0 CB D:CYS91 3.4 27.4 1.0 CB D:HIS62 3.4 20.6 1.0 N D:CYS94 3.8 21.8 1.0 N D:CYS91 3.8 27.0 1.0 OE2 D:GLU64 4.0 38.7 1.0 CA D:CYS91 4.1 26.2 1.0 CA D:CYS94 4.1 21.1 1.0 OE1 D:GLU64 4.2 28.0 1.0 NE2 D:HIS62 4.2 21.1 1.0 CD2 D:HIS62 4.2 21.0 1.0 CD D:GLU64 4.3 33.3 1.0 C2 D:EDO202 4.4 32.4 1.0 CE D:MET93 4.4 29.8 1.0 O2 D:EDO202 4.5 37.4 1.0 C D:CYS91 4.6 26.3 1.0 O D:CYS91 4.7 26.2 1.0 CB D:MET93 4.8 22.9 1.0 O D:HOH361 4.8 24.9 1.0 C D:MET93 4.8 20.7 1.0 O D:HOH380 4.9 29.3 1.0 C D:PRO90 4.9 25.6 1.0 CA D:HIS62 4.9 20.8 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