Zinc in PDB 1ysd: Yeast Cytosine Deaminase Double Mutant

All present enzymatic activity of Yeast Cytosine Deaminase Double Mutant:
3.5.4.1;

The structure of Yeast Cytosine Deaminase Double Mutant, PDB code: 1ysd was solved by A.Korkegian, M.E.Black, D.Baker, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.350, 54.770, 68.400, 90.00, 105.68, 90.00
R / Rfree (%)	16.3 / 20

The structure of Yeast Cytosine Deaminase Double Mutant also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Yeast Cytosine Deaminase Double Mutant (pdb code 1ysd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Yeast Cytosine Deaminase Double Mutant, PDB code: 1ysd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Yeast Cytosine Deaminase Double Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast Cytosine Deaminase Double Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:9.8 occ:1.00 O A:HOH1133 1.9 10.5 1.0 O A:HOH1129 2.0 11.2 1.0 O A:HOH1128 2.2 17.0 1.0 O A:HOH1132 2.3 23.3 1.0 ZN A:ZN501 3.2 11.6 1.0 OE2 A:GLU64 3.6 12.7 1.0 OE1 A:GLU64 3.6 9.4 1.0 O A:HOH1113 3.8 17.0 1.0 ND1 A:HIS62 3.8 7.7 1.0 CD A:GLU64 4.0 11.4 1.0 N A:CYS91 4.1 8.5 1.0 CD1 A:ILE33 4.2 7.4 1.0 CG A:HIS62 4.3 9.1 1.0 CE1 A:HIS62 4.4 9.2 1.0 CB A:CYS91 4.5 8.3 1.0 O A:SER89 4.5 8.4 1.0 CB A:HIS62 4.6 9.9 1.0 SG A:CYS94 4.6 9.7 1.0 CG2 A:ILE33 4.7 10.6 1.0 CA A:PRO90 4.7 9.4 1.0 CE2 A:PHE114 4.7 12.1 1.0 SG A:CYS91 4.7 10.4 1.0 C A:PRO90 4.9 9.8 1.0 CA A:CYS91 4.9 8.6 1.0 CD2 A:PHE114 5.0 13.6 1.0 OD2 A:ASP155 5.0 12.7 1.0

Zinc binding site 2 out of 4 in the Yeast Cytosine Deaminase Double Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast Cytosine Deaminase Double Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:11.6 occ:1.00 O A:HOH1133 2.0 10.5 1.0 ND1 A:HIS62 2.1 7.7 1.0 SG A:CYS94 2.3 9.7 1.0 SG A:CYS91 2.4 10.4 1.0 CE1 A:HIS62 3.1 9.2 1.0 CG A:HIS62 3.2 9.1 1.0 ZN A:ZN500 3.2 9.8 1.0 CB A:CYS94 3.3 8.8 1.0 CB A:CYS91 3.4 8.3 1.0 CB A:HIS62 3.5 9.9 1.0 O A:HOH1129 3.7 11.2 1.0 N A:CYS91 3.8 8.5 1.0 N A:CYS94 3.8 8.6 1.0 CA A:CYS91 4.2 8.6 1.0 CA A:CYS94 4.2 8.8 1.0 NE2 A:HIS62 4.2 9.9 1.0 O A:HOH1128 4.2 17.0 1.0 OE1 A:GLU64 4.3 9.4 1.0 CE A:MET93 4.3 10.6 1.0 CD2 A:HIS62 4.3 9.8 1.0 OE2 A:GLU64 4.4 12.7 1.0 CD A:GLU64 4.5 11.4 1.0 C A:CYS91 4.7 8.2 1.0 CB A:MET93 4.8 9.4 1.0 O A:CYS91 4.8 7.0 1.0 C A:MET93 4.9 8.2 1.0 C A:PRO90 4.9 9.8 1.0

Zinc binding site 3 out of 4 in the Yeast Cytosine Deaminase Double Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast Cytosine Deaminase Double Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:11.9 occ:1.00 O B:HOH1131 2.0 13.4 1.0 ND1 B:HIS262 2.2 11.6 1.0 SG B:CYS294 2.3 9.8 1.0 SG B:CYS291 2.4 10.5 1.0 CE1 B:HIS262 3.1 11.4 1.0 ZN B:ZN503 3.2 13.6 1.0 CG B:HIS262 3.2 11.4 1.0 CB B:CYS294 3.3 9.8 1.0 CB B:CYS291 3.4 9.5 1.0 CB B:HIS262 3.5 10.6 1.0 O B:HOH1135 3.6 13.2 1.0 N B:CYS291 3.8 8.8 1.0 N B:CYS294 3.8 7.9 1.0 CA B:CYS291 4.1 9.2 1.0 CA B:CYS294 4.1 9.4 1.0 O B:HOH1134 4.2 15.9 1.0 OE2 B:GLU264 4.3 12.8 1.0 NE2 B:HIS262 4.3 12.7 1.0 CE B:MET293 4.3 9.2 1.0 CD2 B:HIS262 4.3 11.8 1.0 OE1 B:GLU264 4.5 16.1 1.0 CD B:GLU264 4.6 14.3 1.0 C B:CYS291 4.7 8.2 1.0 CB B:MET293 4.7 9.0 1.0 O B:CYS291 4.8 6.9 1.0 C B:MET293 4.9 9.3 1.0 C B:PRO290 4.9 10.4 1.0

Zinc binding site 4 out of 4 in the Yeast Cytosine Deaminase Double Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast Cytosine Deaminase Double Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:13.6 occ:1.00 O B:HOH1135 2.0 13.2 1.0 O B:HOH1131 2.0 13.4 1.0 O B:HOH1134 2.2 15.9 1.0 O B:HOH1130 2.2 17.4 1.0 ZN B:ZN502 3.2 11.9 1.0 OE2 B:GLU264 3.7 12.8 1.0 OE1 B:GLU264 3.7 16.1 1.0 O B:HOH1030 3.7 14.7 1.0 ND1 B:HIS262 3.8 11.6 1.0 CD B:GLU264 4.1 14.3 1.0 N B:CYS291 4.1 8.8 1.0 CD1 B:ILE233 4.2 11.9 1.0 CG B:HIS262 4.4 11.4 1.0 CE1 B:HIS262 4.4 11.4 1.0 CB B:CYS291 4.5 9.5 1.0 CA B:PRO290 4.6 7.8 1.0 O B:SER289 4.6 8.7 1.0 SG B:CYS294 4.6 9.8 1.0 CB B:HIS262 4.6 10.6 1.0 CG2 B:ILE233 4.7 9.1 1.0 SG B:CYS291 4.7 10.5 1.0 C B:PRO290 4.8 10.4 1.0 CE1 B:PHE314 4.8 13.5 1.0 CA B:CYS291 4.9 9.2 1.0 OD2 B:ASP355 5.0 19.4 1.0

A.Korkegian, M.E.Black, D.Baker, B.L.Stoddard. Computational Thermostabilization of An Enzyme. Science V. 308 857 2005.
ISSN: ISSN 0036-8075
PubMed: 15879217
DOI: 10.1126/SCIENCE.1107387