Zinc in PDB 1rb7: Yeast Cytosine Deaminase Crystal Form P212121 with Sodium Acetate.

All present enzymatic activity of Yeast Cytosine Deaminase Crystal Form P212121 with Sodium Acetate.:
3.5.4.1;

The structure of Yeast Cytosine Deaminase Crystal Form P212121 with Sodium Acetate., PDB code: 1rb7 was solved by G.C.Ireton, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.87 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.489, 72.125, 79.441, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 21.1

The binding sites of Zinc atom in the Yeast Cytosine Deaminase Crystal Form P212121 with Sodium Acetate. (pdb code 1rb7). 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 Crystal Form P212121 with Sodium Acetate., PDB code: 1rb7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Yeast Cytosine Deaminase Crystal Form P212121 with Sodium Acetate.


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 Crystal Form P212121 with Sodium Acetate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:24.1 occ:1.00 O A:HOH704 2.2 29.5 1.0 ND1 A:HIS62 2.2 25.2 1.0 SG A:CYS94 2.4 21.2 1.0 SG A:CYS91 2.4 27.3 1.0 CE1 A:HIS62 3.1 24.1 1.0 CG A:HIS62 3.2 26.7 1.0 ZN A:ZN402 3.3 26.8 1.0 CB A:CYS94 3.4 19.6 1.0 CB A:CYS91 3.5 23.9 1.0 CB A:HIS62 3.5 24.4 1.0 O A:HOH703 3.8 24.6 1.0 N A:CYS94 3.8 18.9 1.0 N A:CYS91 3.9 21.8 1.0 CA A:CYS94 4.2 18.9 1.0 CA A:CYS91 4.3 23.5 1.0 NE2 A:HIS62 4.3 27.0 1.0 O A:HOH701 4.3 30.9 1.0 CD2 A:HIS62 4.3 25.7 1.0 CE A:MET93 4.4 24.0 1.0 OE1 A:GLU64 4.5 26.5 1.0 OE2 A:GLU64 4.5 27.1 1.0 CD A:GLU64 4.7 27.9 1.0 CB A:MET93 4.7 21.0 1.0 C A:CYS91 4.8 21.2 1.0 C A:MET93 4.9 20.8 1.0 O A:CYS91 4.9 23.0 1.0

Zinc binding site 2 out of 4 in the Yeast Cytosine Deaminase Crystal Form P212121 with Sodium Acetate.


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 Crystal Form P212121 with Sodium Acetate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:26.8 occ:1.00 O A:HOH703 2.0 24.6 1.0 O A:HOH704 2.1 29.5 1.0 O A:HOH700 2.3 32.5 1.0 O A:HOH701 2.3 30.9 1.0 ZN A:ZN400 3.3 24.1 1.0 OE2 A:GLU64 3.6 27.1 1.0 OE1 A:GLU64 3.7 26.5 1.0 O A:HOH562 3.8 30.5 1.0 ND1 A:HIS62 3.9 25.2 1.0 CD A:GLU64 4.1 27.9 1.0 N A:CYS91 4.2 21.8 1.0 CD1 A:ILE33 4.2 25.1 1.0 CG A:HIS62 4.5 26.7 1.0 CE1 A:HIS62 4.6 24.1 1.0 CA A:PRO90 4.6 23.0 1.0 CB A:CYS91 4.6 23.9 1.0 O A:SER89 4.6 22.0 1.0 SG A:CYS94 4.6 21.2 1.0 CB A:HIS62 4.6 24.4 1.0 CG2 A:ILE33 4.7 27.0 1.0 SG A:CYS91 4.8 27.3 1.0 C A:PRO90 4.9 23.1 1.0 CE1 A:PHE114 4.9 29.3 1.0

Zinc binding site 3 out of 4 in the Yeast Cytosine Deaminase Crystal Form P212121 with Sodium Acetate.


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 Crystal Form P212121 with Sodium Acetate. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:24.3 occ:1.00 O B:HOH705 2.1 22.3 1.0 ND1 B:HIS62 2.2 23.1 1.0 SG B:CYS94 2.4 19.5 1.0 SG B:CYS91 2.4 20.9 1.0 CE1 B:HIS62 3.2 24.7 1.0 ZN B:ZN403 3.2 26.9 1.0 CG B:HIS62 3.3 24.3 1.0 CB B:CYS94 3.3 20.2 1.0 CB B:CYS91 3.4 21.4 1.0 CB B:HIS62 3.6 23.7 1.0 O B:HOH708 3.7 24.7 1.0 N B:CYS91 3.8 23.0 1.0 N B:CYS94 3.9 21.2 1.0 CA B:CYS91 4.2 21.6 1.0 CA B:CYS94 4.2 20.3 1.0 OE2 B:GLU64 4.3 24.2 1.0 NE2 B:HIS62 4.3 25.8 1.0 O B:HOH707 4.3 29.8 1.0 CE B:MET93 4.4 23.8 1.0 CD2 B:HIS62 4.4 23.9 1.0 OE1 B:GLU64 4.4 25.4 1.0 CD B:GLU64 4.5 27.4 1.0 C B:CYS91 4.7 21.9 1.0 CB B:MET93 4.8 21.7 1.0 O B:CYS91 4.9 20.8 1.0 C B:PRO90 4.9 23.4 1.0 C B:MET93 5.0 21.8 1.0

Zinc binding site 4 out of 4 in the Yeast Cytosine Deaminase Crystal Form P212121 with Sodium Acetate.


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 Crystal Form P212121 with Sodium Acetate. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:26.9 occ:1.00 O B:HOH705 2.0 22.3 1.0 O B:HOH708 2.0 24.7 1.0 O B:HOH706 2.2 33.9 1.0 O B:HOH707 2.3 29.8 1.0 ZN B:ZN401 3.2 24.3 1.0 OE1 B:GLU64 3.5 25.4 1.0 OE2 B:GLU64 3.6 24.2 1.0 ND1 B:HIS62 3.8 23.1 1.0 O B:HOH532 3.8 21.9 1.0 CD B:GLU64 4.0 27.4 1.0 N B:CYS91 4.2 23.0 1.0 CE1 B:HIS62 4.4 24.7 1.0 CG B:HIS62 4.4 24.3 1.0 CD1 B:ILE33 4.5 23.0 1.0 O B:SER89 4.5 21.9 1.0 CB B:HIS62 4.6 23.7 1.0 CA B:PRO90 4.6 23.2 1.0 CB B:CYS91 4.7 21.4 1.0 SG B:CYS94 4.7 19.5 1.0 CG2 B:ILE33 4.8 22.6 1.0 CE1 B:PHE114 4.8 23.1 1.0 C B:PRO90 4.9 23.4 1.0 SG B:CYS91 4.9 20.9 1.0 OD1 B:ASP155 5.0 29.2 1.0

G.C.Ireton, B.L.Stoddard. Microseed Matrix Screening to Improve Crystals of Yeast Cytosine Deaminase. Acta Crystallogr.,Sect.D V. 60 601 2004.
ISSN: ISSN 0907-4449
PubMed: 14993707
DOI: 10.1107/S0907444903029664