Zinc in PDB 8i3p: Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH in Complex with (R)-4-Hydroxy-3,4-Dihydropyrimidin-2(1H)-One

All present enzymatic activity of Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH in Complex with (R)-4-Hydroxy-3,4-Dihydropyrimidin-2(1H)-One:
3.5.4.1;

The structure of Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH in Complex with (R)-4-Hydroxy-3,4-Dihydropyrimidin-2(1H)-One, PDB code: 8i3p was solved by M.M.Qin, H.Z.Deng, L.S.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.41 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.175, 68.9, 49.424, 90, 101.58, 90
R / Rfree (%)	14.1 / 16.1

The binding sites of Zinc atom in the Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH in Complex with (R)-4-Hydroxy-3,4-Dihydropyrimidin-2(1H)-One (pdb code 8i3p). 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 Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH in Complex with (R)-4-Hydroxy-3,4-Dihydropyrimidin-2(1H)-One, PDB code: 8i3p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH in Complex with (R)-4-Hydroxy-3,4-Dihydropyrimidin-2(1H)-One


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 Cytosine Deaminase Mutant Ycd-Rq-1/8SAH in Complex with (R)-4-Hydroxy-3,4-Dihydropyrimidin-2(1H)-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:10.1 occ:1.00 O07 A:OS0601 2.0 10.9 1.0 ND1 A:HIS62 2.1 9.4 1.0 SG A:CYS91 2.3 10.1 1.0 SG A:CYS94 2.3 10.4 1.0 CE1 A:HIS62 3.0 9.2 1.0 CG A:HIS62 3.1 9.4 1.0 C06 A:OS0601 3.1 10.6 1.0 CB A:CYS94 3.2 10.3 1.0 CB A:CYS91 3.4 10.6 1.0 CB A:HIS62 3.4 9.4 1.0 N08 A:OS0601 3.4 10.9 1.0 C05 A:OS0601 3.7 11.3 1.0 OE2 A:GLU64 3.7 10.9 1.0 N A:CYS91 3.8 9.7 1.0 N A:CYS94 3.9 9.6 1.0 C02 A:OS0601 3.9 10.4 1.0 NE2 A:HIS62 4.1 9.6 1.0 C04 A:OS0601 4.1 10.8 1.0 CA A:CYS91 4.2 10.3 1.0 CA A:CYS94 4.2 10.2 1.0 CD2 A:HIS62 4.2 10.0 1.0 CD A:GLU64 4.2 10.5 1.0 N03 A:OS0601 4.3 10.2 1.0 OE1 A:GLU64 4.3 11.1 1.0 CE A:MET93 4.3 13.2 1.0 O01 A:OS0601 4.7 9.7 1.0 CB A:MET93 4.7 10.5 1.0 C A:CYS91 4.7 9.8 1.0 O A:CYS91 4.8 9.9 1.0 C A:PRO90 4.9 9.7 1.0 C A:MET93 5.0 10.7 1.0 CA A:HIS62 5.0 9.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH in Complex with (R)-4-Hydroxy-3,4-Dihydropyrimidin-2(1H)-One


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 Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH in Complex with (R)-4-Hydroxy-3,4-Dihydropyrimidin-2(1H)-One within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:10.1 occ:1.00 ND1 B:HIS62 2.0 9.0 1.0 O07 B:OS0601 2.1 10.2 1.0 SG B:CYS91 2.3 9.6 1.0 SG B:CYS94 2.3 9.7 1.0 CE1 B:HIS62 2.9 9.0 1.0 CG B:HIS62 3.1 9.3 1.0 C06 B:OS0601 3.1 10.3 1.0 CB B:CYS94 3.2 9.0 1.0 N08 B:OS0601 3.4 9.7 1.0 CB B:CYS91 3.4 10.2 1.0 CB B:HIS62 3.5 9.3 1.0 C05 B:OS0601 3.7 10.0 1.0 OE2 B:GLU64 3.7 9.7 1.0 N B:CYS91 3.8 9.8 1.0 N B:CYS94 3.9 9.9 1.0 C02 B:OS0601 4.0 9.4 1.0 NE2 B:HIS62 4.1 9.8 1.0 C04 B:OS0601 4.1 10.0 1.0 CA B:CYS91 4.2 9.8 1.0 CD2 B:HIS62 4.2 9.8 1.0 CA B:CYS94 4.2 8.8 1.0 CD B:GLU64 4.2 10.3 1.0 OE1 B:GLU64 4.3 10.9 1.0 N03 B:OS0601 4.3 9.9 1.0 CE B:MET93 4.3 12.5 1.0 C B:CYS91 4.7 10.0 1.0 O01 B:OS0601 4.7 8.9 1.0 CB B:MET93 4.8 9.9 1.0 O B:CYS91 4.8 10.4 1.0 C B:PRO90 4.9 10.0 1.0 CA B:HIS62 4.9 9.2 1.0 C B:MET93 5.0 9.7 1.0

M.M.Qin, H.Z.Deng, L.S.Yao. Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH in Complex with (R)-4-Hydroxy-3,4-Dihydropyrimidin-2(1H)-One To Be Published.