Zinc in PDB 8i3n: Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq

All present enzymatic activity of Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq:
3.5.4.1;

The structure of Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq, PDB code: 8i3n was solved by M.M.Qin, L.S.Yao, H.Z.Deng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.29 / 1.73
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.669, 64.47, 83.092, 90, 97.97, 90
R / Rfree (%)	20.3 / 21.8

The binding sites of Zinc atom in the Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq (pdb code 8i3n). 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 Yeast Cytosine Deaminase Mutant Ycd-Rq, PDB code: 8i3n:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:22.1 occ:1.00 ND1 A:HIS62 2.1 22.7 1.0 SG A:CYS94 2.3 21.2 1.0 O A:HOH379 2.3 24.1 1.0 SG A:CYS91 2.4 21.6 1.0 CE1 A:HIS62 3.1 24.4 1.0 CG A:HIS62 3.2 20.5 1.0 CB A:CYS94 3.3 20.1 1.0 CB A:CYS91 3.4 19.9 1.0 CB A:HIS62 3.5 18.3 1.0 N A:CYS91 3.9 20.9 1.0 N A:CYS94 3.9 16.3 1.0 OE1 A:GLU64 4.2 32.3 1.0 CA A:CYS91 4.2 21.2 1.0 NE2 A:HIS62 4.2 23.9 1.0 OE2 A:GLU64 4.2 24.7 1.0 CA A:CYS94 4.3 19.1 1.0 CD2 A:HIS62 4.3 24.6 1.0 CE A:MET93 4.4 23.5 1.0 CD A:GLU64 4.4 27.2 1.0 O A:HOH396 4.5 32.2 1.0 O A:HOH411 4.7 27.6 1.0 C A:CYS91 4.7 19.9 1.0 CB A:MET93 4.9 17.3 1.0 O A:CYS91 4.9 18.0 1.0 O A:HOH364 4.9 21.8 1.0 C A:PRO90 5.0 21.1 1.0 C A:MET93 5.0 18.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:23.9 occ:1.00 ND1 B:HIS62 2.1 22.9 1.0 SG B:CYS94 2.3 23.5 1.0 SG B:CYS91 2.4 23.7 1.0 O B:HOH386 2.4 24.5 1.0 CE1 B:HIS62 3.1 24.1 1.0 CG B:HIS62 3.1 23.6 1.0 CB B:CYS94 3.4 22.7 1.0 CB B:CYS91 3.5 20.1 1.0 CB B:HIS62 3.5 22.3 1.0 N B:CYS94 3.9 19.7 1.0 N B:CYS91 3.9 20.6 1.0 OE2 B:GLU64 4.2 26.8 1.0 NE2 B:HIS62 4.2 25.8 1.0 CA B:CYS91 4.2 22.5 1.0 CA B:CYS94 4.2 20.9 1.0 OE1 B:GLU64 4.2 35.8 1.0 CD2 B:HIS62 4.3 22.4 1.0 CE B:MET93 4.3 23.8 1.0 O B:HOH424 4.3 33.9 1.0 CD B:GLU64 4.5 32.3 1.0 O B:HOH423 4.5 29.9 1.0 C B:CYS91 4.8 20.4 1.0 O B:HOH361 4.8 23.1 1.0 CB B:MET93 4.8 19.3 1.0 O B:CYS91 4.9 20.2 1.0 C B:MET93 5.0 18.9 1.0 CA B:HIS62 5.0 22.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq


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 Yeast Cytosine Deaminase Mutant Ycd-Rq within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:23.0 occ:1.00 ND1 C:HIS62 2.1 19.7 1.0 SG C:CYS94 2.3 22.7 1.0 SG C:CYS91 2.3 22.1 1.0 O C:HOH390 2.4 30.0 1.0 CE1 C:HIS62 3.1 23.0 1.0 CG C:HIS62 3.1 22.4 1.0 CB C:CYS94 3.4 22.5 1.0 CB C:CYS91 3.4 23.1 1.0 CB C:HIS62 3.5 22.0 1.0 N C:CYS91 3.9 20.3 1.0 N C:CYS94 3.9 18.4 1.0 CA C:CYS91 4.2 21.0 1.0 NE2 C:HIS62 4.2 23.5 1.0 OE2 C:GLU64 4.3 29.7 1.0 CD2 C:HIS62 4.3 20.2 1.0 CA C:CYS94 4.3 19.2 1.0 OE1 C:GLU64 4.3 37.4 1.0 CE C:MET93 4.3 21.5 1.0 O C:HOH391 4.4 28.6 1.0 CD C:GLU64 4.5 33.4 1.0 O C:HOH364 4.7 23.0 1.0 C C:CYS91 4.8 19.0 1.0 CB C:MET93 4.8 18.8 1.0 O C:CYS91 4.9 19.5 1.0 C C:MET93 5.0 16.8 1.0 CA C:HIS62 5.0 21.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq


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 Yeast Cytosine Deaminase Mutant Ycd-Rq within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:24.3 occ:1.00 ND1 D:HIS62 2.1 24.2 1.0 O D:HOH391 2.1 31.5 1.0 SG D:CYS94 2.3 24.0 1.0 SG D:CYS91 2.3 23.3 1.0 CE1 D:HIS62 3.0 24.9 1.0 CG D:HIS62 3.1 22.6 1.0 CB D:CYS94 3.4 24.4 1.0 CB D:HIS62 3.4 22.9 1.0 CB D:CYS91 3.5 21.0 1.0 N D:CYS94 3.9 19.9 1.0 N D:CYS91 4.0 19.4 1.0 OE2 D:GLU64 4.1 30.2 1.0 NE2 D:HIS62 4.2 23.8 1.0 CD2 D:HIS62 4.2 21.4 1.0 CA D:CYS91 4.3 18.0 1.0 CE D:MET93 4.3 21.0 1.0 CA D:CYS94 4.3 20.9 1.0 O D:HOH387 4.3 30.0 1.0 OE1 D:GLU64 4.4 39.1 1.0 CD D:GLU64 4.5 34.6 1.0 O D:HOH331 4.7 23.1 1.0 C D:CYS91 4.8 21.2 1.0 CB D:MET93 4.8 19.9 1.0 CA D:HIS62 5.0 23.0 1.0 C D:MET93 5.0 19.4 1.0 O D:CYS91 5.0 20.1 1.0

M.M.Qin, L.S.Yao. The Crystal Structure of Rational Designed Ycd Mutant Ycd-Rq To Be Published.