Manganese in PDB 8i3o: Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH

All present enzymatic activity of Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH:
3.5.4.1;

The structure of Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH, PDB code: 8i3o 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)	34.67 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.319, 64.273, 83.092, 90, 97.69, 90
R / Rfree (%)	17.4 / 20.8

The binding sites of Manganese atom in the Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH (pdb code 8i3o). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH, PDB code: 8i3o:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:18.1 occ:1.00 ND1 A:HIS62 2.2 25.9 1.0 SG A:CYS94 2.3 22.5 1.0 O A:HOH381 2.3 27.4 1.0 SG A:CYS91 2.3 21.1 1.0 CG A:HIS62 3.1 24.2 1.0 CE1 A:HIS62 3.1 27.3 1.0 CB A:CYS91 3.4 22.5 1.0 CB A:CYS94 3.4 20.8 1.0 CB A:HIS62 3.4 23.5 1.0 N A:CYS91 3.8 19.1 1.0 N A:CYS94 3.9 18.3 1.0 OE1 A:GLU64 4.1 28.3 1.0 CA A:CYS91 4.1 22.1 1.0 NE2 A:HIS62 4.3 26.0 1.0 CA A:CYS94 4.3 19.2 1.0 CD2 A:HIS62 4.3 23.8 1.0 CE A:MET93 4.4 23.5 1.0 O A:HOH378 4.4 29.8 1.0 CD A:GLU64 4.6 33.3 1.0 O A:HOH351 4.7 23.6 1.0 OE2 A:GLU64 4.7 36.3 1.0 C A:CYS91 4.7 19.4 1.0 CB A:MET93 4.9 19.8 1.0 O A:CYS91 4.9 19.7 1.0 CA A:HIS62 4.9 22.3 1.0 C A:MET93 5.0 18.4 1.0 C A:PRO90 5.0 23.9 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:17.6 occ:1.00 ND1 B:HIS62 2.2 24.0 1.0 SG B:CYS94 2.3 23.3 1.0 SG B:CYS91 2.3 20.8 1.0 O B:HOH378 2.3 25.4 1.0 CE1 B:HIS62 3.1 26.3 1.0 CG B:HIS62 3.1 21.9 1.0 CB B:CYS94 3.4 20.5 1.0 CB B:CYS91 3.4 21.5 1.0 CB B:HIS62 3.5 20.3 1.0 N B:CYS91 3.9 20.4 1.0 N B:CYS94 3.9 17.7 1.0 OE1 B:GLU64 4.1 26.9 1.0 CA B:CYS91 4.2 20.8 1.0 NE2 B:HIS62 4.2 23.0 1.0 CD2 B:HIS62 4.3 21.4 1.0 CA B:CYS94 4.3 19.6 1.0 CE B:MET93 4.3 21.8 1.0 O B:HOH374 4.4 27.6 1.0 CD B:GLU64 4.6 31.6 1.0 OE2 B:GLU64 4.6 33.8 1.0 O B:HOH341 4.7 23.2 1.0 C B:CYS91 4.7 19.1 1.0 CB B:MET93 4.9 19.1 1.0 O B:CYS91 4.9 18.9 1.0 CA B:HIS62 5.0 21.2 1.0 C B:MET93 5.0 17.3 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn201 b:17.3 occ:1.00 ND1 C:HIS62 2.1 21.6 1.0 O C:HOH387 2.1 23.9 1.0 SG C:CYS94 2.3 21.5 1.0 SG C:CYS91 2.3 20.2 1.0 CE1 C:HIS62 3.1 25.1 1.0 CG C:HIS62 3.1 21.9 1.0 CB C:CYS91 3.4 18.2 1.0 CB C:CYS94 3.4 17.1 1.0 CB C:HIS62 3.5 18.9 1.0 N C:CYS91 3.8 18.8 1.0 N C:CYS94 3.9 17.4 1.0 CA C:CYS91 4.1 18.9 1.0 NE2 C:HIS62 4.2 22.9 1.0 OE1 C:GLU64 4.2 26.9 1.0 CD2 C:HIS62 4.2 22.9 1.0 CA C:CYS94 4.3 17.7 1.0 CE C:MET93 4.4 22.0 1.0 O C:HOH417 4.5 27.8 1.0 OE2 C:GLU64 4.6 32.3 1.0 CD C:GLU64 4.6 30.8 1.0 O C:HOH399 4.7 30.0 1.0 C C:CYS91 4.7 17.7 1.0 O C:HOH385 4.8 22.2 1.0 CB C:MET93 4.9 18.7 1.0 O C:CYS91 4.9 17.8 1.0 CA C:HIS62 5.0 21.0 1.0 C C:PRO90 5.0 20.0 1.0 C C:MET93 5.0 17.5 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn201 b:17.7 occ:1.00 ND1 D:HIS62 2.2 22.8 1.0 O D:HOH395 2.2 25.7 1.0 SG D:CYS94 2.3 22.1 1.0 SG D:CYS91 2.3 21.4 1.0 CE1 D:HIS62 3.1 26.9 1.0 CG D:HIS62 3.2 24.0 1.0 CB D:CYS91 3.3 21.2 1.0 CB D:CYS94 3.4 19.3 1.0 CB D:HIS62 3.5 22.7 1.0 N D:CYS91 3.9 19.4 1.0 N D:CYS94 3.9 17.3 1.0 CA D:CYS91 4.1 20.7 1.0 OE1 D:GLU64 4.2 25.9 1.0 NE2 D:HIS62 4.2 26.4 1.0 CA D:CYS94 4.3 18.5 1.0 CD2 D:HIS62 4.3 24.4 1.0 O D:HOH404 4.3 27.3 1.0 CE D:MET93 4.3 22.6 1.0 O D:HOH408 4.4 28.2 1.0 CD D:GLU64 4.6 31.9 1.0 OE2 D:GLU64 4.7 33.9 1.0 C D:CYS91 4.7 18.9 1.0 O D:HOH347 4.7 20.8 1.0 CB D:MET93 4.9 19.5 1.0 O D:CYS91 4.9 17.5 1.0 CA D:HIS62 5.0 21.3 1.0 C D:MET93 5.0 18.2 1.0

M.M.Qin, L.S.Yao, H.Z.Deng. Crystal Structure of Yeast Cytosine Deaminase Mutant Ycd-Rq-1/8SAH To Be Published.