Zinc in PDB 5jfy: Crystal Structure of A Plant Cytidine Deaminase

The structure of Crystal Structure of A Plant Cytidine Deaminase, PDB code: 5jfy was solved by M.W.Taylor, J.E.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.64 / 2.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.808, 99.808, 143.061, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 21.4

The structure of Crystal Structure of A Plant Cytidine Deaminase also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of A Plant Cytidine Deaminase (pdb code 5jfy). 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 A Plant Cytidine Deaminase, PDB code: 5jfy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Plant Cytidine Deaminase


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 A Plant Cytidine Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:30.2 occ:1.00 ND1 A:HIS80 2.1 26.7 1.0 O C:HOH321 2.1 25.7 1.0 SG A:CYS113 2.3 27.9 1.0 SG A:CYS110 2.3 27.0 1.0 HB2 A:CYS113 3.0 29.5 1.0 CE1 A:HIS80 3.1 30.9 1.0 CG A:HIS80 3.1 28.6 1.0 H A:CYS110 3.1 37.3 1.0 HB3 A:HIS80 3.1 24.9 1.0 HE1 A:HIS80 3.2 37.0 1.0 CB A:CYS113 3.3 24.6 1.0 HB3 A:CYS110 3.3 39.8 1.0 HB2 A:HIS80 3.3 24.9 1.0 CB A:HIS80 3.4 20.8 1.0 H A:CYS113 3.4 31.3 1.0 CB A:CYS110 3.4 33.1 1.0 HE1 A:MET112 3.5 34.0 1.0 HD3 C:LYS130 3.6 43.5 1.0 HZ3 C:LYS130 3.7 52.5 1.0 N A:CYS110 3.9 31.1 1.0 HB3 A:CYS113 4.0 29.5 1.0 HE2 A:MET112 4.0 34.0 1.0 N A:CYS113 4.0 26.1 1.0 OE1 A:GLU82 4.0 37.7 1.0 HB3 A:MET112 4.0 34.4 1.0 NE2 A:HIS80 4.2 28.0 1.0 CE A:MET112 4.2 28.4 1.0 CD2 A:HIS80 4.2 31.1 1.0 CA A:CYS110 4.2 32.6 1.0 HB2 A:CYS110 4.2 39.8 1.0 CA A:CYS113 4.2 27.1 1.0 CD C:LYS130 4.5 36.3 1.0 HE3 A:MET112 4.5 34.0 1.0 NZ C:LYS130 4.6 43.7 1.0 HA A:PRO109 4.6 38.6 1.0 HA A:CYS113 4.6 32.5 1.0 CL A:CL201 4.6 27.9 1.0 HD11 B:LEU119 4.6 45.8 1.0 HB2 A:GLU82 4.7 26.2 1.0 CD A:GLU82 4.7 45.5 1.0 C A:CYS110 4.8 32.4 1.0 HZ2 C:LYS130 4.8 52.5 1.0 HD2 C:LYS130 4.8 43.5 1.0 O A:CYS110 4.9 27.3 1.0 HB3 A:PRO109 4.9 44.1 1.0 CA A:HIS80 4.9 26.6 1.0 HB3 C:LYS130 4.9 44.1 1.0 HG23 A:VAL83 4.9 28.9 1.0 HE2 A:HIS80 4.9 33.6 1.0 CE C:LYS130 5.0 36.8 1.0 CB A:MET112 5.0 28.7 1.0 HE2 C:LYS130 5.0 44.2 1.0 H A:GLU82 5.0 29.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Plant Cytidine Deaminase


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 A Plant Cytidine Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:33.6 occ:1.00 ND1 B:HIS80 2.0 29.5 1.0 O B:HOH333 2.1 24.6 1.0 SG B:CYS110 2.3 29.6 1.0 SG B:CYS113 2.3 31.6 1.0 CE1 B:HIS80 3.0 25.9 1.0 HB2 B:CYS113 3.0 27.2 1.0 H B:CYS110 3.0 38.8 1.0 CG B:HIS80 3.1 31.5 1.0 HE1 B:HIS80 3.1 31.1 1.0 HB3 B:HIS80 3.2 29.4 1.0 CB B:CYS113 3.3 22.7 1.0 HB3 B:CYS110 3.3 34.4 1.0 HB2 B:HIS80 3.3 29.4 1.0 HE2 B:MET112 3.4 37.7 1.0 CB B:HIS80 3.4 24.5 1.0 CB B:CYS110 3.4 28.7 1.0 H B:CYS113 3.5 35.5 1.0 N B:CYS110 3.8 32.3 1.0 HB3 B:CYS113 3.9 27.2 1.0 HE3 B:MET112 4.0 37.7 1.0 HB3 B:MET112 4.0 34.3 1.0 N B:CYS113 4.0 29.6 1.0 NE2 B:HIS80 4.1 29.6 1.0 CE B:MET112 4.1 31.4 1.0 CD2 B:HIS80 4.2 29.1 1.0 CA B:CYS110 4.2 29.4 1.0 HB2 B:CYS110 4.2 34.4 1.0 OE1 B:GLU82 4.2 44.3 1.0 CA B:CYS113 4.3 28.0 1.0 HD11 A:LEU119 4.3 40.9 1.0 HE1 B:MET112 4.5 37.7 1.0 HA B:PRO109 4.5 41.0 1.0 HA B:CYS113 4.6 33.6 1.0 C B:CYS110 4.7 29.3 1.0 CL B:CL201 4.7 29.7 1.0 O B:CYS110 4.7 28.1 1.0 HB2 B:GLU82 4.8 33.7 1.0 HB3 B:PRO109 4.9 49.6 1.0 HE2 B:HIS80 4.9 35.5 1.0 HD13 A:LEU119 4.9 40.9 1.0 HG23 B:VAL83 4.9 30.8 1.0 CD B:GLU82 4.9 44.6 1.0 CA B:HIS80 4.9 29.2 1.0 C B:PRO109 5.0 34.9 1.0 CB B:MET112 5.0 28.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Plant Cytidine Deaminase


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 A Plant Cytidine Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:38.0 occ:1.00 ND1 C:HIS80 2.1 40.2 1.0 SG C:CYS110 2.3 32.0 1.0 SG C:CYS113 2.3 41.9 1.0 O A:HOH332 2.3 31.9 1.0 HB3 C:HIS80 3.0 39.3 1.0 HB2 C:CYS113 3.0 44.8 1.0 CG C:HIS80 3.0 35.7 1.0 CE1 C:HIS80 3.1 36.0 1.0 H C:CYS110 3.1 46.3 1.0 HB2 C:HIS80 3.3 39.3 1.0 CB C:CYS113 3.3 37.3 1.0 HE1 C:HIS80 3.3 43.1 1.0 CB C:HIS80 3.3 32.8 1.0 HB3 C:CYS110 3.4 42.8 1.0 HE2 C:MET112 3.5 52.4 1.0 CB C:CYS110 3.5 35.6 1.0 HD3 A:LYS130 3.5 46.1 1.0 H C:CYS113 3.5 48.0 1.0 N C:CYS110 3.9 38.6 1.0 HB3 C:CYS113 4.0 44.8 1.0 HE3 C:MET112 4.0 52.4 1.0 HZ3 A:LYS130 4.0 64.5 1.0 HB3 C:MET112 4.1 65.0 1.0 OE1 C:GLU82 4.1 50.3 1.0 N C:CYS113 4.1 40.0 1.0 CE C:MET112 4.2 43.6 1.0 CD2 C:HIS80 4.2 37.9 1.0 NE2 C:HIS80 4.2 34.9 1.0 CA C:CYS110 4.2 34.8 1.0 HB2 C:CYS110 4.3 42.8 1.0 CA C:CYS113 4.3 37.3 1.0 CD A:LYS130 4.4 38.4 1.0 HE1 C:MET112 4.5 52.4 1.0 HA C:PRO109 4.6 33.2 1.0 CL C:CL201 4.6 31.2 1.0 HD11 D:LEU119 4.6 61.0 1.0 HA C:CYS113 4.6 44.8 1.0 HB2 C:GLU82 4.6 40.0 1.0 HD2 A:LYS130 4.7 46.1 1.0 HB3 A:LYS130 4.8 47.0 1.0 HE2 A:LYS130 4.8 50.0 1.0 HG23 C:VAL83 4.8 38.4 1.0 CD C:GLU82 4.8 59.6 1.0 C C:CYS110 4.8 37.7 1.0 NZ A:LYS130 4.8 53.7 1.0 CA C:HIS80 4.8 35.6 1.0 O C:CYS110 4.9 33.0 1.0 HB3 C:PRO109 4.9 37.3 1.0 H C:GLU82 4.9 42.1 1.0 CE A:LYS130 4.9 41.6 1.0 HE2 C:HIS80 5.0 41.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Plant Cytidine Deaminase


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 A Plant Cytidine Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:42.7 occ:1.00 ND1 D:HIS80 1.9 36.9 1.0 O D:HOH316 2.3 56.1 1.0 SG D:CYS113 2.3 41.8 1.0 SG D:CYS110 2.4 42.6 1.0 CE1 D:HIS80 2.8 38.5 1.0 HE1 D:HIS80 2.9 46.2 1.0 H D:CYS110 2.9 56.5 1.0 HB2 D:CYS113 3.0 53.5 1.0 CG D:HIS80 3.1 39.2 1.0 CB D:CYS113 3.2 44.6 1.0 HB3 D:CYS110 3.3 48.6 1.0 H D:CYS113 3.4 55.6 1.0 HE2 D:MET112 3.4 63.6 1.0 HB3 D:HIS80 3.4 49.6 1.0 CB D:CYS110 3.4 40.5 1.0 HB2 D:HIS80 3.5 49.6 1.0 CB D:HIS80 3.6 41.3 1.0 N D:CYS110 3.7 47.1 1.0 HE3 D:MET112 3.9 63.6 1.0 HB3 D:CYS113 3.9 53.5 1.0 NE2 D:HIS80 4.0 47.2 1.0 O D:HOH308 4.0 50.4 1.0 N D:CYS113 4.0 46.3 1.0 CE D:MET112 4.1 53.0 1.0 HB3 D:MET112 4.1 42.3 1.0 HD11 C:LEU119 4.1 45.8 1.0 CA D:CYS110 4.1 40.8 1.0 CD2 D:HIS80 4.1 48.8 1.0 OE2 D:GLU82 4.2 50.3 1.0 CA D:CYS113 4.2 47.8 1.0 HB2 D:CYS110 4.2 48.6 1.0 HA D:PRO109 4.3 64.2 1.0 HE1 D:MET112 4.4 63.6 1.0 OE1 D:GLU82 4.4 56.9 1.0 CD D:GLU82 4.5 66.9 1.0 HA D:CYS113 4.5 57.4 1.0 HB2 D:GLU82 4.7 80.1 1.0 HE2 D:HIS80 4.7 56.6 1.0 C D:CYS110 4.7 41.5 1.0 O D:HOH326 4.8 40.1 0.9 O D:CYS110 4.8 47.2 1.0 CL D:CL201 4.8 54.4 1.0 HG23 D:VAL83 4.8 42.1 1.0 C D:PRO109 4.8 55.0 1.0 HB3 D:PRO109 4.9 55.9 1.0 HD13 C:LEU119 4.9 45.8 1.0 CD1 C:LEU119 4.9 38.2 1.0 HA D:CYS110 5.0 48.9 1.0 CA D:PRO109 5.0 53.5 1.0 CB D:MET112 5.0 35.2 1.0

M.W.Taylor, J.E.Lee. To Be Published To Be Published.