Zinc in PDB 1zab: Crystal Structure of Mouse Cytidine Deaminase Complexed with 3-Deazauridine

All present enzymatic activity of Crystal Structure of Mouse Cytidine Deaminase Complexed with 3-Deazauridine:
3.5.4.5;

The structure of Crystal Structure of Mouse Cytidine Deaminase Complexed with 3-Deazauridine, PDB code: 1zab was solved by A.H.Teh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.56 / 2.36
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	82.237, 92.361, 180.531, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.6

The binding sites of Zinc atom in the Crystal Structure of Mouse Cytidine Deaminase Complexed with 3-Deazauridine (pdb code 1zab). 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 Mouse Cytidine Deaminase Complexed with 3-Deazauridine, PDB code: 1zab:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Mouse Cytidine Deaminase Complexed with 3-Deazauridine


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 Mouse Cytidine Deaminase Complexed with 3-Deazauridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn147 b:16.5 occ:1.00 O A:HOH1006 2.1 5.8 1.0 SG A:CYS99 2.3 14.8 1.0 SG A:CYS102 2.3 15.5 1.0 SG A:CYS65 2.4 15.4 1.0 CB A:CYS65 3.0 12.9 1.0 CB A:CYS99 3.4 12.6 1.0 CB A:CYS102 3.5 12.2 1.0 SG C:CYS59 3.7 16.8 1.0 N A:CYS99 3.8 12.9 1.0 OE1 A:GLU67 4.0 19.6 1.0 N A:CYS102 4.1 12.4 1.0 NH1 A:ARG68 4.1 17.9 0.5 CA A:CYS99 4.1 13.6 1.0 CA A:CYS102 4.4 12.2 1.0 NE A:ARG68 4.4 19.4 0.5 O A:CYS99 4.5 12.5 1.0 CD A:GLU67 4.5 17.8 1.0 CA A:CYS65 4.5 13.2 1.0 OE2 A:GLU67 4.6 16.8 1.0 C3 A:URD1001 4.6 19.0 1.0 C A:CYS99 4.6 14.2 1.0 CZ A:ARG68 4.6 18.9 0.5 C4 A:URD1001 4.7 18.4 1.0 C2 A:URD1001 4.9 19.5 1.0 C A:PRO98 5.0 15.0 1.0 CB A:ALA101 5.0 10.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Mouse Cytidine Deaminase Complexed with 3-Deazauridine


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 Mouse Cytidine Deaminase Complexed with 3-Deazauridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn147 b:21.0 occ:1.00 O B:HOH1003 2.2 9.4 1.0 SG B:CYS102 2.3 18.3 1.0 SG B:CYS99 2.4 18.3 1.0 SG B:CYS65 2.4 13.4 1.0 CB B:CYS65 3.0 14.8 1.0 CB B:CYS99 3.3 15.6 1.0 CB B:CYS102 3.4 14.0 1.0 N B:CYS99 3.8 14.4 1.0 SG D:CYS59 3.9 15.0 1.0 N B:CYS102 4.0 14.7 1.0 OE1 B:GLU67 4.0 22.0 1.0 CA B:CYS99 4.1 15.5 1.0 NH1 B:ARG68 4.3 20.3 0.5 CA B:CYS102 4.3 14.4 1.0 OE2 B:GLU67 4.3 23.8 1.0 O B:CYS99 4.4 17.5 1.0 CD B:GLU67 4.4 22.4 1.0 CA B:CYS65 4.5 15.5 1.0 NE B:ARG68 4.5 20.2 0.5 C B:CYS99 4.5 16.2 1.0 C3 B:URD1002 4.6 16.3 1.0 CZ B:ARG68 4.8 19.9 0.5 C4 B:URD1002 4.8 19.2 1.0 C2 B:URD1002 4.9 20.2 1.0 CB B:ALA101 4.9 12.0 1.0 C B:PRO98 4.9 14.1 1.0 N B:CYS65 5.0 14.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Mouse Cytidine Deaminase Complexed with 3-Deazauridine


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 Mouse Cytidine Deaminase Complexed with 3-Deazauridine within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn147 b:20.0 occ:1.00 O C:HOH1004 2.1 15.8 1.0 SG C:CYS65 2.3 17.0 1.0 SG C:CYS102 2.4 18.1 1.0 SG C:CYS99 2.4 16.6 1.0 CB C:CYS65 2.9 15.4 1.0 CB C:CYS99 3.3 14.9 1.0 CB C:CYS102 3.4 14.0 1.0 SG A:CYS59 3.7 18.5 1.0 N C:CYS99 3.8 16.2 1.0 OE1 C:GLU67 4.0 18.6 1.0 N C:CYS102 4.0 14.3 1.0 CA C:CYS99 4.1 15.9 1.0 NH1 C:ARG68 4.2 18.8 0.5 OE2 C:GLU67 4.3 20.4 1.0 CA C:CYS102 4.3 15.1 1.0 CD C:GLU67 4.4 17.6 1.0 CA C:CYS65 4.4 16.2 1.0 NE C:ARG68 4.4 21.4 0.5 O C:CYS99 4.5 13.6 1.0 C C:CYS99 4.6 15.7 1.0 C3 C:URD1003 4.6 16.4 1.0 CZ C:ARG68 4.7 21.2 0.5 C4 C:URD1003 4.8 19.1 1.0 C2 C:URD1003 4.9 17.6 1.0 N C:CYS65 5.0 15.1 1.0 C C:PRO98 5.0 17.0 1.0 CB C:ALA101 5.0 14.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Mouse Cytidine Deaminase Complexed with 3-Deazauridine


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 Mouse Cytidine Deaminase Complexed with 3-Deazauridine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn147 b:19.2 occ:1.00 O D:HOH1005 2.2 14.8 1.0 SG D:CYS102 2.3 18.1 1.0 SG D:CYS65 2.4 17.9 1.0 SG D:CYS99 2.4 20.6 1.0 CB D:CYS65 3.0 16.2 1.0 CB D:CYS99 3.4 17.0 1.0 CB D:CYS102 3.4 16.2 1.0 N D:CYS99 3.7 18.7 1.0 SG B:CYS59 3.8 18.9 1.0 OE1 D:GLU67 3.9 22.3 1.0 N D:CYS102 4.0 16.3 1.0 CA D:CYS99 4.1 19.1 1.0 NH1 D:ARG68 4.1 16.5 0.5 OE2 D:GLU67 4.2 21.5 1.0 CA D:CYS102 4.3 15.9 1.0 CD D:GLU67 4.3 20.9 1.0 NE D:ARG68 4.4 17.9 0.5 O D:CYS99 4.5 23.0 1.0 CA D:CYS65 4.5 15.1 1.0 C D:CYS99 4.5 19.9 1.0 CZ D:ARG68 4.6 17.7 0.5 C3 D:URD1004 4.6 18.6 1.0 C4 D:URD1004 4.8 19.0 1.0 C D:PRO98 4.9 20.4 1.0 C2 D:URD1004 4.9 21.2 1.0 CB D:ALA101 4.9 15.4 1.0

A.H.Teh, M.Kimura, M.Yamamoto, N.Tanaka, I.Yamaguchi, T.Kumasaka. The 1.48 A Resolution Crystal Structure of the Homotetrameric Cytidine Deaminase From Mouse Biochemistry V. 45 7825 2006.
ISSN: ISSN 0006-2960
PubMed: 16784234
DOI: 10.1021/BI060345F