Zinc in PDB 2fr5: Crystal Structure of Mouse Cytidine Deaminase Complexed with Tetrahydrouridine

All present enzymatic activity of Crystal Structure of Mouse Cytidine Deaminase Complexed with Tetrahydrouridine:
3.5.4.5;

The structure of Crystal Structure of Mouse Cytidine Deaminase Complexed with Tetrahydrouridine, PDB code: 2fr5 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)	41.49 / 1.48
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	82.238, 93.403, 180.743, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 19

The binding sites of Zinc atom in the Crystal Structure of Mouse Cytidine Deaminase Complexed with Tetrahydrouridine (pdb code 2fr5). 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 Tetrahydrouridine, PDB code: 2fr5:
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 Tetrahydrouridine


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 Tetrahydrouridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn147 b:9.1 occ:1.00 O4 A:TYU1001 2.1 9.4 1.0 SG A:CYS102 2.3 7.2 1.0 SG A:CYS99 2.3 6.7 1.0 SG A:CYS65 2.3 7.1 1.0 CB A:CYS65 3.0 6.7 1.0 C4 A:TYU1001 3.2 9.1 1.0 CB A:CYS102 3.3 7.6 1.0 CB A:CYS99 3.4 6.0 1.0 C5 A:TYU1001 3.6 9.7 1.0 N3 A:TYU1001 3.6 7.9 1.0 OE1 A:GLU67 3.8 7.4 1.0 N A:CYS99 3.8 6.2 1.0 N A:CYS102 4.0 6.5 1.0 SG C:CYS59 4.0 10.6 1.0 CA A:CYS99 4.1 6.4 1.0 CA A:CYS102 4.2 7.2 1.0 C2 A:TYU1001 4.3 7.1 1.0 CD A:GLU67 4.3 7.1 1.0 OE2 A:GLU67 4.3 6.7 1.0 NH1 A:ARG68 4.4 12.5 0.5 NE A:ARG68 4.4 7.8 0.5 CA A:CYS65 4.5 6.8 1.0 O A:CYS99 4.5 5.5 1.0 C A:CYS99 4.6 5.7 1.0 N1 A:TYU1001 4.7 8.0 1.0 CZ A:ARG68 4.8 9.2 0.5 C6 A:TYU1001 4.8 9.8 1.0 O2 A:TYU1001 4.9 7.6 1.0 C A:PRO98 5.0 6.9 1.0

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


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 Tetrahydrouridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn147 b:10.1 occ:1.00 O4 B:TYU1002 2.2 8.5 1.0 SG B:CYS102 2.3 7.7 1.0 SG B:CYS65 2.3 9.1 1.0 SG B:CYS99 2.3 7.5 1.0 CB B:CYS65 3.0 7.7 1.0 C4 B:TYU1002 3.2 8.6 1.0 CB B:CYS102 3.3 7.3 1.0 CB B:CYS99 3.4 6.4 1.0 C5 B:TYU1002 3.5 10.8 1.0 N3 B:TYU1002 3.6 11.0 1.0 N B:CYS99 3.8 7.2 1.0 OE1 B:GLU67 3.9 9.5 1.0 N B:CYS102 4.0 7.2 1.0 SG D:CYS59 4.1 9.1 1.0 CA B:CYS99 4.1 7.2 1.0 CA B:CYS102 4.2 7.2 1.0 C2 B:TYU1002 4.2 9.8 1.0 OE2 B:GLU67 4.3 9.5 1.0 NH1 B:ARG68 4.3 15.1 0.5 CD B:GLU67 4.3 8.3 1.0 NE B:ARG68 4.4 10.0 0.5 CA B:CYS65 4.5 7.9 1.0 O B:CYS99 4.6 7.1 1.0 C B:CYS99 4.6 6.3 1.0 N1 B:TYU1002 4.7 8.8 1.0 C6 B:TYU1002 4.7 9.7 1.0 CZ B:ARG68 4.8 11.9 0.5 O2 B:TYU1002 4.9 8.4 1.0 C B:PRO98 4.9 7.1 1.0

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


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 Tetrahydrouridine within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn147 b:11.5 occ:1.00 O4 C:TYU1003 2.1 11.6 1.0 SG C:CYS102 2.3 11.0 1.0 SG C:CYS99 2.3 11.0 1.0 SG C:CYS65 2.3 9.2 1.0 CB C:CYS65 3.0 7.0 1.0 C4 C:TYU1003 3.2 9.3 1.0 CB C:CYS102 3.3 10.3 1.0 CB C:CYS99 3.4 9.0 1.0 C5 C:TYU1003 3.5 10.5 1.0 N3 C:TYU1003 3.6 8.5 1.0 OE1 C:GLU67 3.8 10.1 1.0 N C:CYS99 3.8 9.5 1.0 SG A:CYS59 4.0 10.1 1.0 N C:CYS102 4.0 9.7 1.0 CA C:CYS99 4.1 9.6 1.0 C2 C:TYU1003 4.2 9.1 1.0 NH1 C:ARG68 4.3 15.9 0.5 CA C:CYS102 4.3 10.4 1.0 OE2 C:GLU67 4.3 9.5 1.0 CD C:GLU67 4.3 9.1 1.0 CA C:CYS65 4.4 8.0 1.0 NE C:ARG68 4.5 9.8 0.5 O C:CYS99 4.5 8.3 1.0 C C:CYS99 4.6 8.4 1.0 N1 C:TYU1003 4.7 10.5 1.0 CZ C:ARG68 4.7 12.1 0.5 C6 C:TYU1003 4.7 10.2 1.0 O2 C:TYU1003 4.9 9.6 1.0 C C:PRO98 4.9 10.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Mouse Cytidine Deaminase Complexed with Tetrahydrouridine


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 Tetrahydrouridine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn147 b:11.0 occ:1.00 O4 D:TYU1004 2.2 11.1 1.0 SG D:CYS102 2.3 9.1 1.0 SG D:CYS99 2.3 9.4 1.0 SG D:CYS65 2.3 8.1 1.0 CB D:CYS65 3.0 6.6 1.0 C4 D:TYU1004 3.2 11.9 1.0 CB D:CYS102 3.3 9.3 1.0 CB D:CYS99 3.3 7.7 1.0 C5 D:TYU1004 3.6 11.7 1.0 N3 D:TYU1004 3.7 10.2 1.0 N D:CYS99 3.8 8.1 1.0 OE1 D:GLU67 3.9 8.9 1.0 N D:CYS102 4.0 8.3 1.0 SG B:CYS59 4.1 10.9 1.0 CA D:CYS99 4.1 8.4 1.0 NH1 D:ARG68 4.2 11.5 0.5 CA D:CYS102 4.2 8.6 1.0 C2 D:TYU1004 4.3 11.6 1.0 OE2 D:GLU67 4.3 8.4 1.0 CD D:GLU67 4.3 7.7 1.0 NE D:ARG68 4.4 6.2 0.5 CA D:CYS65 4.5 6.7 1.0 O D:CYS99 4.6 8.9 1.0 C D:CYS99 4.6 8.5 1.0 CZ D:ARG68 4.7 7.6 0.5 N1 D:TYU1004 4.7 9.8 1.0 C6 D:TYU1004 4.8 11.1 1.0 O2 D:TYU1004 4.9 9.0 1.0 C D:PRO98 4.9 9.1 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