Zinc in PDB 1r5t: The Crystal Structure of Cytidine Deaminase CDD1, An Orphan C to U Editase From Yeast

All present enzymatic activity of The Crystal Structure of Cytidine Deaminase CDD1, An Orphan C to U Editase From Yeast:
3.5.4.5;

The structure of The Crystal Structure of Cytidine Deaminase CDD1, An Orphan C to U Editase From Yeast, PDB code: 1r5t was solved by K.Xie, M.P.Sowden, G.S.C.Dance, A.T.Torelli, H.C.Smith, J.E.Wedekind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.05 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	78.520, 86.370, 156.260, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.2

The binding sites of Zinc atom in the The Crystal Structure of Cytidine Deaminase CDD1, An Orphan C to U Editase From Yeast (pdb code 1r5t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Crystal Structure of Cytidine Deaminase CDD1, An Orphan C to U Editase From Yeast, PDB code: 1r5t:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Crystal Structure of Cytidine Deaminase CDD1, An Orphan C to U Editase From Yeast


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Cytidine Deaminase CDD1, An Orphan C to U Editase From Yeast within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn150 b:35.0 occ:1.00 O A:HOH223 2.1 38.0 1.0 SG A:CYS96 2.2 26.6 1.0 SG A:CYS99 2.2 29.1 1.0 SG A:CYS61 2.4 35.4 1.0 CB A:CYS61 3.1 27.5 1.0 CB A:CYS96 3.3 24.9 1.0 CB A:CYS99 3.3 27.3 1.0 N A:CYS96 3.7 26.9 1.0 N A:CYS99 3.9 25.4 1.0 CA A:CYS96 4.0 24.6 1.0 OE2 A:GLU63 4.1 39.9 1.0 CA A:CYS99 4.2 25.5 1.0 OE1 A:GLU63 4.3 34.9 1.0 O A:CYS96 4.3 22.4 1.0 C A:CYS96 4.4 23.2 1.0 CD A:GLU63 4.4 36.4 1.0 CA A:CYS61 4.6 25.5 1.0 NH2 A:ARG64 4.7 34.9 1.0 O A:HOH222 4.7 62.9 1.0 NE A:ARG64 4.7 35.6 1.0 OG D:SER55 4.8 39.4 1.0 CB A:VAL98 4.8 26.7 1.0 C A:PRO95 4.8 28.7 1.0 C A:VAL98 4.9 25.9 1.0 O A:HOH224 5.0 68.6 1.0

Zinc binding site 2 out of 4 in the The Crystal Structure of Cytidine Deaminase CDD1, An Orphan C to U Editase From Yeast


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Cytidine Deaminase CDD1, An Orphan C to U Editase From Yeast within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn151 b:40.0 occ:1.00 O B:HOH209 2.2 48.8 1.0 SG B:CYS99 2.2 33.5 1.0 SG B:CYS61 2.3 34.5 1.0 SG B:CYS96 2.4 27.1 1.0 CB B:CYS61 3.0 27.5 1.0 CB B:CYS99 3.4 28.4 1.0 CB B:CYS96 3.4 27.7 1.0 N B:CYS96 3.7 27.3 1.0 N B:CYS99 3.9 22.9 1.0 CA B:CYS96 4.1 26.5 1.0 OE2 B:GLU63 4.1 35.6 1.0 CA B:CYS99 4.2 24.9 1.0 OE1 B:GLU63 4.3 31.8 1.0 NH2 B:ARG64 4.4 31.3 1.0 CD B:GLU63 4.4 32.1 1.0 O B:CYS96 4.4 27.6 1.0 CA B:CYS61 4.5 26.5 1.0 C B:CYS96 4.5 25.6 1.0 NE B:ARG64 4.6 35.6 1.0 CB B:VAL98 4.7 23.4 1.0 C B:PRO95 4.8 30.4 1.0 OG C:SER55 4.9 38.3 1.0 C B:VAL98 4.9 22.8 1.0 CZ B:ARG64 5.0 37.0 1.0 N B:CYS61 5.0 26.6 1.0

Zinc binding site 3 out of 4 in the The Crystal Structure of Cytidine Deaminase CDD1, An Orphan C to U Editase From Yeast


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Cytidine Deaminase CDD1, An Orphan C to U Editase From Yeast within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn152 b:35.7 occ:1.00 O C:HOH198 2.1 30.8 1.0 SG C:CYS96 2.3 24.2 1.0 SG C:CYS99 2.3 28.6 1.0 SG C:CYS61 2.3 31.1 1.0 CB C:CYS61 3.1 26.4 1.0 CB C:CYS99 3.3 20.6 1.0 CB C:CYS96 3.4 23.8 1.0 N C:CYS96 3.7 23.8 1.0 N C:CYS99 3.9 20.0 1.0 CA C:CYS96 4.0 22.5 1.0 OE2 C:GLU63 4.0 35.6 1.0 CA C:CYS99 4.2 20.1 1.0 OE1 C:GLU63 4.2 31.6 1.0 CD C:GLU63 4.4 30.5 1.0 O C:HOH197 4.5 53.7 1.0 O C:CYS96 4.5 21.2 1.0 C C:CYS96 4.5 22.1 1.0 NH2 C:ARG64 4.5 33.9 1.0 OG B:SER55 4.6 37.0 1.0 CA C:CYS61 4.6 24.2 1.0 NE C:ARG64 4.7 34.0 1.0 CB C:VAL98 4.8 21.3 1.0 C C:PRO95 4.9 24.9 1.0 C C:VAL98 5.0 21.2 1.0

Zinc binding site 4 out of 4 in the The Crystal Structure of Cytidine Deaminase CDD1, An Orphan C to U Editase From Yeast


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Cytidine Deaminase CDD1, An Orphan C to U Editase From Yeast within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn153 b:35.9 occ:1.00 O D:HOH179 2.0 30.0 1.0 SG D:CYS99 2.3 26.3 1.0 SG D:CYS96 2.4 29.4 1.0 SG D:CYS61 2.4 36.7 1.0 CB D:CYS61 3.1 26.7 1.0 CB D:CYS99 3.3 21.3 1.0 CB D:CYS96 3.4 25.1 1.0 N D:CYS96 3.7 25.6 1.0 N D:CYS99 4.0 21.6 1.0 OE2 D:GLU63 4.0 33.6 1.0 CA D:CYS96 4.1 25.5 1.0 CA D:CYS99 4.2 22.0 1.0 OE1 D:GLU63 4.3 31.9 1.0 CD D:GLU63 4.4 30.7 1.0 NH2 D:ARG64 4.4 30.6 1.0 O D:CYS96 4.6 23.7 1.0 CA D:CYS61 4.6 24.9 1.0 C D:CYS96 4.6 23.3 1.0 OG A:SER55 4.6 35.9 1.0 NE D:ARG64 4.7 32.9 1.0 C D:PRO95 4.9 26.6 1.0 CB D:VAL98 4.9 23.4 1.0 O D:HOH178 4.9 30.5 1.0 O D:HOH177 5.0 60.0 1.0

K.Xie, M.P.Sowden, G.S.Dance, A.T.Torelli, H.C.Smith, J.E.Wedekind. The Structure of A Yeast Rna-Editing Deaminase Provides Insight Into the Fold and Function of Activation-Induced Deaminase and Apobec-1. Proc.Natl.Acad.Sci.Usa V. 101 8114 2004.
ISSN: ISSN 0027-8424
PubMed: 15148397
DOI: 10.1073/PNAS.0400493101