Zinc in PDB 3g8q: A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea

The structure of A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea, PDB code: 3g8q was solved by Y.Xiong, B.J.Stanley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	184.465, 77.060, 109.082, 90.00, 103.57, 90.00
R / Rfree (%)	20.2 / 26.5

The structure of A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea also contains other interesting chemical elements:

Sodium

(Na)

7 atoms

The binding sites of Zinc atom in the A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea (pdb code 3g8q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea, PDB code: 3g8q:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:0.4 occ:1.00 SG A:CYS70 2.3 67.8 1.0 ND1 A:HIS44 2.7 70.8 1.0 SG A:CYS67 2.8 56.4 1.0 O A:HOH326 2.9 40.2 1.0 CG A:HIS44 3.0 66.6 1.0 CE1 A:HIS44 3.3 68.8 1.0 CB A:CYS70 3.4 59.2 1.0 CB A:HIS44 3.4 61.3 1.0 N A:CYS67 3.6 40.2 1.0 OE2 A:GLU46 3.6 59.2 1.0 CB A:CYS67 3.6 47.1 1.0 CD2 A:HIS44 3.7 69.2 1.0 OE1 A:GLU46 3.9 54.0 1.0 NE2 A:HIS44 3.9 69.8 1.0 CD A:GLU46 3.9 52.4 1.0 CA A:CYS67 4.2 42.5 1.0 CA A:CYS70 4.6 60.0 1.0 C A:PRO66 4.6 38.7 1.0 N A:CYS70 4.6 60.5 1.0 CA A:PRO66 4.7 40.7 1.0 O A:CYS67 4.8 43.3 1.0 C A:CYS67 4.8 45.1 1.0 CA A:HIS44 4.8 62.0 1.0

Zinc binding site 2 out of 4 in the A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:0.5 occ:1.00 SG B:CYS70 2.2 67.6 1.0 ND1 B:HIS44 2.4 75.5 1.0 SG B:CYS67 2.8 65.0 1.0 CG B:HIS44 3.0 75.0 1.0 CE1 B:HIS44 3.1 78.1 1.0 CB B:CYS67 3.2 62.6 1.0 CB B:HIS44 3.4 70.4 1.0 O B:HOH305 3.5 57.4 1.0 N B:CYS67 3.5 58.9 1.0 CB B:CYS70 3.5 61.9 1.0 OE2 B:GLU46 3.7 56.1 1.0 CA B:CYS67 3.9 59.9 1.0 CD2 B:HIS44 3.9 81.8 1.0 NE2 B:HIS44 4.0 81.3 1.0 OE1 B:GLU46 4.1 67.1 1.0 CD B:GLU46 4.2 59.4 1.0 N B:CYS70 4.5 62.5 1.0 C B:PRO66 4.5 57.0 1.0 CA B:CYS70 4.6 62.8 1.0 C B:CYS67 4.6 59.0 1.0 O B:CYS67 4.7 57.9 1.0 CA B:PRO66 4.8 53.9 1.0 CA B:HIS44 4.9 70.4 1.0

Zinc binding site 3 out of 4 in the A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:0.1 occ:1.00 SG C:CYS70 2.5 65.2 1.0 CG C:HIS44 2.6 68.9 1.0 ND1 C:HIS44 2.7 73.2 1.0 SG C:CYS67 2.8 64.1 1.0 CD2 C:HIS44 3.0 67.3 1.0 CB C:HIS44 3.1 65.7 1.0 O C:HOH304 3.1 49.8 1.0 CE1 C:HIS44 3.1 72.5 1.0 NE2 C:HIS44 3.3 68.8 1.0 CB C:CYS67 3.4 55.4 1.0 CB C:CYS70 3.6 60.0 1.0 OE1 C:GLU46 3.7 62.1 1.0 N C:CYS67 3.9 52.0 1.0 OE2 C:GLU46 4.1 65.8 1.0 CD C:GLU46 4.2 63.7 1.0 CA C:CYS67 4.3 54.1 1.0 NE C:ARG47 4.5 0.7 1.0 N C:CYS70 4.5 63.4 1.0 CA C:HIS44 4.5 66.2 1.0 CA C:CYS70 4.7 62.9 1.0 NH2 C:ARG47 4.7 0.5 1.0 CZ C:ARG47 4.8 0.5 1.0 O C:CYS67 4.9 52.4 1.0 C C:CYS67 4.9 55.5 1.0

Zinc binding site 4 out of 4 in the A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Cytidine Deaminase Edits C-to-U in Transfer Rnas in Archaea within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:88.7 occ:1.00 SG D:CYS70 2.4 55.3 1.0 SG D:CYS67 2.5 49.8 1.0 ND1 D:HIS44 2.9 58.6 1.0 O D:HOH305 3.0 39.2 1.0 CB D:CYS70 3.1 42.4 1.0 CG D:HIS44 3.2 54.1 1.0 CB D:CYS67 3.2 40.5 1.0 CE1 D:HIS44 3.4 55.1 1.0 N D:CYS67 3.5 41.1 1.0 CB D:HIS44 3.6 53.1 1.0 CD2 D:HIS44 3.7 55.0 1.0 CA D:CYS67 3.8 40.2 1.0 NE2 D:HIS44 3.9 58.5 1.0 OE1 D:GLU46 4.1 49.6 1.0 OE2 D:GLU46 4.1 49.7 1.0 N D:CYS70 4.2 40.1 1.0 CD D:GLU46 4.2 46.5 1.0 CA D:CYS70 4.2 41.2 1.0 O D:CYS67 4.3 39.2 1.0 C D:CYS67 4.4 40.3 1.0 C D:PRO66 4.6 38.4 1.0 O D:HOH314 4.8 72.8 1.0 CA D:PRO66 4.8 37.7 1.0

L.Randau, B.J.Stanley, A.Kohlway, S.Mechta, Y.Xiong, D.Soll. A Cytidine Deaminase Edits C to U in Transfer Rnas in Archaea Science V. 324 657 2009.
ISSN: ISSN 0036-8075
PubMed: 19407206
DOI: 10.1126/SCIENCE.1170123