Zinc in PDB 1wwr: Crystal Structure of Trna Adenosine Deaminase Tada From Aquifex Aeolicus

The structure of Crystal Structure of Trna Adenosine Deaminase Tada From Aquifex Aeolicus, PDB code: 1wwr was solved by M.Kuratani, R.Ishii, Y.Bessho, R.Fukunaga, T.Sengoku, S.Sekine, S.Yokoyama, Riken Structural Genomics/Proteomics Initiative(Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.47 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.176, 151.953, 54.133, 90.00, 113.42, 90.00
R / Rfree (%)	19.8 / 24.8

The binding sites of Zinc atom in the Crystal Structure of Trna Adenosine Deaminase Tada From Aquifex Aeolicus (pdb code 1wwr). 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 Trna Adenosine Deaminase Tada From Aquifex Aeolicus, PDB code: 1wwr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Trna Adenosine Deaminase Tada From Aquifex Aeolicus


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 Trna Adenosine Deaminase Tada From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:24.6 occ:1.00 ND1 A:HIS52 2.2 20.0 1.0 SG A:CYS85 2.3 17.8 1.0 O A:HOH225 2.3 18.5 1.0 SG A:CYS82 2.4 17.4 1.0 CE1 A:HIS52 3.1 22.7 1.0 CG A:HIS52 3.1 19.8 1.0 CB A:CYS85 3.2 14.8 1.0 CB A:CYS82 3.4 14.7 1.0 CB A:HIS52 3.5 15.2 1.0 N A:CYS85 3.9 13.2 1.0 N A:CYS82 3.9 15.4 1.0 OE1 A:GLU54 4.0 19.4 1.0 CA A:CYS85 4.1 14.9 1.0 O A:HOH266 4.2 22.8 1.0 CA A:CYS82 4.2 15.7 1.0 OE2 A:GLU54 4.2 16.8 1.0 NE2 A:HIS52 4.2 17.8 1.0 CD2 A:HIS52 4.3 20.3 1.0 CD A:GLU54 4.3 16.1 1.0 C A:CYS82 4.7 16.6 1.0 O A:CYS82 4.8 15.2 1.0 CB A:MET84 4.9 12.7 1.0 O D:HOH208 5.0 21.7 1.0 CA A:HIS52 5.0 15.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Trna Adenosine Deaminase Tada From Aquifex Aeolicus


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 Trna Adenosine Deaminase Tada From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:33.6 occ:1.00 SG B:CYS85 2.3 22.1 1.0 ND1 B:HIS52 2.3 22.8 1.0 SG B:CYS82 2.3 20.4 1.0 O B:HOH333 2.4 44.5 1.0 CB B:CYS85 3.1 18.8 1.0 CE1 B:HIS52 3.2 22.9 1.0 CG B:HIS52 3.3 18.5 1.0 CB B:CYS82 3.4 18.8 1.0 CB B:HIS52 3.5 17.9 1.0 N B:CYS82 3.7 18.6 1.0 N B:CYS85 3.8 12.2 1.0 OE1 B:GLU54 4.0 19.9 1.0 CA B:CYS85 4.0 13.8 1.0 CE B:MET84 4.1 17.9 1.0 CA B:CYS82 4.1 16.3 1.0 O B:HOH315 4.3 22.3 1.0 OE2 B:GLU54 4.3 17.3 1.0 CD B:GLU54 4.3 22.1 1.0 NE2 B:HIS52 4.3 20.4 1.0 CD2 B:HIS52 4.4 22.7 1.0 C B:CYS82 4.6 15.6 1.0 O B:CYS82 4.7 15.9 1.0 O B:HOH218 4.9 23.0 1.0 CB B:MET84 4.9 12.2 1.0 C B:PRO81 4.9 16.8 1.0 C B:MET84 4.9 12.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Trna Adenosine Deaminase Tada From Aquifex Aeolicus


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 Trna Adenosine Deaminase Tada From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn203 b:33.4 occ:1.00 SG C:CYS85 2.2 18.7 1.0 SG C:CYS82 2.3 20.9 1.0 ND1 C:HIS52 2.3 24.8 1.0 O C:HOH329 2.4 27.8 1.0 CB C:CYS85 2.9 16.1 1.0 CE1 C:HIS52 3.3 21.2 1.0 CG C:HIS52 3.3 20.9 1.0 CB C:CYS82 3.5 16.2 1.0 CB C:HIS52 3.6 16.0 1.0 N C:CYS85 3.8 14.2 1.0 N C:CYS82 3.8 17.2 1.0 CA C:CYS85 3.9 14.5 1.0 OE1 C:GLU54 4.0 23.6 1.0 CE C:MET84 4.1 15.8 1.0 CA C:CYS82 4.2 16.7 1.0 O C:HOH288 4.3 27.9 1.0 OE2 C:GLU54 4.4 16.4 1.0 NE2 C:HIS52 4.4 21.1 1.0 CD C:GLU54 4.4 18.4 1.0 CD2 C:HIS52 4.4 22.1 1.0 C C:CYS82 4.6 18.6 1.0 O C:CYS82 4.8 15.8 1.0 CB C:MET84 4.8 10.9 1.0 C C:PRO81 4.9 15.6 1.0 C C:MET84 4.9 14.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Trna Adenosine Deaminase Tada From Aquifex Aeolicus


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 Trna Adenosine Deaminase Tada From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn204 b:19.8 occ:1.00 ND1 D:HIS52 2.1 12.6 1.0 SG D:CYS82 2.3 14.8 1.0 O D:HOH241 2.3 15.3 1.0 SG D:CYS85 2.3 13.8 1.0 CE1 D:HIS52 3.0 14.3 1.0 CB D:CYS85 3.1 9.5 1.0 CG D:HIS52 3.1 11.6 1.0 CB D:CYS82 3.4 12.2 1.0 CB D:HIS52 3.5 12.4 1.0 N D:CYS82 3.8 11.5 1.0 N D:CYS85 3.8 11.6 1.0 CE D:MET84 4.0 18.4 1.0 OE1 D:GLU54 4.0 15.0 1.0 CA D:CYS85 4.1 12.7 1.0 CA D:CYS82 4.1 13.3 1.0 NE2 D:HIS52 4.2 11.4 1.0 O D:HOH280 4.2 16.9 1.0 CD2 D:HIS52 4.3 14.2 1.0 OE2 D:GLU54 4.3 12.1 1.0 CD D:GLU54 4.4 11.2 1.0 C D:CYS82 4.6 14.1 1.0 O D:CYS82 4.8 14.9 1.0 CB D:MET84 4.8 12.8 1.0 O D:HOH223 4.9 17.6 1.0 O D:HOH217 4.9 22.0 1.0 C D:MET84 4.9 15.5 1.0 C D:PRO81 4.9 12.1 1.0

M.Kuratani, R.Ishii, Y.Bessho, R.Fukunaga, T.Sengoku, M.Shirouzu, S.Sekine, S.Yokoyama. Crystal Structure of Trna Adenosine Deaminase (Tada) From Aquifex Aeolicus J.Biol.Chem. V. 280 16002 2005.
ISSN: ISSN 0021-9258
PubMed: 15677468
DOI: 10.1074/JBC.M414541200