Zinc in PDB 3ay0: Crystal Structure of Methanocaldococcus Jannaschii TRM5 in Complex with Adenosine

The structure of Crystal Structure of Methanocaldococcus Jannaschii TRM5 in Complex with Adenosine, PDB code: 3ay0 was solved by S.Goto-Ito, T.Ito, Y.M.Hou, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.490, 67.127, 92.239, 90.00, 93.75, 90.00
R / Rfree (%)	21.4 / 29.3

The binding sites of Zinc atom in the Crystal Structure of Methanocaldococcus Jannaschii TRM5 in Complex with Adenosine (pdb code 3ay0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Methanocaldococcus Jannaschii TRM5 in Complex with Adenosine, PDB code: 3ay0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Methanocaldococcus Jannaschii TRM5 in Complex with Adenosine


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 Methanocaldococcus Jannaschii TRM5 in Complex with Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn337 b:78.4 occ:1.00 OE1 A:GLU111 2.2 82.9 1.0 NE2 B:HIS271 2.5 54.8 1.0 OE2 A:GLU111 2.6 83.7 1.0 CD A:GLU111 2.7 83.0 1.0 O A:HOH347 2.8 23.8 1.0 CD2 B:HIS271 3.0 54.1 1.0 CD B:LYS272 3.5 54.8 1.0 CE1 B:HIS271 3.6 54.4 1.0 CG B:LYS272 3.7 52.4 1.0 CD1 A:LEU92 4.1 77.3 1.0 CG A:GLU111 4.2 81.3 1.0 CG B:HIS271 4.2 53.8 1.0 ND1 B:HIS271 4.5 54.2 1.0 CE B:LYS272 4.7 54.5 1.0 CB A:GLU111 4.8 80.7 1.0 NZ B:LYS272 5.0 56.5 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Methanocaldococcus Jannaschii TRM5 in Complex with Adenosine


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 Methanocaldococcus Jannaschii TRM5 in Complex with Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn338 b:77.0 occ:1.00 OE2 A:GLU230 2.2 65.2 1.0 ND1 A:HIS227 2.3 65.0 1.0 O A:HOH346 2.6 26.3 1.0 NZ A:LYS175 2.8 63.2 1.0 CE1 A:HIS227 2.9 65.5 1.0 CE A:LYS175 2.9 62.8 1.0 CD A:GLU230 3.1 64.8 1.0 OE1 A:GLU230 3.4 65.4 1.0 CG A:HIS227 3.5 64.0 1.0 CB A:HIS227 4.1 61.0 1.0 NE2 A:HIS227 4.1 66.4 1.0 O A:HOH345 4.3 41.1 1.0 CG A:GLU230 4.4 62.4 1.0 CD2 A:HIS227 4.4 64.4 1.0 CD A:LYS175 4.4 60.5 1.0 CA A:HIS227 4.5 58.4 1.0 CB A:GLU230 4.6 60.0 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Methanocaldococcus Jannaschii TRM5 in Complex with Adenosine


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 Methanocaldococcus Jannaschii TRM5 in Complex with Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn339 b:80.4 occ:1.00 ND1 A:HIS11 2.0 67.0 1.0 O A:HOH341 2.5 25.6 1.0 O A:HOH343 2.9 26.7 1.0 CG A:HIS11 3.0 65.4 1.0 CE1 A:HIS11 3.0 67.8 1.0 CB A:HIS11 3.3 63.7 1.0 CA A:HIS11 3.5 63.6 1.0 CB A:GLN14 3.9 73.8 1.0 CG A:GLN14 4.0 76.0 1.0 NE2 A:HIS11 4.1 66.6 1.0 CD2 A:HIS11 4.1 65.5 1.0 N A:HIS11 4.3 63.1 1.0 O A:LYS10 4.3 63.3 1.0 CG2 A:ILE56 4.5 69.7 1.0 C A:HIS11 4.7 63.5 1.0 OE1 A:GLN14 4.7 80.2 1.0 C A:LYS10 4.7 62.8 1.0 CD A:GLN14 4.8 78.1 1.0 O A:HIS11 4.9 61.8 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Methanocaldococcus Jannaschii TRM5 in Complex with Adenosine


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 Methanocaldococcus Jannaschii TRM5 in Complex with Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn337 b:65.4 occ:1.00 OE1 B:GLU230 2.2 57.9 1.0 ND1 B:HIS227 2.6 66.8 1.0 CD B:GLU230 3.3 56.3 1.0 CE1 B:HIS227 3.5 68.2 1.0 CG B:HIS227 3.6 64.3 1.0 OE2 B:GLU230 3.8 58.0 1.0 CD B:LYS175 3.8 66.7 1.0 CB B:HIS227 3.9 58.4 1.0 NZ B:LYS175 4.0 65.0 1.0 CA B:HIS227 4.2 54.1 1.0 CE B:LYS175 4.5 67.2 1.0 CG B:GLU230 4.6 51.8 1.0 NE2 B:HIS227 4.6 68.5 1.0 CD2 B:HIS227 4.7 66.5 1.0 O B:HIS227 4.7 51.7 1.0 CB B:GLU230 4.8 46.2 1.0 CB B:LYS175 4.8 64.5 1.0 CG B:LYS175 4.9 64.1 1.0 C B:HIS227 5.0 51.9 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Methanocaldococcus Jannaschii TRM5 in Complex with Adenosine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Methanocaldococcus Jannaschii TRM5 in Complex with Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn338 b:78.1 occ:1.00 ND1 B:HIS243 2.4 58.0 1.0 O B:HOH340 2.7 34.1 1.0 CG B:HIS243 3.2 58.5 1.0 CB B:HIS243 3.3 56.6 1.0 CE1 B:HIS243 3.5 60.6 1.0 CA B:HIS243 3.5 56.5 1.0 O B:HIS243 3.8 52.8 1.0 C B:HIS243 4.2 54.9 1.0 CD2 B:HIS243 4.4 60.6 1.0 NE2 B:HIS243 4.5 61.9 1.0 N B:HIS243 4.8 57.6 1.0

G.Lahoud, S.Goto-Ito, K.Yoshida, T.Ito, S.Yokoyama, Y.M.Hou. Differentiating Analogous Trna Methyltransferases By Fragments of the Methyl Donor. Rna V. 17 1236 2011.
ISSN: ISSN 1355-8382
PubMed: 21602303
DOI: 10.1261/RNA.2706011