Zinc in PDB 1j2b: Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val)

All present enzymatic activity of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val):
2.4.2.29;

The structure of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val), PDB code: 1j2b was solved by R.Ishitani, O.Nureki, N.Nameki, N.Okada, S.Nishimura, 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)	48.54 / 3.30
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	230.834, 230.834, 269.255, 90.00, 90.00, 120.00
R / Rfree (%)	22.5 / 28.8

The structure of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val) also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val) (pdb code 1j2b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val), PDB code: 1j2b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val)


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 Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn600 b:76.7 occ:1.00 ND1 A:HIS307 2.1 73.2 1.0 SG A:CYS284 2.5 74.9 1.0 SG A:CYS281 2.7 54.9 1.0 CG A:HIS307 2.9 74.1 1.0 SG A:CYS279 2.9 75.3 1.0 CB A:HIS307 3.1 62.3 1.0 CE1 A:HIS307 3.1 81.8 1.0 OH A:TYR262 3.4 75.2 1.0 CB A:CYS279 3.6 73.8 1.0 CA A:HIS307 3.8 62.8 1.0 CB A:CYS284 3.9 76.7 1.0 CD2 A:HIS307 4.0 72.7 1.0 CB A:CYS281 4.1 72.0 1.0 CZ A:TYR262 4.1 71.5 1.0 NE2 A:HIS307 4.1 76.1 1.0 CE1 A:TYR262 4.1 70.7 1.0 O A:HIS307 4.3 73.0 1.0 C A:HIS307 4.3 69.3 1.0 N A:CYS284 4.4 86.8 1.0 CG2 A:VAL311 4.6 78.2 1.0 CB A:VAL283 4.8 74.8 1.0 CA A:CYS284 4.8 79.5 1.0 N A:CYS281 5.0 97.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val)


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 Archaeosine Trna-Guanine Transglycosylase Complexed with Lambda-Form Trna(Val) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn600 b:70.6 occ:1.00 ND1 B:HIS307 2.1 65.7 1.0 SG B:CYS284 2.3 0.5 1.0 SG B:CYS279 2.3 66.2 1.0 SG B:CYS281 2.5 90.9 1.0 CE1 B:HIS307 2.7 59.2 1.0 CB B:CYS279 3.0 74.1 1.0 CG B:HIS307 3.2 64.8 1.0 CB B:CYS284 3.4 1.0 1.0 CB B:CYS281 3.8 97.6 1.0 CB B:HIS307 3.9 60.9 1.0 NE2 B:HIS307 3.9 66.6 1.0 N B:CYS284 4.0 0.6 1.0 OH B:TYR262 4.1 68.1 1.0 CD2 B:HIS307 4.1 61.5 1.0 CA B:CYS284 4.3 0.6 1.0 CA B:HIS307 4.4 73.3 1.0 N B:CYS281 4.4 97.7 1.0 CE1 B:TYR262 4.5 50.9 1.0 CA B:CYS279 4.5 84.0 1.0 CZ B:TYR262 4.6 57.0 1.0 CA B:CYS281 4.7 92.8 1.0 C B:CYS279 4.9 85.8 1.0 O B:HIS307 4.9 58.5 1.0 N B:SER280 4.9 82.1 1.0 C B:HIS307 5.0 71.0 1.0

R.Ishitani, O.Nureki, N.Nameki, N.Okada, S.Nishimura, S.Yokoyama. Alternative Tertiary Structure of Trna For Recognition By A Posttranscriptional Modification Enzyme Cell(Cambridge,Mass.) V. 113 383 2003.
ISSN: ISSN 0092-8674
PubMed: 12732145
DOI: 10.1016/S0092-8674(03)00280-0