Magnesium in PDB 1it7: Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Guanine

All present enzymatic activity of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Guanine:
2.4.2.29;

The structure of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Guanine, PDB code: 1it7 was solved by R.Ishitani, O.Nureki, S.Fukai, T.Kijimoto, N.Nameki, M.Watanabe, H.Kondo, M.Sekine, N.Okada, S.Nishimura, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.201, 100.201, 364.658, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 27.1

The structure of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Guanine also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Guanine (pdb code 1it7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Guanine, PDB code: 1it7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Guanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:18.8 occ:1.00 O A:ILE567 2.5 23.3 1.0 O A:ALA528 2.5 28.2 1.0 O A:PHE569 2.6 24.8 1.0 O A:MET566 2.6 23.8 1.0 O A:VAL531 3.3 29.2 1.0 C A:ILE567 3.3 23.1 1.0 NE2 A:GLN570 3.4 31.2 1.0 C A:ALA528 3.4 29.8 1.0 C A:PHE569 3.8 25.0 1.0 C A:MET566 3.8 22.9 1.0 CA A:ILE567 3.8 23.4 1.0 CA A:LYS529 4.0 33.6 1.0 N A:LYS529 4.1 31.2 1.0 CD A:GLN570 4.2 30.7 1.0 C A:VAL531 4.3 28.2 1.0 N A:ILE567 4.3 22.8 1.0 C A:LYS529 4.3 33.0 1.0 N A:VAL531 4.3 27.8 1.0 N A:PHE569 4.3 25.8 1.0 CB A:VAL531 4.3 25.6 1.0 CA A:ALA528 4.3 29.2 1.0 C A:VAL568 4.3 26.4 1.0 N A:VAL568 4.3 23.4 1.0 O A:LYS529 4.5 33.2 1.0 CB A:ALA528 4.5 28.1 1.0 CA A:VAL531 4.5 26.6 1.0 O A:VAL568 4.5 28.4 1.0 CA A:PHE569 4.6 24.3 1.0 OE1 A:GLN570 4.6 34.1 1.0 N A:GLN570 4.7 25.5 1.0 N A:PHE530 4.8 32.5 1.0 CA A:VAL568 4.8 25.5 1.0 CA A:GLN570 4.9 26.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Guanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:21.4 occ:1.00 O B:ALA528 2.5 42.2 1.0 O B:ILE567 2.5 30.6 1.0 O B:MET566 2.6 31.7 1.0 O B:PHE569 2.7 38.3 1.0 O B:VAL531 3.2 29.5 1.0 C B:ILE567 3.3 31.0 1.0 C B:ALA528 3.3 41.9 1.0 NE2 B:GLN570 3.4 48.8 1.0 CA B:ILE567 3.6 31.2 1.0 C B:MET566 3.6 31.5 1.0 CA B:LYS529 3.8 41.0 1.0 C B:PHE569 3.9 37.5 1.0 N B:LYS529 3.9 41.8 1.0 N B:ILE567 4.1 30.6 1.0 C B:LYS529 4.1 39.2 1.0 CB B:VAL531 4.2 29.9 1.0 C B:VAL531 4.2 30.3 1.0 CA B:ALA528 4.2 41.9 1.0 N B:VAL531 4.2 32.1 1.0 O B:LYS529 4.2 39.8 1.0 N B:PHE569 4.2 33.9 1.0 N B:VAL568 4.3 30.9 1.0 CB B:ALA528 4.3 41.9 1.0 CD B:GLN570 4.4 46.0 1.0 CA B:VAL531 4.4 30.2 1.0 C B:VAL568 4.4 33.5 1.0 CA B:PHE569 4.6 35.6 1.0 OE1 B:GLN570 4.7 48.9 1.0 N B:PHE530 4.8 37.5 1.0 CA B:VAL568 4.8 32.8 1.0 CG1 B:VAL531 4.8 29.4 1.0 O B:VAL568 4.9 33.4 1.0 N B:GLN570 4.9 38.0 1.0 CA B:MET566 4.9 32.3 1.0

R.Ishitani, O.Nureki, S.Fukai, T.Kijimoto, N.Nameki, M.Watanabe, H.Kondo, M.Sekine, N.Okada, S.Nishimura, S.Yokoyama. Crystal Structure of Archaeosine Trna-Guanine Transglycosylase. J.Mol.Biol. V. 318 665 2002.
ISSN: ISSN 0022-2836
PubMed: 12054814
DOI: 10.1016/S0022-2836(02)00090-6