Zinc 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:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase Complexed with Guanine, PDB code: 1it7:
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 Guanine


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 Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn600 b:23.1 occ:1.00 ND1 A:HIS307 2.1 18.7 1.0 SG A:CYS284 2.3 27.1 1.0 SG A:CYS281 2.4 22.5 1.0 SG A:CYS279 2.5 23.5 1.0 CE1 A:HIS307 2.9 17.9 1.0 CG A:HIS307 3.3 18.8 1.0 CB A:CYS284 3.3 26.8 1.0 CB A:CYS279 3.3 22.0 1.0 CB A:CYS281 3.4 21.3 1.0 CB A:HIS307 3.7 18.9 1.0 N A:CYS284 4.0 27.9 1.0 OH A:TYR262 4.0 15.5 1.0 N A:CYS281 4.0 21.7 1.0 NE2 A:HIS307 4.1 22.1 1.0 CA A:HIS307 4.2 20.5 1.0 CA A:CYS281 4.2 22.2 1.0 CA A:CYS284 4.3 27.9 1.0 CD2 A:HIS307 4.3 19.1 1.0 O A:HIS307 4.6 21.2 1.0 CE1 A:TYR262 4.6 16.0 1.0 CZ A:TYR262 4.6 15.6 1.0 CA A:CYS279 4.6 26.2 1.0 CG2 A:VAL311 4.7 23.8 1.0 C A:HIS307 4.8 21.2 1.0 C A:CYS279 4.8 26.6 1.0 C A:CYS281 4.8 22.9 1.0 N A:SER280 4.8 26.4 1.0 CB A:VAL283 4.9 24.1 1.0 O A:CYS281 4.9 23.0 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn600 b:25.2 occ:1.00 ND1 B:HIS307 2.2 22.8 1.0 SG B:CYS284 2.3 27.6 1.0 SG B:CYS281 2.3 22.9 1.0 SG B:CYS279 2.4 25.6 1.0 CE1 B:HIS307 3.0 22.1 1.0 CG B:HIS307 3.2 21.8 1.0 CB B:CYS279 3.3 25.6 1.0 CB B:CYS284 3.3 30.0 1.0 CB B:CYS281 3.4 22.9 1.0 CB B:HIS307 3.7 19.4 1.0 OH B:TYR262 3.9 21.4 1.0 N B:CYS284 3.9 29.0 1.0 N B:CYS281 4.1 25.3 1.0 CA B:HIS307 4.2 19.8 1.0 NE2 B:HIS307 4.2 23.6 1.0 CA B:CYS284 4.2 30.4 1.0 CA B:CYS281 4.3 24.0 1.0 CD2 B:HIS307 4.3 23.0 1.0 CE1 B:TYR262 4.5 20.2 1.0 CZ B:TYR262 4.5 20.7 1.0 O B:HIS307 4.6 22.6 1.0 CA B:CYS279 4.6 26.5 1.0 C B:HIS307 4.7 20.5 1.0 C B:CYS279 4.8 25.7 1.0 CB B:VAL283 4.8 27.9 1.0 C B:CYS281 4.9 22.8 1.0 N B:SER280 5.0 25.3 1.0 CG2 B:VAL311 5.0 19.4 1.0 O B:CYS281 5.0 22.5 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