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Magnesium in PDB 1it8: Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0

Enzymatic activity of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0

All present enzymatic activity of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0:
2.4.2.29;

Protein crystallography data

The structure of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0, PDB code: 1it8 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) 34.87 / 2.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.467, 100.467, 366.168, 90.00, 90.00, 90.00
R / Rfree (%) 23.2 / 27.8

Other elements in 1it8:

The structure of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0 (pdb code 1it8). 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 From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0, PDB code: 1it8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1it8

Go back to Magnesium Binding Sites List in 1it8
Magnesium binding site 1 out of 2 in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0


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 From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:15.6
occ:1.00
 O A:ILE567 2.5 21.5 1.0
O A:ALA528 2.6 30.3 1.0
O A:PHE569 2.7 30.4 1.0
O A:MET566 2.9 21.6 1.0
NE2 A:GLN570 3.1 36.5 1.0
O A:VAL531 3.2 25.9 1.0
C A:ILE567 3.2 21.6 1.0
C A:ALA528 3.6 29.8 1.0
CA A:ILE567 3.6 20.9 1.0
C A:PHE569 3.9 28.3 1.0
C A:MET566 3.9 20.6 1.0
CA A:LYS529 4.1 34.3 1.0
CD A:GLN570 4.2 34.0 1.0
C A:VAL531 4.2 27.2 1.0
N A:LYS529 4.2 31.9 1.0
N A:ILE567 4.3 20.3 1.0
N A:VAL568 4.3 22.7 1.0
N A:VAL531 4.3 27.8 1.0
CB A:VAL531 4.3 27.2 1.0
N A:PHE569 4.3 27.1 1.0
C A:VAL568 4.3 25.4 1.0
C A:LYS529 4.4 33.5 1.0
O A:LYS529 4.5 34.6 1.0
CA A:ALA528 4.5 29.6 1.0
CA A:VAL531 4.5 27.4 1.0
O A:VAL568 4.6 25.5 1.0
OE1 A:GLN570 4.6 35.9 1.0
CB A:ALA528 4.6 29.8 1.0
CA A:PHE569 4.6 28.1 1.0
CA A:VAL568 4.8 23.9 1.0
N A:GLN570 4.9 28.2 1.0
CB A:ILE567 4.9 20.4 1.0

Magnesium binding site 2 out of 2 in 1it8

Go back to Magnesium Binding Sites List in 1it8
Magnesium binding site 2 out of 2 in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0


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 From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:22.2
occ:1.00
 O B:ILE567 2.3 25.6 1.0
O B:ALA528 2.5 42.3 1.0
O B:PHE569 2.9 33.7 1.0
O B:VAL531 3.1 31.6 1.0
O B:MET566 3.1 28.7 1.0
NE2 B:GLN570 3.2 39.8 1.0
C B:ILE567 3.3 26.5 1.0
C B:ALA528 3.5 42.6 1.0
CA B:LYS529 3.8 41.6 1.0
CA B:ILE567 3.9 27.1 1.0
C B:PHE569 4.0 32.9 1.0
N B:LYS529 4.1 41.5 1.0
C B:LYS529 4.1 41.1 1.0
C B:VAL531 4.1 32.2 1.0
C B:MET566 4.2 29.2 1.0
O B:LYS529 4.2 42.5 1.0
N B:PHE569 4.3 30.9 1.0
C B:VAL568 4.3 29.4 1.0
N B:VAL531 4.3 34.5 1.0
N B:VAL568 4.3 26.1 1.0
CD B:GLN570 4.4 38.6 1.0
CB B:VAL531 4.4 31.4 1.0
N B:ILE567 4.5 28.0 1.0
CA B:VAL531 4.5 32.6 1.0
CA B:ALA528 4.6 43.2 1.0
O B:VAL568 4.6 29.2 1.0
CA B:VAL568 4.7 28.3 1.0
CA B:PHE569 4.7 32.5 1.0
N B:PHE530 4.8 39.8 1.0
CB B:ALA528 4.9 43.5 1.0
N B:GLN570 4.9 34.3 1.0
OE1 B:GLN570 4.9 39.3 1.0

Reference:

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
Page generated: Tue Aug 13 05:39:10 2024

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