Atomistry » Magnesium » PDB 1it7-1jbz » 1it8
Atomistry »
  Magnesium »
    PDB 1it7-1jbz »
      1it8 »

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: Mon Dec 14 06:05:45 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy