Magnesium in PDB 4qyt: Schizosaccharomyces Pombe Dj-1

The structure of Schizosaccharomyces Pombe Dj-1, PDB code: 4qyt was solved by M.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.69 / 1.05
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.507, 51.913, 82.705, 89.07, 88.98, 66.83
R / Rfree (%)	11 / 13.2

The binding sites of Magnesium atom in the Schizosaccharomyces Pombe Dj-1 (pdb code 4qyt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Schizosaccharomyces Pombe Dj-1, PDB code: 4qyt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Schizosaccharomyces Pombe Dj-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Schizosaccharomyces Pombe Dj-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:36.6 occ:1.00 O B:HOH491 1.7 53.4 1.0 O B:HOH428 1.7 40.0 1.0 O B:HOH489 1.8 39.8 1.0 O B:HOH490 2.1 40.5 1.0 O B:HOH478 4.0 51.8 1.0 OD1 B:ASP41 4.0 25.2 1.0 OD2 B:ASP41 4.1 28.1 1.0 O C:HOH367 4.5 19.4 1.0 CG B:ASP41 4.5 23.6 1.0 O C:HOH469 4.7 34.0 1.0

Magnesium binding site 2 out of 5 in the Schizosaccharomyces Pombe Dj-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Schizosaccharomyces Pombe Dj-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg204 b:18.1 occ:0.50 O C:HOH479 2.0 21.3 0.5 O C:HOH446 2.0 22.9 0.5 O C:HOH445 2.1 24.3 0.5 O C:HOH470 2.1 21.8 0.5 O D:HOH344 2.1 25.9 1.0 O D:HOH350 2.3 24.9 1.0 O D:HOH429 3.7 27.7 1.0 O C:HOH335 4.0 13.8 1.0 O D:MET190 4.1 13.7 1.0 OD1 C:ASP146 4.2 19.3 1.0 OE1 C:GLN159 4.5 15.3 1.0 O D:HOH357 4.8 25.9 1.0 OD2 C:ASP146 4.9 28.4 1.0 CG C:ASP146 4.9 19.9 1.0

Magnesium binding site 3 out of 5 in the Schizosaccharomyces Pombe Dj-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Schizosaccharomyces Pombe Dj-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg205 b:16.5 occ:0.50 O C:HOH504 1.5 65.3 0.5 O C:HOH505 2.0 26.5 0.5 O C:HOH503 2.0 17.2 0.5 O C:HOH301 2.0 19.3 0.5 O A:HOH457 2.0 18.8 0.5 OE1 C:GLU153 4.0 17.6 1.0 OE2 C:GLU153 4.1 22.2 1.0 O A:HOH423 4.2 26.7 1.0 O A:HOH446 4.3 24.8 1.0 O C:HOH514 4.3 31.5 1.0 O A:HOH324 4.3 15.9 1.0 CE C:LYS101 4.4 27.4 0.5 CD C:GLU153 4.5 15.2 1.0 O A:HOH458 4.6 37.2 0.5 NZ C:LYS101 4.7 28.4 0.5

Magnesium binding site 4 out of 5 in the Schizosaccharomyces Pombe Dj-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Schizosaccharomyces Pombe Dj-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg206 b:29.4 occ:1.00 O C:HOH517 1.8 22.1 1.0 O C:HOH487 2.1 32.4 1.0 O B:HOH475 2.2 40.4 1.0 O C:HOH430 2.4 29.0 1.0 O C:HOH392 3.4 32.9 1.0 CE B:LYS45 3.8 18.8 1.0 O B:HOH462 4.1 45.6 1.0 NZ B:LYS45 4.3 20.1 1.0 O C:HOH521 4.3 37.0 1.0 OE1 C:GLU98 4.4 18.9 1.0 OD1 B:ASP49 4.4 14.2 1.0 OD1 C:ASP65 4.4 18.1 1.0 OD2 C:ASP65 4.5 18.8 1.0 O C:HOH356 4.6 23.5 1.0 CG C:ASP65 4.9 16.5 1.0

Magnesium binding site 5 out of 5 in the Schizosaccharomyces Pombe Dj-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Schizosaccharomyces Pombe Dj-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg203 b:20.9 occ:1.00 O D:HOH450 2.0 24.1 1.0 O D:GLY141 2.1 22.1 1.0 O D:HOH449 2.1 25.3 1.0 C D:GLY141 3.2 20.1 1.0 CA D:GLY141 3.8 24.4 1.0 O D:HOH379 4.3 28.5 1.0 N D:TYR142 4.3 16.8 1.0 O D:HOH481 4.3 37.7 1.0 O D:HOH355 4.4 22.3 1.0 O D:LYS125 4.5 16.9 0.5 O D:LYS125 4.5 13.6 0.5 CA D:TYR142 4.5 16.4 1.0 N D:LYS143 4.6 15.5 0.5 C D:TYR142 4.7 14.8 1.0 N D:LYS143 4.7 14.9 0.5 CD D:LYS125 4.8 19.0 0.5

P.Madzelan, T.Labunska, M.A.Wilson. Influence of Peptide Dipoles and Hydrogen Bonds on Reactive Cysteine Pk(A) Values in Fission Yeast Dj-1. Febs J. V. 279 4111 2012.
ISSN: ISSN 1742-464X
PubMed: 22971103
DOI: 10.1111/FEBS.12004