Magnesium in PDB 5hx1: Crystal Structure of DR2231_E46A Mutant in Complex with Dump and Magnesium

The structure of Crystal Structure of DR2231_E46A Mutant in Complex with Dump and Magnesium, PDB code: 5hx1 was solved by C.S.Mota, A.M.D.Goncalves, D.De Sanctis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.39 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	148.827, 77.813, 52.266, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 21.3

The binding sites of Magnesium atom in the Crystal Structure of DR2231_E46A Mutant in Complex with Dump and Magnesium (pdb code 5hx1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of DR2231_E46A Mutant in Complex with Dump and Magnesium, PDB code: 5hx1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of DR2231_E46A Mutant in Complex with Dump and Magnesium


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 DR2231_E46A Mutant in Complex with Dump and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:25.6 occ:1.00 OE1 A:GLU50 2.1 33.3 1.0 OE1 A:GLU79 2.3 28.2 1.0 OD2 A:ASP82 2.4 18.6 1.0 OE1 A:GLU47 2.5 30.7 1.0 CD A:GLU50 3.3 33.0 1.0 CG A:ASP82 3.4 21.2 1.0 CD A:GLU79 3.4 31.5 1.0 O A:HOH375 3.5 34.8 1.0 CD A:GLU47 3.6 32.8 1.0 CB A:ASP82 3.6 13.0 1.0 OE2 A:GLU79 3.8 37.7 1.0 OE2 A:GLU50 3.9 36.1 1.0 OE2 A:GLU47 3.9 36.5 1.0 CG A:GLU50 4.4 26.4 1.0 CB A:GLU50 4.5 15.8 1.0 OD1 A:ASP82 4.5 18.3 1.0 CA A:GLU79 4.7 8.8 1.0 CG A:GLU79 4.7 14.7 1.0 CG A:GLU47 4.9 19.9 1.0 CB A:GLU79 4.9 11.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of DR2231_E46A Mutant in Complex with Dump and Magnesium


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 DR2231_E46A Mutant in Complex with Dump and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:19.0 occ:1.00 O B:HOH368 1.9 29.4 1.0 OE1 B:GLU50 2.1 34.0 1.0 OE1 B:GLU79 2.2 22.4 1.0 O B:HOH366 2.2 44.8 1.0 OD2 B:ASP82 2.3 18.2 1.0 OE1 B:GLU47 2.3 20.6 1.0 CD B:GLU79 3.2 24.5 1.0 CD B:GLU47 3.3 22.3 1.0 CG B:ASP82 3.4 20.5 1.0 CD B:GLU50 3.4 32.6 1.0 OE2 B:GLU79 3.5 25.3 1.0 OE2 B:GLU47 3.6 27.6 1.0 CB B:ASP82 3.7 12.0 1.0 OE2 B:GLU50 4.2 37.0 1.0 CB B:GLU50 4.3 14.9 1.0 CG B:GLU50 4.4 16.4 1.0 OD1 B:ASP82 4.5 19.2 1.0 CG B:GLU79 4.6 12.6 1.0 O B:HOH478 4.6 49.9 1.0 O B:HOH449 4.7 41.3 1.0 O B:HOH485 4.7 45.4 1.0 CG B:GLU47 4.7 13.8 1.0 CA B:GLU79 4.8 14.1 1.0 CB B:GLU79 4.9 10.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of DR2231_E46A Mutant in Complex with Dump and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of DR2231_E46A Mutant in Complex with Dump and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:23.9 occ:0.53 O C:HOH314 1.8 39.1 1.0 OE1 C:GLU50 2.2 33.3 0.5 OE1 C:GLU47 2.2 17.2 1.0 OE1 C:GLU79 2.3 18.1 1.0 OD2 C:ASP82 2.4 13.7 1.0 O A:HOH325 2.8 22.8 1.0 CD C:GLU47 3.1 19.2 1.0 O A:HOH414 3.2 36.2 1.0 CD C:GLU50 3.2 27.9 0.5 CD C:GLU79 3.3 19.7 1.0 OE2 C:GLU47 3.3 16.1 1.0 CG C:ASP82 3.4 15.1 1.0 OE2 C:GLU79 3.6 22.9 1.0 OE2 C:GLU50 3.7 33.7 0.5 CB C:ASP82 3.8 9.7 1.0 CG C:GLU50 4.1 24.2 0.5 O A:HOH345 4.2 35.8 1.0 CB C:GLU50 4.3 18.6 0.5 CG C:GLU50 4.3 24.5 0.5 CB C:GLU50 4.4 18.5 0.5 OD1 C:ASP82 4.5 12.1 1.0 O C:HOH369 4.6 43.9 1.0 CG C:GLU47 4.6 11.5 1.0 CG C:GLU79 4.6 13.2 1.0 C5' A:UMP201 4.8 13.0 1.0 CA C:GLU79 4.9 9.4 1.0 OP1 A:UMP201 5.0 16.4 1.0 CB C:GLU79 5.0 9.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of DR2231_E46A Mutant in Complex with Dump and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of DR2231_E46A Mutant in Complex with Dump and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:22.1 occ:0.54 O D:HOH302 1.8 36.7 1.0 OE2 D:GLU50 2.1 29.9 0.4 OE1 D:GLU79 2.2 11.8 1.0 OE1 D:GLU47 2.2 17.1 1.0 OD2 D:ASP82 2.2 12.9 1.0 CD D:GLU47 3.2 22.9 1.0 CD D:GLU79 3.2 19.9 1.0 O B:HOH307 3.2 31.3 1.0 CG D:ASP82 3.3 10.6 1.0 CD D:GLU50 3.3 27.1 0.4 O D:HOH367 3.4 22.3 1.0 OE2 D:GLU47 3.5 19.6 1.0 OE2 D:GLU79 3.6 22.1 1.0 CB D:ASP82 3.6 7.6 1.0 OE1 D:GLU50 3.9 34.0 0.4 CB D:GLU50 4.3 13.7 0.6 CB D:GLU50 4.3 14.2 0.4 OD1 D:ASP82 4.4 13.0 1.0 CG D:GLU50 4.4 21.2 0.4 CG D:GLU50 4.4 21.5 0.6 O B:HOH326 4.4 39.2 1.0 CG D:GLU47 4.6 14.0 1.0 CG D:GLU79 4.6 15.2 1.0 CA D:GLU79 4.7 8.7 1.0 C5' B:UMP201 4.7 9.0 1.0 CB D:GLU79 4.9 12.6 1.0 CA D:GLU47 5.0 14.3 1.0

C.S.Mota, A.M.Goncalves, D.De Sanctis. Deinococcus Radiodurans DR2231 Is A Two-Metal-Ion Mechanism Hydrolase with Exclusive Activity on Dutp. Febs J. V. 283 4274 2016.
ISSN: ISSN 1742-4658
PubMed: 27739259
DOI: 10.1111/FEBS.13923