Magnesium in PDB 5hva: Crystal Structure of DR2231 in Complex with Dumpnpp and Magnesium.

The structure of Crystal Structure of DR2231 in Complex with Dumpnpp and Magnesium., PDB code: 5hva 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)	43.56 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	148.827, 77.841, 52.560, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 23.3

The binding sites of Magnesium atom in the Crystal Structure of DR2231 in Complex with Dumpnpp and Magnesium. (pdb code 5hva). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of DR2231 in Complex with Dumpnpp and Magnesium., PDB code: 5hva:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of DR2231 in Complex with Dumpnpp 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 in Complex with Dumpnpp and Magnesium. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:41.7 occ:1.00 O A:HOH318 1.9 46.2 1.0 OE1 A:GLU79 2.1 39.2 1.0 OE1 A:GLU50 2.1 47.5 1.0 OD2 A:ASP82 2.2 29.9 1.0 OE2 A:GLU47 2.3 33.6 1.0 CD A:GLU79 3.1 36.8 1.0 CG A:ASP82 3.2 35.7 1.0 CD A:GLU47 3.3 32.6 1.0 CD A:GLU50 3.3 52.5 1.0 OE2 A:GLU79 3.5 44.2 1.0 OE1 A:GLU47 3.5 30.0 1.0 CB A:ASP82 3.6 32.1 1.0 OE2 A:GLU50 4.0 62.3 1.0 CB A:GLU50 4.3 34.8 1.0 OD1 A:ASP82 4.4 34.3 1.0 CG A:GLU50 4.4 42.4 1.0 CG A:GLU79 4.5 26.3 1.0 CA A:GLU79 4.6 24.8 1.0 CG A:GLU47 4.7 30.0 1.0 CB A:GLU79 4.8 23.7 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of DR2231 in Complex with Dumpnpp 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 in Complex with Dumpnpp and Magnesium. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:50.8 occ:1.00 OE1 B:GLU79 2.2 54.7 1.0 OD2 B:ASP82 2.2 37.7 1.0 OE1 B:GLU50 2.3 53.8 1.0 OE2 B:GLU47 2.4 34.8 1.0 CD B:GLU79 3.0 50.0 1.0 CG B:ASP82 3.1 34.1 1.0 OE2 B:GLU79 3.1 55.1 1.0 CB B:ASP82 3.3 29.8 1.0 CD B:GLU47 3.5 34.6 1.0 CD B:GLU50 3.5 55.2 1.0 OE1 B:GLU47 3.8 39.1 1.0 OE2 B:GLU50 4.1 70.0 1.0 OD1 B:ASP82 4.3 30.1 1.0 CG B:GLU79 4.4 38.1 1.0 CA B:GLU79 4.4 22.7 1.0 CB B:GLU50 4.5 34.5 1.0 CG B:GLU50 4.6 43.1 1.0 CB B:GLU79 4.7 27.0 1.0 CG B:GLU47 4.8 28.5 1.0 CA B:ASP82 4.8 26.7 1.0 O B:GLU79 4.9 24.7 1.0 CB B:GLU47 4.9 26.0 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of DR2231 in Complex with Dumpnpp 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 in Complex with Dumpnpp and Magnesium. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:22.9 occ:1.00 OE1 C:GLU47 2.1 24.8 1.0 OE2 C:GLU50 2.1 43.9 1.0 OE1 C:GLU79 2.1 23.4 1.0 O C:HOH310 2.2 45.5 1.0 OD2 C:ASP82 2.2 20.4 1.0 O2B C:DUP201 2.3 12.7 0.6 CD C:GLU47 3.1 27.9 1.0 CD C:GLU79 3.1 25.5 1.0 CD C:GLU50 3.1 43.3 1.0 CG C:ASP82 3.2 17.3 1.0 OE2 C:GLU47 3.4 26.0 1.0 PB C:DUP201 3.4 24.7 0.6 OE2 C:GLU79 3.4 31.1 1.0 O1B C:DUP201 3.5 30.6 0.6 CB C:ASP82 3.5 13.7 1.0 OE1 C:GLU50 3.7 49.0 1.0 O2B C:DUP201 3.7 26.4 0.4 MG C:MG203 3.7 30.6 1.0 CB C:GLU50 4.2 22.3 1.0 CG C:GLU50 4.3 27.7 1.0 O3B C:DUP201 4.3 25.2 0.6 OD1 C:ASP82 4.3 20.8 1.0 CG C:GLU47 4.4 19.1 1.0 O C:HOH372 4.4 39.0 1.0 CG C:GLU79 4.5 22.0 1.0 O3G C:DUP201 4.6 25.7 0.6 CA C:GLU79 4.7 20.8 1.0 O2G C:DUP201 4.7 35.7 0.6 O2G C:DUP201 4.7 34.4 0.4 C5' C:DUP201 4.7 23.5 0.6 N3A C:DUP201 4.8 22.6 0.4 CB C:GLU79 4.8 27.1 1.0 N3A C:DUP201 4.8 21.5 0.6 PG C:DUP201 4.8 33.1 0.6 PB C:DUP201 4.9 24.6 0.4 C5' C:DUP201 4.9 23.0 0.4 CB C:GLU47 4.9 18.1 1.0 O C:HOH317 4.9 25.2 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of DR2231 in Complex with Dumpnpp 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 in Complex with Dumpnpp and Magnesium. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg203 b:30.6 occ:1.00 O3G C:DUP201 1.9 25.7 0.6 O1A C:DUP201 2.1 18.4 0.6 O C:HOH328 2.1 32.2 1.0 OE1 C:GLU50 2.2 49.0 1.0 O2B C:DUP201 2.2 12.7 0.6 OE2 C:GLU47 2.3 26.0 1.0 O1A C:DUP201 2.7 18.6 0.4 CD C:GLU50 3.1 43.3 1.0 PG C:DUP201 3.2 33.1 0.6 PB C:DUP201 3.2 24.7 0.6 OE2 C:GLU50 3.3 43.9 1.0 CD C:GLU47 3.3 27.9 1.0 PA C:DUP201 3.3 22.1 0.6 N3A C:DUP201 3.5 22.6 0.4 PA C:DUP201 3.6 21.4 0.4 OE1 C:GLU47 3.6 24.8 1.0 N3A C:DUP201 3.7 21.5 0.6 O3B C:DUP201 3.7 25.2 0.6 MG C:MG202 3.7 22.9 1.0 O2G C:DUP201 3.8 35.7 0.6 O C:HOH354 3.9 23.4 1.0 C5' C:DUP201 4.0 23.0 0.4 C5' C:DUP201 4.1 23.5 0.6 O C:HOH392 4.2 31.3 1.0 NZ A:LYS122 4.2 27.4 1.0 O5' C:DUP201 4.3 23.0 0.6 O1G C:DUP201 4.4 27.5 0.6 O5' C:DUP201 4.4 23.1 0.4 OE1 C:GLU46 4.4 29.9 1.0 O2A C:DUP201 4.5 19.3 0.6 CG C:GLU50 4.5 27.7 1.0 O1B C:DUP201 4.6 30.6 0.6 O C:HOH310 4.6 45.5 1.0 CG C:GLU47 4.6 19.1 1.0 CB C:GLU46 4.7 20.2 1.0 O2B C:DUP201 4.7 26.4 0.4 PB C:DUP201 4.8 24.6 0.4 O2A C:DUP201 4.9 19.1 0.4 O3G C:DUP201 5.0 35.0 0.4

Magnesium binding site 5 out of 6 in the Crystal Structure of DR2231 in Complex with Dumpnpp and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of DR2231 in Complex with Dumpnpp and Magnesium. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:30.1 occ:1.00 OE2 D:GLU50 2.0 36.2 1.0 OE1 D:GLU79 2.2 29.4 1.0 OE2 D:GLU47 2.2 29.3 1.0 OD2 D:ASP82 2.2 20.9 1.0 O D:HOH305 2.3 34.4 1.0 O1B D:DUP201 2.3 13.6 0.6 CD D:GLU50 3.1 36.7 1.0 O2B D:DUP201 3.1 31.7 0.6 CD D:GLU79 3.1 27.0 1.0 CD D:GLU47 3.2 30.5 1.0 CG D:ASP82 3.2 26.2 1.0 PB D:DUP201 3.3 26.9 0.6 OE2 D:GLU79 3.4 30.1 1.0 OE1 D:GLU47 3.5 30.8 1.0 MG D:MG203 3.6 32.2 1.0 CB D:ASP82 3.6 16.8 1.0 OE1 D:GLU50 3.7 43.9 1.0 O1B D:DUP201 3.8 29.1 0.4 O D:HOH353 4.1 42.6 1.0 O3B D:DUP201 4.2 25.6 0.6 CG D:GLU50 4.3 31.9 1.0 CB D:GLU50 4.3 20.9 1.0 C5' D:DUP201 4.4 26.0 0.6 OD1 D:ASP82 4.4 25.1 1.0 CG D:GLU47 4.5 25.6 1.0 O2G D:DUP201 4.5 25.4 0.6 CG D:GLU79 4.5 21.7 1.0 O2G D:DUP201 4.6 24.1 0.4 N3A D:DUP201 4.6 23.6 0.4 O D:HOH301 4.7 22.9 1.0 N3A D:DUP201 4.7 24.1 0.6 CA D:GLU79 4.8 23.8 1.0 PG D:DUP201 4.8 30.1 0.6 O1G D:DUP201 4.8 38.2 0.6 PB D:DUP201 4.9 24.8 0.4 O2A D:DUP201 4.9 24.1 0.6 CB D:GLU79 4.9 21.4 1.0 CD2 D:HIS78 5.0 35.8 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of DR2231 in Complex with Dumpnpp and Magnesium.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of DR2231 in Complex with Dumpnpp and Magnesium. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg203 b:32.2 occ:1.00 O1B D:DUP201 2.0 13.6 0.6 O2A D:DUP201 2.2 24.1 0.6 OE1 D:GLU50 2.2 43.9 1.0 O2G D:DUP201 2.2 25.4 0.6 OE2 D:GLU46 2.4 13.3 0.4 OE1 D:GLU47 2.4 30.8 1.0 O2A D:DUP201 2.8 22.7 0.4 CD D:GLU46 3.1 17.5 0.4 CD D:GLU50 3.1 36.7 1.0 OE2 D:GLU50 3.3 36.2 1.0 PB D:DUP201 3.3 26.9 0.6 CD D:GLU47 3.3 30.5 1.0 CG D:GLU46 3.4 19.0 0.4 PA D:DUP201 3.4 23.2 0.6 OE2 D:GLU47 3.5 29.3 1.0 PG D:DUP201 3.6 30.1 0.6 MG D:MG202 3.6 30.1 1.0 N3A D:DUP201 3.6 23.6 0.4 PA D:DUP201 3.8 24.2 0.4 N3A D:DUP201 3.8 24.1 0.6 O D:HOH345 3.9 23.3 1.0 O3B D:DUP201 3.9 25.6 0.6 C5' D:DUP201 4.0 26.0 0.6 OE1 D:GLU46 4.0 22.2 0.4 O D:HOH324 4.1 31.0 1.0 O5' D:DUP201 4.2 23.2 0.6 C5' D:DUP201 4.2 23.4 0.4 O1G D:DUP201 4.2 38.2 0.6 NZ B:LYS122 4.2 21.3 1.0 O2B D:DUP201 4.4 31.7 0.6 CG D:GLU50 4.5 31.9 1.0 O D:HOH305 4.6 34.4 1.0 O5' D:DUP201 4.6 24.1 0.4 O1A D:DUP201 4.6 23.2 0.6 OE1 D:GLU46 4.6 21.4 0.6 O3G D:DUP201 4.7 32.2 0.6 CG D:GLU47 4.7 25.6 1.0 CB D:GLU46 4.8 23.3 0.4 CB D:GLU46 4.8 23.6 0.6 O1B D:DUP201 4.9 29.1 0.4 PB D:DUP201 5.0 24.8 0.4 O1A D:DUP201 5.0 21.2 0.4

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