Magnesium in PDB 5dk8: Human Ubiquitin in the P1 Space Group

The structure of Human Ubiquitin in the P1 Space Group, PDB code: 5dk8 was solved by A.Camara-Artigas, J.Bacarizo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.82 / 1.32
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	29.961, 30.182, 41.414, 88.52, 79.12, 67.37
R / Rfree (%)	17.8 / 20.1

The binding sites of Magnesium atom in the Human Ubiquitin in the P1 Space Group (pdb code 5dk8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Human Ubiquitin in the P1 Space Group, PDB code: 5dk8:

Magnesium binding site 1 out of 1 in the Human Ubiquitin in the P1 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Ubiquitin in the P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:15.0 occ:1.00 O A:HOH206 2.0 16.6 1.0 O A:HOH214 2.1 14.3 1.0 O A:HOH209 2.1 31.8 1.0 O A:HOH204 2.1 16.7 1.0 HZ2 A:LYS29 3.2 28.3 1.0 HZ3 A:LYS29 3.8 28.3 1.0 NZ A:LYS29 3.9 23.6 1.0 OD1 A:ASP21 4.0 15.1 1.0 OE2 A:GLU18 4.1 18.5 1.0 O A:HOH252 4.2 19.8 1.0 OD2 A:ASP21 4.2 12.8 1.0 HZ1 A:LYS29 4.3 28.3 1.0 OD1 A:ASN25 4.4 17.9 1.0 CD A:GLU18 4.5 17.1 1.0 CG A:ASP21 4.5 12.2 1.0 HD21 A:ASN25 4.6 20.1 1.0 OE1 A:GLU18 4.6 18.7 1.0 HE3 A:LYS29 4.8 28.5 1.0 CE A:LYS29 5.0 23.8 1.0 O A:HOH211 5.0 15.6 1.0

A.Camara-Artigas, M.Plaza-Garrido, S.Martinez-Rodriguez, J.Bacarizo. New Crystal Form of Human Ubiquitin in the Presence of Magnesium. Acta Crystallogr.,Sect.F V. 72 29 2016.
ISSN: ESSN 2053-230X
PubMed: 26750481
DOI: 10.1107/S2053230X15023390