Magnesium in PDB 5e5a: Crystal Structure of the Chromatin-Tethering Domain of Human Cytomegalovirus IE1 Protein Bound to the Nucleosome Core Particle

The structure of Crystal Structure of the Chromatin-Tethering Domain of Human Cytomegalovirus IE1 Protein Bound to the Nucleosome Core Particle, PDB code: 5e5a was solved by Q.Fang, P.Chen, M.Wang, J.Fang, N.Yang, G.Li, R.M.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.700, 109.474, 181.976, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24.3

The binding sites of Magnesium atom in the Crystal Structure of the Chromatin-Tethering Domain of Human Cytomegalovirus IE1 Protein Bound to the Nucleosome Core Particle (pdb code 5e5a). 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 the Chromatin-Tethering Domain of Human Cytomegalovirus IE1 Protein Bound to the Nucleosome Core Particle, PDB code: 5e5a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Chromatin-Tethering Domain of Human Cytomegalovirus IE1 Protein Bound to the Nucleosome Core Particle


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 the Chromatin-Tethering Domain of Human Cytomegalovirus IE1 Protein Bound to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg201 b:52.8 occ:1.00 O I:HOH306 2.0 53.9 1.0 O J:HOH313 2.2 50.3 1.0 O J:HOH314 2.3 49.5 1.0 C5' I:DC88 4.0 55.3 1.0 C4' I:DC88 4.2 53.2 1.0 O4' I:DC88 4.2 54.7 1.0 O4' J:DT208 4.3 44.4 1.0 O4' I:DG87 4.5 56.3 1.0 C4' I:DG87 4.7 55.6 1.0 C4' J:DT208 4.7 41.5 1.0 O2 I:DT86 4.8 58.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Chromatin-Tethering Domain of Human Cytomegalovirus IE1 Protein Bound to the Nucleosome Core Particle


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 the Chromatin-Tethering Domain of Human Cytomegalovirus IE1 Protein Bound to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:35.0 occ:1.00 OD1 C:ASP90 2.1 36.9 1.0 CG C:ASP90 2.9 32.8 1.0 OD2 C:ASP90 3.2 32.5 1.0 CB C:GLU92 4.2 30.7 1.0 CB C:ASP90 4.2 26.8 1.0 N C:GLU92 4.3 31.0 1.0 OE1 C:GLU92 4.3 41.6 1.0 CG C:GLU92 4.4 33.8 1.0 N C:GLU91 4.5 34.2 1.0 CD C:GLU92 4.6 39.4 1.0 CA C:ASP90 4.6 25.6 1.0 C C:ASP90 4.7 28.9 1.0 CA C:GLU92 4.9 29.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Chromatin-Tethering Domain of Human Cytomegalovirus IE1 Protein Bound to the Nucleosome Core Particle


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 the Chromatin-Tethering Domain of Human Cytomegalovirus IE1 Protein Bound to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:52.0 occ:1.00 OE1 D:GLU102 2.4 52.4 1.0 O D:HOH301 2.6 57.8 1.0 NZ D:LYS105 2.7 49.0 1.0 NE2 D:HIS106 2.9 45.6 1.0 CE D:LYS105 3.2 49.9 1.0 CD D:GLU102 3.3 51.7 1.0 CE1 D:HIS106 3.4 45.8 1.0 OE2 D:GLU102 3.6 47.9 1.0 CD2 D:HIS106 4.1 40.5 1.0 ND1 D:HIS106 4.6 42.8 1.0 CD D:LYS105 4.7 51.0 1.0 CG D:GLU102 4.7 54.0 1.0 CG D:HIS106 5.0 37.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Chromatin-Tethering Domain of Human Cytomegalovirus IE1 Protein Bound to the Nucleosome Core Particle


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 the Chromatin-Tethering Domain of Human Cytomegalovirus IE1 Protein Bound to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:23.3 occ:1.00 O E:HOH307 1.9 26.3 1.0 OD1 E:ASP77 2.0 27.0 1.0 O E:HOH310 2.1 24.0 1.0 CG E:ASP77 3.0 26.5 1.0 OD2 E:ASP77 3.4 24.1 1.0 O E:HOH309 4.0 25.3 1.0 CB E:ASP77 4.3 28.3 1.0 O E:GLU73 4.3 26.7 1.0 OE1 E:GLN76 4.4 32.2 1.0 N E:ASP77 4.5 27.5 1.0 CA E:ASP77 4.5 28.2 1.0 O F:LEU22 4.6 29.6 1.0 CG E:GLN76 4.7 27.9 1.0 CB E:GLN76 4.7 27.6 1.0 CG E:GLU73 4.8 22.9 1.0 C E:GLN76 5.0 29.4 1.0 CD E:GLN76 5.0 33.9 1.0

Q.Fang, P.Chen, M.Wang, J.Fang, N.Yang, G.Li, R.M.Xu. Human Cytomegalovirus IE1 Protein Alters the Higher-Order Chromatin Structure By Targeting the Acidic Patch of the Nucleosome Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 26812545
DOI: 10.7554/ELIFE.11911