Manganese in PDB 5b0z: The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution

The structure of The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution, PDB code: 5b0z was solved by Y.Suzuki, N.Horikoshi, D.Kato, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.94 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.685, 108.204, 168.286, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 25.4

The structure of The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Manganese atom in the The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution (pdb code 5b0z). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution, PDB code: 5b0z:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn301 b:24.0 occ:1.00 OD1 E:ASP77 2.2 27.4 1.0 O E:HOH423 2.2 25.7 1.0 CG E:ASP77 3.1 28.4 1.0 OD2 E:ASP77 3.4 25.1 1.0 OE1 E:GLN76 4.2 35.3 1.0 O F:LEU22 4.3 31.6 1.0 O E:GLU73 4.4 23.0 1.0 CB E:ASP77 4.5 24.6 1.0 N E:ASP77 4.7 25.0 1.0 O E:HOH417 4.7 33.8 1.0 CA E:ASP77 4.7 25.1 1.0 CG E:GLU73 4.9 24.7 1.0 O E:HOH440 5.0 30.4 1.0

Manganese binding site 2 out of 3 in the The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn301 b:48.7 occ:1.00 O I:HOH404 2.3 36.4 1.0 O I:HOH425 2.3 46.0 1.0 N7 I:DG121 2.3 42.0 1.0 C8 I:DG121 3.2 38.0 1.0 C5 I:DG121 3.4 37.9 1.0 O6 I:DG121 3.7 36.8 1.0 C6 I:DG121 3.9 38.8 1.0 C2' I:DT120 4.2 47.3 1.0 OP2 I:DG121 4.3 39.6 1.0 O6 I:DG122 4.4 38.3 1.0 N9 I:DG121 4.5 37.4 1.0 C4 I:DG121 4.6 36.2 1.0

Manganese binding site 3 out of 3 in the The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn301 b:48.6 occ:1.00 O J:HOH425 1.9 26.5 1.0 N7 J:DG185 2.3 38.1 1.0 O6 J:DG186 2.3 39.2 1.0 C5 J:DG185 3.2 36.8 1.0 C6 J:DG186 3.2 40.8 1.0 C8 J:DG185 3.3 34.7 1.0 O6 J:DG185 3.3 40.4 1.0 C6 J:DG185 3.6 40.5 1.0 N4 I:DC107 3.6 41.0 1.0 C5 J:DG186 3.8 36.7 1.0 N7 J:DG186 3.9 34.8 1.0 N1 J:DG186 4.3 39.3 1.0 C4 J:DG185 4.3 33.3 1.0 N9 J:DG185 4.4 36.9 1.0 OP2 J:DG185 4.4 38.7 1.0 C4 I:DC107 4.7 44.4 1.0 C2' J:DT184 4.8 35.5 1.0 O4 I:DT106 4.9 47.1 1.0 N1 J:DG185 4.9 38.6 1.0

Y.Suzuki, N.Horikoshi, D.Kato, H.Kurumizaka. Crystal Structure of the Nucleosome Containing Histone H3 with Crotonylated Lysine 122 Biochem.Biophys.Res.Commun. V. 469 483 2016.
ISSN: ESSN 1090-2104
PubMed: 26694698
DOI: 10.1016/J.BBRC.2015.12.041