Manganese in PDB 3wkj: The Nucleosome Containing Human TSH2B

The structure of The Nucleosome Containing Human TSH2B, PDB code: 3wkj was solved by T.Urahama, N.Horikoshi, A.Osakabe, H.Tachiwana, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	107.037, 109.926, 182.961, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 29.1

The structure of The Nucleosome Containing Human TSH2B also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Manganese atom in the The Nucleosome Containing Human TSH2B (pdb code 3wkj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the The Nucleosome Containing Human TSH2B, PDB code: 3wkj:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the The Nucleosome Containing Human TSH2B


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Nucleosome Containing Human TSH2B within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn401 b:0.2 occ:1.00 O6 I:DG68 3.0 87.1 1.0 N4 J:DC225 3.2 99.5 1.0 C6 I:DG68 4.2 85.2 1.0 N7 J:DG224 4.4 98.6 1.0 O6 J:DG224 4.4 97.7 1.0 C4 J:DC225 4.6 99.2 1.0 C5 J:DG224 4.9 98.5 1.0 C6 J:DG224 5.0 98.7 1.0 C5 I:DG68 5.0 84.1 1.0

Manganese binding site 2 out of 5 in the The Nucleosome Containing Human TSH2B


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Nucleosome Containing Human TSH2B within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn402 b:1.0 occ:1.00 N7 I:DG121 2.3 98.9 1.0 O6 I:DG121 2.9 0.6 1.0 C5 I:DG121 2.9 99.5 1.0 C6 I:DG121 3.2 99.9 1.0 O6 I:DG122 3.2 0.1 1.0 C8 I:DG121 3.4 98.0 1.0 N4 J:DC171 3.5 0.3 1.0 C6 I:DT120 4.0 0.9 1.0 C4 I:DG121 4.2 98.8 1.0 C5 I:DT120 4.2 0.1 1.0 C6 I:DG122 4.3 0.1 1.0 N9 I:DG121 4.4 97.2 1.0 C7 I:DT120 4.4 0.4 1.0 N1 I:DG121 4.5 98.8 1.0 N1 I:DT120 4.5 0.2 1.0 C2' I:DT120 4.6 99.5 1.0 C4 J:DC171 4.7 0.9 1.0 C4 I:DT120 4.9 0.3 1.0

Manganese binding site 3 out of 5 in the The Nucleosome Containing Human TSH2B


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Nucleosome Containing Human TSH2B within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn403 b:95.5 occ:1.00 O4' I:DC88 3.8 78.4 1.0 O2 I:DT86 3.9 82.2 1.0 O4' I:DG87 4.0 72.8 1.0 C4' I:DC88 4.0 76.9 1.0 O4' J:DT208 4.2 53.8 1.0 C2 J:DA207 4.2 60.5 1.0 C5' I:DC88 4.3 75.8 1.0 N3 J:DA207 4.5 59.1 1.0 C4' I:DG87 4.5 72.3 1.0 O2 J:DT208 4.9 63.2 1.0 N3 I:DG87 4.9 77.0 1.0 C1' J:DT208 5.0 55.7 1.0 C4' J:DT208 5.0 53.9 1.0

Manganese binding site 4 out of 5 in the The Nucleosome Containing Human TSH2B


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Nucleosome Containing Human TSH2B within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn301 b:99.2 occ:1.00 N7 J:DG267 2.7 94.2 1.0 C8 J:DG267 3.5 93.0 1.0 C5 J:DG267 3.7 92.6 1.0 O6 J:DG268 3.8 83.2 1.0 O6 J:DG267 4.0 90.9 1.0 C6 J:DG267 4.2 91.9 1.0 OP2 J:DG267 4.4 96.4 1.0 C2' J:DT266 4.5 0.7 1.0 N4 I:DC25 4.7 0.9 1.0 N9 J:DG267 4.7 91.6 1.0 C6 J:DG268 4.8 82.8 1.0 C4 J:DG267 4.9 92.0 1.0

Manganese binding site 5 out of 5 in the The Nucleosome Containing Human TSH2B


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Nucleosome Containing Human TSH2B within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn302 b:84.3 occ:1.00 N7 J:DG217 2.3 64.7 1.0 C8 J:DG217 3.2 63.9 1.0 C5 J:DG217 3.4 65.2 1.0 O6 J:DG217 3.7 64.5 1.0 C6 J:DG217 3.9 65.0 1.0 C2' J:DT216 4.0 58.4 1.0 OP2 J:DG217 4.2 44.8 1.0 N6 J:DA218 4.3 72.0 1.0 N9 J:DG217 4.4 62.3 1.0 C6 J:DT216 4.5 65.2 1.0 C4 J:DG217 4.6 64.5 1.0 C1' J:DT216 4.9 61.2 1.0 N1 J:DT216 4.9 64.0 1.0

T.Urahama, N.Horikoshi, A.Osakabe, H.Tachiwana, H.Kurumizaka. Structure of Human Nucleosome Containing the Testis-Specific Histone Variant TSH2B Acta Crystallogr.,Sect.F V. 70 444 2014.
ISSN: ESSN 1744-3091
DOI: 10.1107/S2053230X14004695