Manganese in PDB 5b2j: Human Nucleosome Containing Cpg Methylated Dna

The structure of Human Nucleosome Containing Cpg Methylated Dna, PDB code: 5b2j was solved by Y.Fujii, M.Wakamori, T.Umehara, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.90 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.540, 109.670, 181.350, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 25.2

The binding sites of Manganese atom in the Human Nucleosome Containing Cpg Methylated Dna (pdb code 5b2j). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Human Nucleosome Containing Cpg Methylated Dna, PDB code: 5b2j:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in the Human Nucleosome Containing Cpg Methylated Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Nucleosome Containing Cpg Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn301 b:58.7 occ:1.00 OD1 E:ASP77 2.1 83.5 1.0 OD2 E:ASP77 2.2 68.0 1.0 CG E:ASP77 2.4 79.8 1.0 CB E:ASP77 3.9 49.0 1.0 OE1 E:GLN76 3.9 68.1 1.0 O F:LEU22 4.1 68.2 1.0 O E:HOH403 4.5 49.4 1.0 CA E:ASP77 4.5 51.0 1.0 O E:GLU73 4.5 65.6 1.0 CD E:GLN76 4.7 59.5 1.0 N E:ASP77 4.7 47.8 1.0 CG E:GLU73 4.8 56.1 1.0 CG E:GLN76 4.9 51.6 1.0

Manganese binding site 2 out of 7 in the Human Nucleosome Containing Cpg Methylated Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Nucleosome Containing Cpg Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn101 b:0.5 occ:1.00 O2 I:DT13 3.7 94.0 1.0 O4' I:DG14 4.0 87.9 1.0 C2 J:DA-13 4.2 74.6 1.0 O4' I:DC15 4.3 95.2 1.0 C5' I:DC15 4.4 81.9 1.0 N3 J:DA-13 4.4 70.7 1.0 C4' I:DG14 4.5 79.0 1.0 O2 J:DT-12 4.5 78.3 1.0 C4' I:DC15 4.5 95.0 1.0 O4' J:DT-12 4.5 69.3 1.0 C1' I:DG14 4.7 0.6 1.0 N3 I:DG14 4.8 0.0 1.0 C2 I:DT13 4.9 92.3 1.0 C1' J:DT-12 4.9 70.0 1.0

Manganese binding site 3 out of 7 in the Human Nucleosome Containing Cpg Methylated Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human Nucleosome Containing Cpg Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn102 b:0.8 occ:1.00 N7 I:DG48 2.1 0.4 1.0 O6 I:DG48 2.9 0.5 1.0 C5 I:DG48 3.0 0.2 1.0 C8 I:DG48 3.2 0.4 1.0 C6 I:DG48 3.3 0.7 1.0 C6 I:DT47 4.1 0.2 1.0 C5 I:DT47 4.2 0.5 1.0 C4 I:DG48 4.2 0.8 1.0 C7 I:DT47 4.3 0.8 1.0 C2' I:DT47 4.3 0.7 1.0 N9 I:DG48 4.4 0.8 1.0 N1 I:DG48 4.7 0.7 1.0 N1 I:DT47 4.7 0.1 1.0 OP2 I:DG48 4.8 0.5 1.0 O6 I:DG49 4.9 0.6 1.0

Manganese binding site 4 out of 7 in the Human Nucleosome Containing Cpg Methylated Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Human Nucleosome Containing Cpg Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn103 b:0.5 occ:1.00 N7 I:DG27 2.4 0.2 1.0 O I:HOH205 2.9 70.8 1.0 C8 I:DG27 3.4 95.6 1.0 C5 I:DG27 3.5 99.9 1.0 O6 I:DG27 3.6 0.3 1.0 C6 I:DG27 3.9 99.7 1.0 C8 I:DA26 4.5 98.8 1.0 N7 I:DA26 4.5 95.4 1.0 N9 I:DG27 4.6 98.8 1.0 C4 I:DG27 4.6 95.9 1.0

Manganese binding site 5 out of 7 in the Human Nucleosome Containing Cpg Methylated Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Human Nucleosome Containing Cpg Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn101 b:0.4 occ:1.00 N7 J:DG26 2.5 0.8 1.0 C8 J:DG26 3.3 0.3 1.0 C5 J:DG26 3.6 0.1 1.0 O6 J:DG26 4.0 0.4 1.0 C6 J:DG26 4.2 0.9 1.0 C8 J:DA25 4.5 0.6 1.0 N9 J:DG26 4.5 0.4 1.0 OP2 J:DA25 4.7 0.1 1.0 C4 J:DG26 4.7 0.4 1.0 N7 J:DA25 4.8 0.6 1.0 C2' J:DA25 5.0 0.5 1.0

Manganese binding site 6 out of 7 in the Human Nucleosome Containing Cpg Methylated Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Human Nucleosome Containing Cpg Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn102 b:0.7 occ:1.00 N7 J:DG-3 2.2 76.9 1.0 C8 J:DG-3 3.1 82.2 1.0 C5 J:DG-3 3.3 81.5 1.0 O6 J:DG-3 3.6 87.3 1.0 C6 J:DG-3 3.8 79.6 1.0 N6 J:DA-2 3.9 88.3 1.0 N9 J:DG-3 4.4 82.2 1.0 C2' J:DT-4 4.4 58.5 1.0 C4 J:DG-3 4.4 80.0 1.0 OP2 J:DG-3 4.7 81.4 1.0 C6 J:DA-2 4.8 82.3 1.0 C6 J:DT-4 4.8 75.8 1.0

Manganese binding site 7 out of 7 in the Human Nucleosome Containing Cpg Methylated Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Human Nucleosome Containing Cpg Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn103 b:0.1 occ:1.00 N7 J:DG47 2.2 0.5 1.0 O6 J:DG47 2.8 0.9 1.0 C5 J:DG47 3.0 0.7 1.0 C6 J:DG47 3.2 0.8 1.0 C8 J:DG47 3.4 0.6 1.0 O6 J:DG48 3.9 0.4 1.0 C4 J:DG47 4.2 0.3 1.0 C6 J:DT46 4.3 0.0 1.0 N9 J:DG47 4.4 0.7 1.0 C5 J:DT46 4.5 1.0 1.0 C2' J:DT46 4.6 0.2 1.0 N1 J:DG47 4.6 0.4 1.0 C7 J:DT46 4.7 0.8 1.0 C6 J:DG48 4.8 0.2 1.0 N1 J:DT46 4.8 0.6 1.0

Y.Fujii, M.Wakamori, T.Umehara, S.Yokoyama. Crystal Structure of Human Nucleosome Core Particle Containing Enzymatically Introduced Cpg Methylation Febs Open Bio V. 6 498 2016.
ISSN: ESSN 2211-5463
DOI: 10.1002/2211-5463.12064