Manganese in PDB 5avb: Human Nucleosome Core Particle

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

Resolution Low / High (Å)	20.00 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.950, 110.090, 181.610, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 23.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Manganese atom in the Human Nucleosome Core Particle (pdb code 5avb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 14 binding sites of Manganese where determined in the Human Nucleosome Core Particle, PDB code: 5avb:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 14 in the Human Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn201 b:40.2 occ:1.00 O F:HOH206 2.0 47.3 1.0 O E:HOH329 2.1 47.3 1.0 OD1 E:ASP77 2.2 42.4 1.0 O E:HOH316 2.3 47.3 1.0 CG E:ASP77 3.1 49.2 1.0 OD2 E:ASP77 3.4 41.7 1.0 O F:LEU22 4.2 45.3 1.0 O E:HOH311 4.4 53.5 1.0 CB E:ASP77 4.5 31.7 1.0 OE1 E:GLN76 4.5 38.0 1.0 O E:GLU73 4.5 41.8 1.0 CA E:ASP77 4.7 36.1 1.0 O E:HOH328 4.7 41.0 1.0 N E:ASP77 4.8 39.9 1.0 CG E:GLU73 4.9 35.1 1.0

Manganese binding site 2 out of 14 in the Human Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn101 b:75.0 occ:0.72 O J:HOH215 2.4 55.8 1.0 O2 I:DT13 3.9 71.4 1.0 O4' I:DG14 3.9 66.2 1.0 C4' I:DG14 4.3 68.0 1.0 O4' I:DC15 4.4 72.1 1.0 C2 J:DA-13 4.4 63.8 1.0 C5' I:DC15 4.5 59.8 1.0 C4' I:DC15 4.6 79.8 1.0 O2 J:DT-12 4.6 58.6 1.0 N3 J:DA-13 4.6 58.0 1.0 O4' J:DT-12 4.7 59.1 1.0 N3 I:DG14 4.8 74.9 1.0 C1' I:DG14 4.9 77.4 1.0 C5' I:DG14 5.0 64.7 1.0

Manganese binding site 3 out of 14 in the Human Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn102 b:0.8 occ:1.00 N7 I:DG48 2.3 95.7 1.0 C8 I:DG48 3.3 96.2 1.0 C5 I:DG48 3.3 95.1 1.0 O6 I:DG48 3.4 0.5 1.0 C6 I:DG48 3.7 0.8 1.0 C2' I:DT47 4.4 92.1 1.0 O6 I:DG49 4.4 95.1 1.0 N9 I:DG48 4.4 94.5 1.0 C4 I:DG48 4.5 90.4 1.0 OP2 I:DG48 4.6 83.8 1.0

Manganese binding site 4 out of 14 in the Human Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Human Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn103 b:76.3 occ:0.90 O I:HOH209 2.3 68.6 1.0 O I:HOH211 2.3 62.0 1.0 N7 I:DG61 2.6 78.7 1.0 O I:HOH210 2.6 62.9 1.0 C8 I:DG61 3.6 87.7 1.0 C5 I:DG61 3.6 81.0 1.0 O6 I:DG61 3.6 66.3 1.0 C6 I:DG61 4.0 79.5 1.0 C8 I:DA60 4.3 84.7 1.0 N7 I:DA60 4.3 84.4 1.0 O6 I:DG62 4.4 80.5 1.0 N9 I:DG61 4.8 87.0 1.0 C4 I:DG61 4.8 80.7 1.0 OP2 I:DA60 5.0 80.6 1.0

Manganese binding site 5 out of 14 in the Human Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Human Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn104 b:99.9 occ:0.72 N7 I:DG27 2.4 89.5 1.0 C8 I:DG27 3.3 84.2 1.0 C5 I:DG27 3.4 80.4 1.0 O6 I:DG27 3.5 97.0 1.0 C6 I:DG27 3.8 87.4 1.0 C8 I:DA26 4.1 85.6 1.0 N7 I:DA26 4.2 88.5 1.0 N9 I:DG27 4.5 84.3 1.0 C4 I:DG27 4.6 80.8 1.0 N9 I:DA26 5.0 86.3 1.0 O6 J:DG-28 5.0 91.3 1.0

Manganese binding site 6 out of 14 in the Human Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Human Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn105 b:76.1 occ:0.63 O I:HOH206 1.9 65.8 1.0 O6 I:DG5 2.5 76.4 1.0 C6 I:DG5 3.6 69.0 1.0 O6 J:DG-6 3.7 67.0 1.0 N7 J:DG-6 3.9 63.1 1.0 N4 J:DC-5 3.9 68.6 1.0 C5 I:DG5 4.3 68.7 1.0 N7 I:DG5 4.3 71.4 1.0 C6 J:DG-6 4.4 61.3 1.0 C5 J:DG-6 4.5 61.1 1.0 N1 I:DG5 4.6 73.9 1.0

Manganese binding site 7 out of 14 in the Human Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Human Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn106 b:71.4 occ:0.64 N7 I:DG-3 2.2 54.5 1.0 C8 I:DG-3 3.2 59.7 1.0 C5 I:DG-3 3.3 60.6 1.0 O6 I:DG-3 3.4 59.0 1.0 O6 I:DG-2 3.7 67.7 1.0 C6 I:DG-3 3.7 59.4 1.0 C2' I:DT-4 4.2 59.7 1.0 N9 I:DG-3 4.4 59.3 1.0 C4 I:DG-3 4.4 61.1 1.0 C6 I:DT-4 4.5 47.6 1.0 C6 I:DG-2 4.6 62.8 1.0 OP2 I:DG-3 4.7 47.2 1.0 N7 I:DG-2 4.9 65.0 1.0 C5 I:DT-4 4.9 63.0 1.0 N1 I:DT-4 5.0 56.2 1.0

Manganese binding site 8 out of 14 in the Human Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Human Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn107 b:99.4 occ:1.00 O6 I:DG-34 2.5 87.5 1.0 N7 I:DG-35 2.6 85.9 1.0 C6 I:DG-34 3.4 84.1 1.0 C8 I:DG-35 3.4 86.0 1.0 C5 I:DG-35 3.7 89.5 1.0 O6 I:DG-35 4.0 89.7 1.0 C5 I:DG-34 4.0 86.0 1.0 N7 I:DG-34 4.0 69.5 1.0 N4 J:DC34 4.2 83.2 1.0 C6 I:DG-35 4.2 87.4 1.0 OP2 I:DG-35 4.3 72.7 1.0 N1 I:DG-34 4.5 84.2 1.0 C2' I:DT-36 4.5 77.3 1.0 N9 I:DG-35 4.6 90.5 1.0 C4 I:DG-35 4.8 86.0 1.0 O3' I:DT-36 4.9 82.9 1.0 O4 J:DT33 5.0 99.9 1.0

Manganese binding site 9 out of 14 in the Human Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Human Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn101 b:82.5 occ:1.00 N7 J:DG61 2.4 84.2 1.0 O6 J:DG61 3.0 90.2 1.0 C5 J:DG61 3.2 82.8 1.0 C6 J:DG61 3.4 90.9 1.0 C8 J:DG61 3.5 91.5 1.0 N7 J:DA60 4.3 75.4 1.0 O6 J:DG62 4.4 91.8 1.0 C8 J:DA60 4.4 79.6 1.0 C4 J:DG61 4.5 83.9 1.0 N9 J:DG61 4.6 96.9 1.0 N1 J:DG61 4.8 88.7 1.0

Manganese binding site 10 out of 14 in the Human Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Human Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn102 b:78.9 occ:0.97 N7 J:DG27 2.4 82.1 1.0 O6 J:DG27 3.2 88.9 1.0 C5 J:DG27 3.2 86.4 1.0 C8 J:DG27 3.4 78.3 1.0 C6 J:DG27 3.5 87.1 1.0 O6 I:DG-28 4.2 88.6 1.0 N7 J:DA26 4.4 86.5 1.0 C4 J:DG27 4.4 86.2 1.0 C8 J:DA26 4.5 82.3 1.0 N9 J:DG27 4.5 85.3 1.0 N1 J:DG27 4.9 84.1 1.0 N4 J:DC28 5.0 80.6 1.0

M.Wakamori, Y.Fujii, N.Suka, M.Shirouzu, K.Sakamoto, T.Umehara, S.Yokoyama. Intra- and Inter-Nucleosomal Interactions of the Histone H4 Tail Revealed with A Human Nucleosome Core Particle with Genetically-Incorporated H4 Tetra-Acetylation Sci Rep V. 5 17204 2015.
ISSN: ESSN 2045-2322
PubMed: 26607036
DOI: 10.1038/SREP17204