Manganese in PDB 5omx: X-Ray Structure of the H2A-N38C Nucleosome Core Particle

The structure of X-Ray Structure of the H2A-N38C Nucleosome Core Particle, PDB code: 5omx was solved by T.D.Frouws, T.J.Richmond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.14 / 2.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.753, 182.578, 109.645, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 25.9

The structure of X-Ray Structure of the H2A-N38C Nucleosome Core Particle also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 33;

Binding sites:

The binding sites of Manganese atom in the X-Ray Structure of the H2A-N38C Nucleosome Core Particle (pdb code 5omx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 33 binding sites of Manganese where determined in the X-Ray Structure of the H2A-N38C Nucleosome Core Particle, PDB code: 5omx:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 33 in the X-Ray Structure of the H2A-N38C 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 X-Ray Structure of the H2A-N38C Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn101 b:0.9 occ:1.00 O4' I:DG5 3.9 77.8 1.0 C4' I:DG5 3.9 86.5 1.0 C5' I:DG5 4.0 90.6 1.0 N3 I:DA4 4.1 71.5 1.0 O I:HOH210 4.3 53.4 1.0 C2 I:DA4 4.6 79.5 1.0 N2 J:DG-3 4.6 57.6 1.0

Manganese binding site 2 out of 33 in the X-Ray Structure of the H2A-N38C 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 X-Ray Structure of the H2A-N38C Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn102 b:0.3 occ:1.00 O2 I:DT33 3.2 0.3 1.0 C5' I:DC34 3.7 0.6 1.0 C4' I:DC34 3.9 0.6 1.0 O4' I:DC34 4.1 0.1 1.0 O4' I:DT33 4.2 0.8 1.0 N3 J:DA-32 4.3 0.5 1.0 C2 I:DT33 4.3 0.4 1.0 C1' I:DT33 4.3 0.6 1.0 C2 J:DA-32 4.6 0.7 1.0 O4' J:DA-31 4.9 0.8 1.0 N1 I:DT33 4.9 0.4 1.0 O5' I:DC34 5.0 0.4 1.0

Manganese binding site 3 out of 33 in the X-Ray Structure of the H2A-N38C 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 X-Ray Structure of the H2A-N38C Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn103 b:0.2 occ:1.00 C4' I:DG-2 4.2 67.8 1.0 C5' I:DG-2 4.3 67.3 1.0 C4' J:DG5 4.4 97.3 1.0 O4' I:DG-2 4.5 72.0 1.0 O4' J:DG5 4.6 0.2 1.0 C5' J:DG5 4.8 86.4 1.0 N2 I:DG-3 5.0 81.5 1.0

Manganese binding site 4 out of 33 in the X-Ray Structure of the H2A-N38C 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 X-Ray Structure of the H2A-N38C Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn104 b:0.7 occ:1.00 N2 I:DG-2 4.1 70.5 1.0 O4' J:DA4 4.2 95.7 1.0 O2 J:DC3 4.3 84.6 1.0 O4' I:DA-1 4.3 80.7 1.0 N2 I:DG-3 4.5 81.5 1.0 C4' J:DA4 4.7 86.8 1.0 C4' I:DA-1 4.8 87.9 1.0 N3 I:DG-2 4.9 68.1 1.0 O4' J:DC3 4.9 0.3 1.0 C2 I:DG-2 5.0 64.2 1.0

Manganese binding site 5 out of 33 in the X-Ray Structure of the H2A-N38C 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 X-Ray Structure of the H2A-N38C Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn105 b:0.6 occ:1.00 C5' I:DT55 3.1 0.2 1.0 O4' I:DA54 3.4 0.6 1.0 C4' I:DT55 3.8 0.8 1.0 C1' I:DA54 3.9 0.2 1.0 N3 I:DA54 3.9 0.5 1.0 C4' I:DA54 4.0 0.1 1.0 O4' I:DT55 4.1 0.7 1.0 O3' I:DA54 4.1 0.2 1.0 O5' I:DT55 4.4 0.8 1.0 N9 I:DA54 4.6 0.6 1.0 C4 I:DA54 4.6 0.1 1.0 C3' I:DA54 4.6 0.1 1.0 N3 J:DA-53 4.7 0.3 1.0 C2 I:DA54 4.8 1.0 1.0 C2 J:DA-53 4.9 0.4 1.0 C2' I:DA54 4.9 0.3 1.0 P I:DT55 5.0 0.9 1.0

Manganese binding site 6 out of 33 in the X-Ray Structure of the H2A-N38C 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 X-Ray Structure of the H2A-N38C Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn106 b:0.4 occ:1.00 C5' I:DT67 3.9 94.4 1.0 O2 J:DC-65 4.0 94.9 1.0 C4' I:DT67 4.2 97.0 1.0 O4' I:DT67 4.2 86.0 1.0 N3 I:DA66 4.3 85.0 1.0 O4' J:DC-64 4.5 95.9 1.0 C5' J:DC-64 4.6 88.0 1.0 O4' J:DC-65 4.7 91.1 1.0 C4' J:DC-64 4.7 95.5 1.0 C2 I:DA66 4.7 86.2 1.0 N2 I:DG65 4.8 89.1 1.0 C1' J:DC-65 5.0 86.0 1.0

Manganese binding site 7 out of 33 in the X-Ray Structure of the H2A-N38C 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 X-Ray Structure of the H2A-N38C Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn107 b:0.5 occ:1.00 O4' I:DC-58 3.0 96.7 1.0 N2 I:DG-59 3.4 84.8 1.0 C4' I:DC-58 3.5 95.8 1.0 N3 I:DG-59 3.6 0.3 1.0 C2 I:DG-59 4.0 97.3 1.0 C5' I:DC-58 4.0 1.0 1.0 O2 I:DC-58 4.0 94.1 1.0 C1' I:DC-58 4.2 97.5 1.0 C2 I:DC-58 4.6 96.1 1.0 N1 I:DC-58 4.7 93.8 1.0 C4 I:DG-59 4.8 0.3 1.0 N3 J:DA60 4.9 71.2 1.0 C3' I:DC-58 4.9 92.3 1.0 C1' I:DG-59 5.0 0.3 1.0

Manganese binding site 8 out of 33 in the X-Ray Structure of the H2A-N38C 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 X-Ray Structure of the H2A-N38C Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn108 b:0.4 occ:1.00 N7 I:DG65 2.4 96.7 1.0 O6 I:DG65 3.0 88.0 1.0 N7 I:DG64 3.1 96.8 1.0 C5 I:DG65 3.1 98.9 1.0 C8 I:DG64 3.3 0.5 1.0 C6 I:DG65 3.4 87.5 1.0 C8 I:DG65 3.5 0.1 1.0 C5 I:DG64 3.8 0.6 1.0 N9 I:DG64 4.1 0.6 1.0 C4 I:DG64 4.4 0.0 1.0 C4 I:DG65 4.4 0.3 1.0 N9 I:DG65 4.6 0.3 1.0 C6 I:DG64 4.6 85.4 1.0 N1 I:DG65 4.8 83.6 1.0 N6 I:DA66 4.8 87.1 1.0 O6 I:DG64 4.8 82.7 1.0 C2' I:DG64 4.8 0.2 1.0

Manganese binding site 9 out of 33 in the X-Ray Structure of the H2A-N38C 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 X-Ray Structure of the H2A-N38C Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn109 b:0.6 occ:1.00 C5' I:DA-31 3.7 0.4 1.0 O4' I:DA-31 3.9 99.4 1.0 N3 I:DA-32 4.0 99.7 1.0 C4' I:DA-31 4.0 0.0 1.0 C1' I:DA-32 4.4 0.4 1.0 O4' I:DA-32 4.5 0.1 1.0 O2 J:DT33 4.5 99.2 1.0 C2 I:DA-32 4.8 0.7 1.0 O5' I:DA-31 4.9 0.8 1.0 C4 I:DA-32 4.9 94.1 1.0 O3' I:DA-32 5.0 0.3 1.0

Manganese binding site 10 out of 33 in the X-Ray Structure of the H2A-N38C 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 X-Ray Structure of the H2A-N38C Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn110 b:0.1 occ:1.00 C4' J:DT55 4.0 0.8 1.0 N3 I:DA-53 4.1 0.3 1.0 O4' J:DT55 4.2 0.2 1.0 C5' J:DT55 4.2 0.6 1.0 C5' I:DC-52 4.3 0.9 1.0 O4' I:DC-52 4.3 0.2 1.0 C4' I:DC-52 4.5 0.1 1.0 N3 J:DA54 4.5 0.5 1.0 C1' I:DA-53 4.6 1.0 1.0 O4' I:DA-53 4.7 0.3 1.0 C2 I:DA-53 4.8 0.5 1.0

T.D.Frouws, P.D.Barth, T.J.Richmond. Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability. J. Mol. Biol. V. 430 45 2018.
ISSN: ESSN 1089-8638
PubMed: 29113904
DOI: 10.1016/J.JMB.2017.10.029