Manganese in PDB 5ong: X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer

The structure of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer, PDB code: 5ong was solved by T.D.Frouws, P.D.Barth, T.J.Richmond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.50 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.240, 183.130, 109.490, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.7

The structure of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Manganese atom in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer (pdb code 5ong). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 20 binding sites of Manganese where determined in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer, PDB code: 5ong:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 20 in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn101 b:0.3 occ:1.00 O6 I:DG71 2.1 0.8 1.0 C6 I:DG71 3.0 0.1 1.0 N7 I:DG71 3.4 0.8 1.0 C5 I:DG71 3.5 0.6 1.0 N7 I:G4770 3.7 0.8 1.0 N4 J:DC-71 4.1 0.8 1.0 N1 I:DG71 4.3 0.0 1.0 O6 I:G4770 4.4 0.3 1.0 C5 I:G4770 4.5 0.2 1.0 C8 I:G4770 4.5 0.3 1.0 C8 I:DG71 4.6 0.9 1.0 C6 I:G4770 4.8 0.2 1.0 O4 J:DT-72 4.9 0.7 1.0 C4 I:DG71 4.9 0.9 1.0

Manganese binding site 2 out of 20 in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn102 b:1.0 occ:1.00 O6 I:DG-58 2.3 0.7 1.0 C6 I:DG-58 3.4 0.6 1.0 N7 I:DG-59 3.6 0.3 1.0 N1 I:DG-58 4.2 0.7 1.0 C8 I:DG-59 4.3 0.7 1.0 OP2 I:DG-59 4.4 0.9 1.0 C5 I:DG-58 4.5 1.0 1.0 C5 I:DG-59 4.6 0.5 1.0 O6 I:DG-59 4.6 0.6 1.0 C2' I:DT-60 4.8 1.0 1.0 N7 I:DG-58 4.9 0.4 1.0 C6 I:DG-59 5.0 0.1 1.0

Manganese binding site 3 out of 20 in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn103 b:0.2 occ:1.00 N7 I:DG56 2.5 0.8 1.0 N7 I:DG55 2.6 0.8 1.0 C8 I:DG55 2.8 0.3 1.0 C5 I:DG55 3.1 0.8 1.0 C5 I:DG56 3.3 0.3 1.0 O6 I:DG56 3.3 0.9 1.0 N9 I:DG55 3.4 0.4 1.0 C8 I:DG56 3.4 0.2 1.0 C4 I:DG55 3.6 0.8 1.0 C6 I:DG56 3.6 0.5 1.0 C6 I:DG55 3.8 0.6 1.0 O6 I:DG55 4.2 0.7 1.0 C2' I:DG55 4.3 0.7 1.0 C4 I:DG56 4.4 0.7 1.0 C1' I:DG55 4.4 1.0 1.0 N9 I:DG56 4.5 0.2 1.0 N3 I:DG55 4.6 0.9 1.0 N1 I:DG55 4.8 0.2 1.0 N1 I:DG56 4.9 0.6 1.0

Manganese binding site 4 out of 20 in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn104 b:0.7 occ:1.00 N7 I:DG-6 3.9 0.2 1.0 C2' I:DA-7 4.0 0.2 1.0 N4 I:DC-5 4.2 0.4 1.0 OP2 I:DG-6 4.2 0.1 1.0 C8 I:DG-6 4.4 0.3 1.0 C3' I:DA-7 4.6 0.4 1.0 O6 J:DG5 4.6 0.5 1.0 O3' I:DA-7 4.7 0.5 1.0

Manganese binding site 5 out of 20 in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn105 b:0.4 occ:1.00 N7 I:DG48 2.7 0.5 1.0 C8 I:DG48 3.3 1.0 1.0 C2' I:DT47 3.7 0.8 1.0 C5 I:DG48 3.9 0.8 1.0 OP2 I:DG48 4.1 0.6 1.0 C3' I:DT47 4.4 0.8 1.0 O6 I:DG48 4.5 0.6 1.0 N9 I:DG48 4.6 0.8 1.0 C6 I:DG48 4.6 0.9 1.0 O3' I:DT47 4.7 0.6 1.0 C1' I:DT47 4.9 0.5 1.0 C4 I:DG48 4.9 0.5 1.0

Manganese binding site 6 out of 20 in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn106 b:0.1 occ:1.00 N7 I:DG61 3.3 0.4 1.0 C8 I:DG61 4.1 0.7 1.0 C5 I:DG61 4.3 0.4 1.0 O6 I:DG62 4.3 0.0 1.0 O6 I:DG61 4.3 0.0 1.0 C6 I:DG61 4.6 0.1 1.0 C8 I:DA60 4.9 0.5 1.0

Manganese binding site 7 out of 20 in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn107 b:0.8 occ:1.00 O J:HOH208 2.5 80.6 1.0 N7 I:DG27 2.7 0.1 1.0 O6 I:DG27 3.1 0.8 1.0 C5 I:DG27 3.4 0.8 1.0 C6 I:DG27 3.6 0.2 1.0 C8 I:DG27 3.8 0.1 1.0 O6 J:DG-28 4.6 98.9 1.0 C4 I:DG27 4.7 0.3 1.0 N7 I:DA26 4.7 1.0 1.0 C8 I:DA26 4.7 0.4 1.0 N9 I:DG27 4.8 96.4 1.0 N4 I:DC28 4.8 98.0 1.0 N1 I:DG27 4.9 0.2 1.0

Manganese binding site 8 out of 20 in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn108 b:0.7 occ:0.86 O6 I:DG5 2.2 0.5 1.0 C6 I:DG5 3.1 0.9 1.0 N7 I:DG5 3.5 0.5 1.0 C5 I:DG5 3.6 0.4 1.0 N4 J:DC-5 4.1 0.0 1.0 N1 I:DG5 4.4 0.1 1.0 N7 I:DA4 4.5 0.6 1.0 O6 J:DG-6 4.7 97.1 1.0 C8 I:DG5 4.8 0.6 1.0 C8 I:DA4 4.8 0.5 1.0

Manganese binding site 9 out of 20 in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn109 b:0.2 occ:0.74 N7 I:DG-3 3.0 0.3 1.0 O6 I:DG-2 3.6 0.2 1.0 O6 I:DG-3 3.9 0.5 1.0 C8 I:DG-3 3.9 96.0 1.0 C5 I:DG-3 4.0 99.8 1.0 C6 I:DG-3 4.3 0.1 1.0 C6 I:DG-2 4.6 0.3 1.0 N4 J:DC2 4.7 0.9 1.0 C2' I:DT-4 4.8 96.4 1.0 N7 I:DG-2 4.9 0.5 1.0 OP2 I:DG-3 5.0 89.0 1.0

Manganese binding site 10 out of 20 in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn110 b:0.0 occ:1.00 N7 I:DG-35 2.7 0.1 1.0 O6 I:DG-34 2.8 0.4 1.0 C8 I:DG-35 3.5 99.3 1.0 C6 I:DG-34 3.6 0.9 1.0 C5 I:DG-35 3.7 0.2 1.0 N7 I:DG-34 3.9 96.1 1.0 C5 I:DG-34 4.1 97.5 1.0 O6 I:DG-35 4.1 0.9 1.0 C6 I:DG-35 4.3 0.3 1.0 N4 J:DC34 4.4 0.8 1.0 OP2 I:DG-35 4.5 0.4 1.0 C2' I:DT-36 4.6 96.2 1.0 N9 I:DG-35 4.6 96.5 1.0 O3' I:DT-36 4.7 95.4 1.0 N1 I:DG-34 4.8 0.1 1.0 C4 I:DG-35 4.8 99.6 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