Manganese in PDB 6l9h: The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties

The structure of The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties, PDB code: 6l9h was solved by A.Soman, C.W.Liew, H.L.Teo, N.Berezhnoy, N.Korolev, D.Rhodes, L.Nordenskiold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.00 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.455, 109.388, 176.376, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 27.8

The binding sites of Manganese atom in the The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties (pdb code 6l9h). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties, PDB code: 6l9h:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn101 b:0.4 occ:1.00 N7 I:DG38 2.7 0.3 1.0 C8 I:DG38 3.5 0.3 1.0 C5 I:DG38 3.6 0.3 1.0 O6 I:DG38 3.8 0.4 1.0 C7 I:DT39 4.0 0.7 1.0 C6 I:DG38 4.1 0.4 1.0 O4 I:DT39 4.1 0.9 1.0 N9 I:DG38 4.7 0.2 1.0 C4 I:DG38 4.7 0.3 1.0 C8 I:DG37 4.8 0.3 1.0 C4 I:DT39 4.8 0.9 1.0 C5 I:DT39 4.8 0.8 1.0 N7 I:DG37 4.9 0.4 1.0

Manganese binding site 2 out of 4 in the The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn102 b:0.7 occ:1.00 N7 I:DG-4 2.8 0.4 1.0 C8 I:DG-4 3.5 0.3 1.0 C2' I:DG-5 4.0 0.1 1.0 C5 I:DG-4 4.0 0.4 1.0 O6 I:DG-4 4.5 0.5 1.0 C6 I:DG-4 4.6 0.5 1.0 N6 J:DA2 4.7 1.0 1.0 OP2 I:DG-4 4.7 0.8 1.0 C3' I:DG-5 4.7 0.2 1.0 N9 I:DG-4 4.7 0.1 1.0 C7 I:DT-3 4.8 0.6 1.0 O3' I:DG-5 4.8 0.6 1.0

Manganese binding site 3 out of 4 in the The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn103 b:0.8 occ:1.00 N7 I:DG50 2.5 0.1 1.0 C8 I:DG50 3.4 0.1 1.0 C5 I:DG50 3.6 0.1 1.0 C8 I:DG49 3.8 0.8 1.0 N7 I:DG49 3.8 0.8 1.0 O6 I:DG50 3.8 0.2 1.0 C6 I:DG50 4.1 0.2 1.0 C5 I:DG49 4.4 0.8 1.0 N9 I:DG49 4.4 0.7 1.0 C2' I:DG49 4.5 0.7 1.0 N9 I:DG50 4.7 0.1 1.0 C4 I:DG50 4.8 0.1 1.0 OP2 I:DG49 4.8 0.6 1.0 C4 I:DG49 4.8 0.9 1.0

Manganese binding site 4 out of 4 in the The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn104 b:0.1 occ:1.00 N7 I:DG7 2.2 0.2 1.0 O6 I:DG7 2.8 0.2 1.0 C5 I:DG7 2.9 0.2 1.0 C6 I:DG7 3.2 0.2 1.0 C8 I:DG7 3.3 0.3 1.0 C8 I:DG6 3.3 0.6 1.0 N7 I:DG6 3.6 0.7 1.0 OP2 I:DG6 4.0 1.0 1.0 C4 I:DG7 4.2 0.2 1.0 N9 I:DG6 4.3 0.4 1.0 N9 I:DG7 4.4 0.2 1.0 C2' I:DG6 4.5 0.8 1.0 N1 I:DG7 4.5 0.1 1.0 C5 I:DG6 4.7 0.8 1.0

A.Soman, C.W.Liew, H.L.Teo, N.Berezhnoy, V.Olieric, N.Korolev, D.Rhodes, L.Nordenskiold. Crystal Structure and Solution Properties of the Telomeric Nucleosome Biorxiv 2019.
DOI: 10.1101/2019.12.18.881755