Potassium in PDB 1eqz: X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution

The structure of X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution, PDB code: 1eqz was solved by B.L.Hanson, J.M.Harp, D.E.Timm, G.J.Bunick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.34 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.280, 109.710, 181.120, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 28.2

The structure of X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution also contains other interesting chemical elements:

Manganese	(Mn)	15 atoms
Arsenic	(As)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Potassium atom in the X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution (pdb code 1eqz). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution, PDB code: 1eqz:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in the X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:K458 b:0.2 occ:1.00 O6 I:DG98 3.2 60.3 1.0 N7 I:DG98 3.5 69.9 1.0 N7 I:DG97 3.6 67.7 1.0 C8 I:DG97 3.9 73.0 1.0 C6 I:DG98 4.0 64.7 1.0 C5 I:DG98 4.1 69.0 1.0 C5 I:DG97 4.6 71.0 1.0 C8 I:DG98 4.7 70.5 1.0 OP2 I:DG97 4.7 77.2 1.0

Potassium binding site 2 out of 7 in the X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ J:K452 b:0.4 occ:1.00 C8 J:DA255 3.5 62.4 1.0 N7 J:DA256 3.5 64.8 1.0 C8 J:DA256 4.0 64.5 1.0 N7 J:DA255 4.0 57.2 1.0 OP2 J:DA255 4.1 77.3 1.0 C2' J:DA255 4.2 55.5 1.0 N9 J:DA255 4.4 60.8 1.0 C5 J:DA256 4.8 61.9 1.0 C1' J:DA255 4.9 57.3 1.0

Potassium binding site 3 out of 7 in the X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ J:K453 b:83.9 occ:1.00 N7 J:DG216 3.4 45.2 1.0 O A:LYS124 3.6 88.6 1.0 C8 J:DG216 3.8 37.2 1.0 C2' J:DC215 3.9 42.2 1.0 OP2 J:DG216 4.1 48.5 1.0 K J:K454 4.4 78.2 1.0 O3' J:DC215 4.5 45.9 1.0 C3' J:DC215 4.6 46.9 1.0 C A:LYS124 4.6 90.9 1.0 C5 J:DG216 4.7 38.9 1.0 C1' J:DC215 5.0 47.5 1.0

Potassium binding site 4 out of 7 in the X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ J:K454 b:78.2 occ:1.00 N7 J:DG217 3.2 40.5 1.0 O6 J:DG217 3.8 48.2 1.0 C5 J:DG217 4.1 46.8 1.0 C8 J:DG217 4.2 41.1 1.0 N6 J:DA218 4.3 41.9 1.0 C8 J:DG216 4.3 37.2 1.0 C6 J:DG217 4.3 45.1 1.0 C2' J:DG216 4.3 41.6 1.0 K J:K453 4.4 83.9 1.0 N7 J:DG216 4.7 45.2 1.0 N9 J:DG216 4.8 43.9 1.0

Potassium binding site 5 out of 7 in the X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ J:K455 b:95.1 occ:1.00 N7 J:DG227 3.0 43.9 1.0 C8 J:DG227 3.9 37.0 1.0 C5 J:DG227 4.1 47.2 1.0 O6 J:DG227 4.2 57.4 1.0 C6 J:DG227 4.5 45.9 1.0 C2' J:DT226 4.6 58.0 1.0 K J:K456 4.9 83.8 1.0 N6 J:DA228 4.9 36.6 1.0 O4 I:DT65 4.9 56.8 1.0

Potassium binding site 6 out of 7 in the X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ J:K456 b:83.8 occ:1.00 N7 J:DA228 3.3 38.9 1.0 NZ D:LYS31 3.7 39.5 1.0 C2' J:DG227 3.8 34.9 1.0 N6 J:DA228 4.0 36.6 1.0 C8 J:DG227 4.1 37.0 1.0 C8 J:DA228 4.3 38.5 1.0 C5 J:DA228 4.3 39.8 1.0 N9 J:DG227 4.4 39.2 1.0 N7 J:DG227 4.5 43.9 1.0 C6 J:DA228 4.6 37.5 1.0 N6 J:DA229 4.7 45.2 1.0 C1' J:DG227 4.8 42.8 1.0 K J:K455 4.9 95.1 1.0 OP2 J:DA228 4.9 20.6 1.0

Potassium binding site 7 out of 7 in the X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ J:K457 b:0.9 occ:1.00 N7 J:DA175 3.5 85.8 1.0 C8 J:DA175 3.7 86.9 1.0 N6 J:DA176 3.9 72.5 1.0 C5 J:DA175 4.3 85.5 1.0 N7 J:DA176 4.4 77.0 1.0 N9 J:DA175 4.6 88.8 1.0 C4 J:DA175 4.9 85.0 1.0 C6 J:DA176 4.9 78.5 1.0 C6 J:DA175 5.0 86.2 1.0

J.M.Harp, B.L.Hanson, D.E.Timm, G.J.Bunick. Asymmetries in the Nucleosome Core Particle at 2.5 A Resolution. Acta Crystallogr.,Sect.D V. 56 1513 2000.
ISSN: ISSN 0907-4449
PubMed: 11092917
DOI: 10.1107/S0907444900011847