Manganese 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:

Potassium	(K)	7 atoms
Arsenic	(As)	1 atom
Chlorine	(Cl)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Manganese 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 Manganese atom.
In total 15 binding sites of Manganese where determined in the X-Ray Structure of the Nucleosome Core Particle at 2.5 A Resolution, PDB code: 1eqz:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 15 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 Manganese with other atoms in the Mn 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:Mn460 b:57.4 occ:1.00 O I:HOH505 2.4 49.7 1.0 N7 I:DG134 2.5 49.7 1.0 C8 I:DG134 3.5 56.7 1.0 C5 I:DG134 3.6 54.3 1.0 O6 I:DG134 3.8 54.4 1.0 C6 I:DG134 4.1 54.4 1.0 C8 I:DA133 4.2 56.0 1.0 N7 I:DA133 4.3 54.2 1.0 O6 I:DG135 4.3 61.2 1.0 N9 I:DG134 4.7 58.7 1.0 C4 I:DG134 4.8 56.6 1.0 OP2 I:DA133 4.8 52.1 1.0

Manganese binding site 2 out of 15 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 Manganese with other atoms in the Mn 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 I:Mn463 b:73.3 occ:1.00 N7 I:DG121 2.4 58.1 1.0 O I:HOH513 3.1 39.1 1.0 C5 I:DG121 3.3 58.0 1.0 C8 I:DG121 3.3 58.5 1.0 O6 I:DG121 3.5 62.5 1.0 C6 I:DG121 3.7 59.7 1.0 O6 I:DG122 4.4 60.6 1.0 C4 I:DG121 4.5 55.5 1.0 N9 I:DG121 4.5 60.8 1.0 C2' I:DT120 4.6 65.7 1.0 OP2 I:DG121 5.0 62.4 1.0

Manganese binding site 3 out of 15 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 Manganese with other atoms in the Mn 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 I:Mn464 b:72.9 occ:1.00 N7 I:DG70 2.1 39.6 1.0 C8 I:DG70 3.0 49.7 1.0 O6 I:DG71 3.0 42.7 1.0 C5 I:DG70 3.1 42.4 1.0 O6 I:DG70 3.6 42.7 1.0 C6 I:DG70 3.7 43.5 1.0 O J:HOH478 3.8 56.3 1.0 C6 I:DG71 3.9 46.0 1.0 N9 I:DG70 4.2 41.2 1.0 C4 I:DG70 4.3 43.1 1.0 O I:HOH498 4.3 40.9 1.0 N7 I:DG71 4.4 43.8 1.0 C2' I:DC69 4.4 39.6 1.0 C5 I:DG71 4.5 48.1 1.0 N4 J:DC222 4.5 49.4 1.0 C6 I:DC69 4.6 36.7 1.0 C5 I:DC69 4.8 42.1 1.0 N1 I:DC69 4.9 40.2 1.0

Manganese binding site 4 out of 15 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 Manganese with other atoms in the Mn 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 I:Mn465 b:97.7 occ:1.00 N7 I:DG39 2.5 66.1 1.0 O6 I:DG40 2.6 50.4 1.0 O I:HOH514 2.6 51.7 1.0 C8 I:DG39 3.3 65.0 1.0 C6 I:DG40 3.3 46.4 1.0 C5 I:DG39 3.6 65.4 1.0 C5 I:DG40 3.9 48.8 1.0 O6 I:DG39 3.9 60.2 1.0 N7 I:DG40 3.9 47.9 1.0 C6 I:DG39 4.1 62.6 1.0 N4 J:DC253 4.3 81.7 1.0 N1 I:DG40 4.4 49.3 1.0 OP2 I:DG39 4.4 58.9 1.0 N9 I:DG39 4.6 67.5 1.0 C2' I:DT38 4.6 60.5 1.0 C4 I:DG39 4.7 65.9 1.0

Manganese binding site 5 out of 15 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 Manganese with other atoms in the Mn 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 I:Mn466 b:0.5 occ:1.00 O I:HOH488 2.4 49.2 1.0 N7 I:DG137 3.2 71.9 1.0 O6 I:DG138 3.2 39.5 1.0 N7 I:DG138 3.5 53.9 1.0 C8 I:DG137 3.5 75.3 1.0 O J:HOH491 3.8 49.1 1.0 C6 I:DG138 4.0 46.8 1.0 C5 I:DG137 4.1 68.0 1.0 C5 I:DG138 4.1 48.8 1.0 N9 I:DG137 4.4 75.8 1.0 C8 I:DG138 4.6 59.8 1.0 C4 I:DG137 4.8 71.8 1.0 C6 I:DG137 4.8 64.3 1.0 O6 I:DG137 4.9 66.2 1.0 N6 I:DA139 4.9 43.5 1.0 O4 J:DT154 4.9 46.5 1.0

Manganese binding site 6 out of 15 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 Manganese with other atoms in the Mn 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 I:Mn470 b:97.2 occ:1.00 N7 I:DG100 2.4 55.6 1.0 C8 I:DG100 3.3 49.6 1.0 C5 I:DG100 3.5 53.9 1.0 O6 I:DG100 3.7 57.4 1.0 C6 I:DG100 3.9 54.4 1.0 C8 I:DA99 4.0 55.7 1.0 N7 I:DA99 4.2 56.9 1.0 N9 I:DG100 4.5 44.7 1.0 C4 I:DG100 4.6 53.5 1.0 OP2 I:DA99 4.7 60.4 1.0 N9 I:DA99 4.9 52.4 1.0

Manganese binding site 7 out of 15 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 Manganese with other atoms in the Mn 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 I:Mn471 b:0.8 occ:1.00 N7 I:DA1 2.7 86.0 1.0 N6 I:DA1 3.2 87.0 1.0 C5 I:DA1 3.5 89.4 1.0 C6 I:DA1 3.8 87.6 1.0 C8 I:DA1 3.8 91.5 1.0 OP3 I:DA1 4.5 0.8 1.0 C4 I:DA1 4.8 92.0 1.0 CG2 A:THR120 4.9 83.3 1.0 N9 I:DA1 5.0 93.6 1.0

Manganese binding site 8 out of 15 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 Manganese with other atoms in the Mn binding site number 8 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:Mn472 b:0.2 occ:1.00 N7 I:DG18 2.5 62.5 1.0 C8 I:DG18 3.4 61.2 1.0 C5 I:DG18 3.5 63.6 1.0 C8 I:DA17 3.6 77.8 1.0 O6 I:DG18 3.7 67.1 1.0 C2' I:DA17 4.0 77.6 1.0 C6 I:DG18 4.0 64.2 1.0 N9 I:DA17 4.1 73.5 1.0 N7 I:DA17 4.1 79.2 1.0 C1' I:DA17 4.5 75.2 1.0 N9 I:DG18 4.6 61.8 1.0 C4 I:DG18 4.7 61.2 1.0 C5 I:DA17 4.8 74.7 1.0 C4 I:DA17 4.8 73.2 1.0 N6 I:DA19 4.9 72.3 1.0

Manganese binding site 9 out of 15 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 Manganese with other atoms in the Mn binding site number 9 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:Mn473 b:1.0 occ:1.00 N7 I:DA124 3.0 98.5 1.0 N7 I:DG125 3.2 0.8 1.0 C8 I:DA124 3.4 96.1 1.0 O6 I:DG125 3.6 0.3 1.0 C5 I:DA124 4.0 97.5 1.0 C5 I:DG125 4.0 0.2 1.0 C6 I:DG125 4.1 0.1 1.0 C8 I:DG125 4.3 0.6 1.0 N9 I:DA124 4.4 95.8 1.0 N6 I:DA126 4.6 0.5 1.0 C6 I:DA124 4.8 98.4 1.0 C4 I:DA124 4.8 95.2 1.0 N6 I:DA124 4.8 96.5 1.0

Manganese binding site 10 out of 15 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 Manganese with other atoms in the Mn binding site number 10 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:Mn459 b:61.2 occ:1.00 N7 J:DG280 2.3 42.4 1.0 O J:HOH507 2.4 38.6 1.0 O J:HOH500 2.4 43.2 1.0 C8 J:DG280 3.2 45.6 1.0 C5 J:DG280 3.3 44.1 1.0 O6 J:DG280 3.6 48.8 1.0 C6 J:DG280 3.8 44.9 1.0 O6 J:DG281 3.9 77.1 1.0 N7 J:DA279 4.3 52.7 1.0 C8 J:DA279 4.4 52.3 1.0 N9 J:DG280 4.4 52.0 1.0 C4 J:DG280 4.5 45.5 1.0 C6 J:DG281 4.8 75.3 1.0 N4 I:DC12 4.8 33.8 1.0 N7 J:DG281 4.9 78.6 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