Manganese in PDB 1kx4: X-Ray Structure of the Nucleosome Core Particle, NCP146B, at 2.6 A Resolution

The structure of X-Ray Structure of the Nucleosome Core Particle, NCP146B, at 2.6 A Resolution, PDB code: 1kx4 was solved by C.A.Davey, D.F.Sargent, K.Luger, A.W.Maeder, T.J.Richmond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.300, 175.690, 109.530, 90.00, 90.00, 90.00
R / Rfree (%)	24.6 / 30

The structure of X-Ray Structure of the Nucleosome Core Particle, NCP146B, at 2.6 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Manganese atom in the X-Ray Structure of the Nucleosome Core Particle, NCP146B, at 2.6 A Resolution (pdb code 1kx4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the X-Ray Structure of the Nucleosome Core Particle, NCP146B, at 2.6 A Resolution, PDB code: 1kx4:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the X-Ray Structure of the Nucleosome Core Particle, NCP146B, at 2.6 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, NCP146B, at 2.6 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn436 b:72.0 occ:1.00 N7 I:DG-53 2.4 68.9 1.0 C8 I:DG-53 3.3 67.5 1.0 C5 I:DG-53 3.4 69.0 1.0 O6 I:DG-53 3.6 69.4 1.0 C6 I:DG-53 3.8 69.4 1.0 N9 I:DG-53 4.5 66.7 1.0 C4 I:DG-53 4.6 68.2 1.0 OP2 I:DC-54 4.6 53.7 1.0 C6 I:DC-54 4.6 47.4 1.0 O6 I:DG-52 4.7 71.8 1.0 C5 I:DC-54 4.8 48.1 1.0

Manganese binding site 2 out of 6 in the X-Ray Structure of the Nucleosome Core Particle, NCP146B, at 2.6 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, NCP146B, at 2.6 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn437 b:85.4 occ:1.00 O6 I:DG69 2.8 76.3 1.0 N7 I:DG68 3.6 78.8 1.0 C6 I:DG69 3.7 74.2 1.0 N7 I:DG69 3.7 73.5 1.0 C5 I:DG69 4.0 73.2 1.0 N4 J:DC-69 4.2 72.6 1.0 C8 I:DG68 4.4 78.7 1.0 O6 I:DG68 4.5 74.6 1.0 C5 I:DG68 4.5 77.7 1.0 C6 I:DG68 4.8 76.6 1.0 N1 I:DG69 4.9 74.8 1.0 C8 I:DG69 5.0 73.2 1.0

Manganese binding site 3 out of 6 in the X-Ray Structure of the Nucleosome Core Particle, NCP146B, at 2.6 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, NCP146B, at 2.6 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn438 b:74.2 occ:1.00 N7 I:DG27 2.7 55.2 1.0 C8 I:DG27 3.5 53.5 1.0 C5 I:DG27 3.9 56.2 1.0 O6 I:DG27 4.3 58.8 1.0 C6 I:DG27 4.5 57.1 1.0 OP2 I:DC26 4.6 64.8 1.0 N9 I:DG27 4.8 53.4 1.0 C6 I:DC26 4.8 56.7 1.0 C5 I:DC26 4.9 57.0 1.0 C4 I:DG27 5.0 54.8 1.0

Manganese binding site 4 out of 6 in the X-Ray Structure of the Nucleosome Core Particle, NCP146B, at 2.6 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, NCP146B, at 2.6 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn439 b:82.1 occ:1.00 N7 I:DG-14 2.7 39.3 1.0 O I:HOH452 3.3 60.4 1.0 C8 I:DG-14 3.4 37.7 1.0 C5 I:DG-14 3.8 41.0 1.0 O6 I:DG-14 4.2 41.9 1.0 C6 I:DG-14 4.4 41.2 1.0 C8 I:DG-15 4.7 44.4 1.0 N9 I:DG-14 4.7 38.9 1.0 C2' I:DG-15 4.8 49.0 1.0 O I:HOH471 4.9 37.0 1.0 C4 I:DG-14 4.9 39.8 1.0

Manganese binding site 5 out of 6 in the X-Ray Structure of the Nucleosome Core Particle, NCP146B, at 2.6 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, NCP146B, at 2.6 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn435 b:77.4 occ:1.00 OP2 J:DT66 3.7 61.7 1.0 OP1 J:DT65 4.8 65.2 1.0 C3' J:DT65 4.8 61.4 1.0 C2' J:DT65 5.0 60.0 1.0

Manganese binding site 6 out of 6 in the X-Ray Structure of the Nucleosome Core Particle, NCP146B, at 2.6 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, NCP146B, at 2.6 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn434 b:24.0 occ:1.00 OD1 A:ASP77 2.3 30.4 1.0 O A:HOH457 2.4 24.7 1.0 O A:HOH460 2.5 21.9 1.0 CG A:ASP77 3.4 26.9 1.0 OD2 A:ASP77 3.8 30.2 1.0 OE1 A:GLN76 4.3 30.7 1.0 O A:GLU73 4.4 17.8 1.0 O A:HOH485 4.4 14.0 1.0 O B:LEU22 4.5 27.6 1.0 CB A:ASP77 4.6 20.4 1.0 CA A:ASP77 4.7 24.4 1.0 O A:HOH480 4.7 41.7 1.0 N A:ASP77 4.8 25.0 1.0

C.A.Davey, D.F.Sargent, K.Luger, A.W.Maeder, T.J.Richmond. Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 A Resolution J.Mol.Biol. V. 319 1097 2002.
ISSN: ISSN 0022-2836
PubMed: 12079350
DOI: 10.1016/S0022-2836(02)00386-8