Manganese in PDB 3mgr: Binding of Rubidium Ions to the Nucleosome Core Particle

The structure of Binding of Rubidium Ions to the Nucleosome Core Particle, PDB code: 3mgr was solved by K.Mohideen, R.Muhammad, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.462, 109.681, 182.213, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 26.7

The structure of Binding of Rubidium Ions to the Nucleosome Core Particle also contains other interesting chemical elements:

Rubidium	(Rb)	5 atoms
Chlorine	(Cl)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Manganese atom in the Binding of Rubidium Ions to the Nucleosome Core Particle (pdb code 3mgr). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 14 binding sites of Manganese where determined in the Binding of Rubidium Ions to the Nucleosome Core Particle, PDB code: 3mgr:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 14 in the Binding of Rubidium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Binding of Rubidium Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn3132 b:33.6 occ:1.00 OD1 E:ASP77 2.3 31.3 1.0 CG E:ASP77 3.2 32.3 1.0 OD2 E:ASP77 3.5 31.1 1.0 OE1 E:GLN76 4.1 37.1 1.0 O F:LEU22 4.4 34.6 1.0 CB E:ASP77 4.5 33.1 1.0 O E:GLU73 4.5 27.7 1.0 N E:ASP77 4.6 33.3 1.0 CA E:ASP77 4.7 33.8 1.0 CD E:GLN76 4.8 37.3 1.0 CG E:GLN76 4.9 34.8 1.0 CG E:GLU73 4.9 27.8 1.0

Manganese binding site 2 out of 14 in the Binding of Rubidium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Binding of Rubidium Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn3137 b:89.3 occ:1.00 N7 I:DG48 2.4 72.8 1.0 C8 I:DG48 3.3 72.6 1.0 C5 I:DG48 3.4 73.2 1.0 O6 I:DG48 3.6 72.6 1.0 C6 I:DG48 3.9 72.8 1.0 O6 I:DG49 4.0 69.4 1.0 C2' I:DT47 4.2 80.2 1.0 N9 I:DG48 4.5 73.0 1.0 C4 I:DG48 4.6 73.2 1.0 OP2 I:DG48 4.9 73.6 1.0 C6 I:DG49 4.9 70.1 1.0 N7 I:DG49 4.9 70.2 1.0

Manganese binding site 3 out of 14 in the Binding of Rubidium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Binding of Rubidium Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn3138 b:69.5 occ:0.90 N7 I:DG61 2.3 71.9 1.0 C8 I:DG61 3.2 72.3 1.0 C5 I:DG61 3.4 72.1 1.0 O6 I:DG61 3.8 71.6 1.0 C6 I:DG61 4.0 71.8 1.0 C8 I:DA60 4.1 74.5 1.0 N7 I:DA60 4.2 74.2 1.0 O6 I:DG62 4.4 87.0 1.0 N9 I:DG61 4.4 72.4 1.0 C4 I:DG61 4.5 72.4 1.0 N9 I:DA60 4.9 74.7 1.0

Manganese binding site 4 out of 14 in the Binding of Rubidium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Binding of Rubidium Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn3140 b:82.7 occ:0.72 N7 I:DG27 2.4 57.3 1.0 C8 I:DG27 3.3 57.0 1.0 C5 I:DG27 3.5 57.0 1.0 O6 I:DG27 3.7 57.3 1.0 C6 I:DG27 3.9 56.9 1.0 C8 I:DA26 4.0 73.2 1.0 N7 I:DA26 4.2 73.3 1.0 N9 I:DG27 4.6 57.4 1.0 C4 I:DG27 4.6 56.9 1.0 N9 I:DA26 4.8 73.0 1.0 C2' I:DA26 4.9 72.5 1.0 N4 I:DC28 5.0 65.1 1.0

Manganese binding site 5 out of 14 in the Binding of Rubidium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Binding of Rubidium Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn3141 b:80.5 occ:0.63 O6 I:DG5 2.7 60.9 1.0 C6 I:DG5 3.7 61.1 1.0 N4 J:DC-5 3.8 48.9 1.0 O6 J:DG-6 4.1 49.7 1.0 N7 I:DG5 4.2 61.5 1.0 N7 J:DG-6 4.2 50.1 1.0 C5 I:DG5 4.3 60.9 1.0 N7 I:DA4 4.7 61.8 1.0 C6 J:DG-6 4.8 49.1 1.0 C5 J:DG-6 4.8 48.9 1.0 N1 I:DG5 4.9 60.9 1.0

Manganese binding site 6 out of 14 in the Binding of Rubidium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Binding of Rubidium Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn3142 b:82.5 occ:0.64 N7 I:DG-3 2.2 49.4 1.0 C8 I:DG-3 3.1 48.9 1.0 C5 I:DG-3 3.3 48.7 1.0 O6 I:DG-3 3.5 49.4 1.0 O6 I:DG-2 3.7 53.4 1.0 C6 I:DG-3 3.7 48.5 1.0 C2' I:DT-4 4.3 47.5 1.0 N9 I:DG-3 4.3 48.5 1.0 C4 I:DG-3 4.4 49.1 1.0 C6 I:DG-2 4.5 53.5 1.0 N7 I:DG-2 4.7 53.3 1.0 C6 I:DT-4 4.8 47.7 1.0 OP2 I:DG-3 4.8 41.9 1.0 C5 I:DG-2 4.8 53.5 1.0

Manganese binding site 7 out of 14 in the Binding of Rubidium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Binding of Rubidium Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn3143 b:99.9 occ:1.00 N7 I:DG-35 2.4 61.8 1.0 O6 I:DG-34 2.8 58.2 1.0 C8 I:DG-35 3.2 61.6 1.0 C5 I:DG-35 3.6 61.8 1.0 C6 I:DG-34 3.7 58.7 1.0 O6 I:DG-35 3.9 61.8 1.0 N7 I:DG-34 3.9 58.6 1.0 C5 I:DG-34 4.1 58.9 1.0 C6 I:DG-35 4.1 61.7 1.0 C2' I:DT-36 4.3 68.8 1.0 N4 J:DC34 4.4 90.2 1.0 N9 I:DG-35 4.5 61.7 1.0 OP2 I:DG-35 4.6 63.3 1.0 C4 I:DG-35 4.7 61.9 1.0 O3' I:DT-36 4.7 65.7 1.0 N1 I:DG-34 4.9 57.9 1.0 C3' I:DT-36 4.9 68.4 1.0

Manganese binding site 8 out of 14 in the Binding of Rubidium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Binding of Rubidium Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn3131 b:74.3 occ:1.00 N7 J:DG61 2.4 71.8 1.0 C8 J:DG61 3.2 72.3 1.0 C5 J:DG61 3.5 72.0 1.0 O6 J:DG61 3.9 72.1 1.0 C6 J:DG61 4.1 72.3 1.0 C8 J:DA60 4.1 59.2 1.0 N7 J:DA60 4.2 58.3 1.0 O6 J:DG62 4.2 83.6 1.0 N9 J:DG61 4.5 72.6 1.0 C4 J:DG61 4.6 72.2 1.0 N9 J:DA60 5.0 59.1 1.0 OP2 J:DA60 5.0 51.6 1.0

Manganese binding site 9 out of 14 in the Binding of Rubidium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Binding of Rubidium Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn3133 b:68.5 occ:0.97 N7 J:DG27 2.5 62.9 1.0 C8 J:DG27 3.4 62.4 1.0 C5 J:DG27 3.7 62.8 1.0 O6 J:DG27 3.9 62.9 1.0 C6 J:DG27 4.2 63.0 1.0 O6 I:DG-28 4.4 86.0 1.0 C8 J:DA26 4.6 75.9 1.0 N9 J:DG27 4.6 62.6 1.0 N7 J:DA26 4.7 76.1 1.0 C4 J:DG27 4.8 62.4 1.0 C7 I:DT-29 4.8 82.5 1.0 N4 J:DC28 5.0 60.3 1.0

Manganese binding site 10 out of 14 in the Binding of Rubidium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Binding of Rubidium Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn3134 b:71.4 occ:1.00 N7 J:DG-3 2.2 44.9 1.0 C8 J:DG-3 3.1 44.7 1.0 C5 J:DG-3 3.3 45.9 1.0 O6 J:DG-3 3.5 45.8 1.0 C6 J:DG-3 3.8 45.5 1.0 C2' J:DT-4 4.1 42.4 1.0 O6 J:DG-2 4.3 55.7 1.0 N9 J:DG-3 4.4 45.4 1.0 C4 J:DG-3 4.4 45.5 1.0 C6 J:DT-4 4.5 45.8 1.0 C5 J:DT-4 4.9 45.8 1.0 N1 J:DT-4 5.0 45.4 1.0

K.Mohideen, R.Muhammad, C.A.Davey. Perturbations in Nucleosome Structure From Heavy Metal Association. Nucleic Acids Res. V. 38 6301 2010.
ISSN: ISSN 0305-1048
PubMed: 20494975
DOI: 10.1093/NAR/GKQ420