Cobalt in PDB 3mgp: Binding of Cobalt Ions to the Nucleosome Core Particle

The structure of Binding of Cobalt Ions to the Nucleosome Core Particle, PDB code: 3mgp 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)	52.60 / 2.44
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.502, 109.940, 183.352, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 28.2

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

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 43;

Binding sites:

The binding sites of Cobalt atom in the Binding of Cobalt Ions to the Nucleosome Core Particle (pdb code 3mgp). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 43 binding sites of Cobalt where determined in the Binding of Cobalt Ions to the Nucleosome Core Particle, PDB code: 3mgp:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 43 in the Binding of Cobalt Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Binding of Cobalt Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ C:Co120 b:97.2 occ:0.15 OD1 C:ASP90 2.3 53.2 1.0 CG C:ASP90 3.1 49.0 1.0 OD2 C:ASP90 3.2 51.2 1.0 CB C:ASP90 4.6 46.8 1.0 OE2 C:GLU61 4.6 57.1 1.0 CB C:GLU92 5.0 46.6 1.0

Cobalt binding site 2 out of 43 in the Binding of Cobalt Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Binding of Cobalt Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ D:Co123 b:90.0 occ:0.44 OE2 D:GLU102 2.3 57.8 1.0 NE2 D:HIS106 2.5 62.5 1.0 CE1 D:HIS106 3.1 61.4 1.0 CD D:GLU102 3.4 57.4 1.0 CD2 D:HIS106 3.4 60.5 1.0 OE1 D:GLU102 3.9 57.4 1.0 ND1 D:HIS106 4.2 60.2 1.0 CG D:HIS106 4.3 57.1 1.0 CG D:GLU102 4.5 55.8 1.0

Cobalt binding site 3 out of 43 in the Binding of Cobalt Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Binding of Cobalt Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ D:Co124 b:96.0 occ:0.34 NE2 D:HIS79 2.4 68.5 1.0 CD2 D:HIS79 2.9 67.0 1.0 CE1 D:HIS79 3.6 68.4 1.0 CG D:HIS79 4.1 65.2 1.0 ND1 D:HIS79 4.5 67.8 1.0 OE2 H:GLU68 4.5 57.9 1.0

Cobalt binding site 4 out of 43 in the Binding of Cobalt Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Binding of Cobalt Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ E:Co136 b:79.5 occ:1.00 OD1 E:ASP77 2.2 46.6 1.0 CG E:ASP77 3.2 45.8 1.0 OD2 E:ASP77 3.6 45.3 1.0 O F:LEU22 4.0 51.5 1.0 OE1 E:GLN76 4.2 50.1 1.0 CB E:ASP77 4.6 43.6 1.0 O E:GLU73 4.7 42.7 1.0 N E:ASP77 4.7 44.5 1.0 CG E:GLU73 4.8 38.5 1.0 CA E:ASP77 4.8 44.5 1.0 CD E:GLN76 4.9 48.2 1.0 CG E:GLN76 5.0 46.9 1.0

Cobalt binding site 5 out of 43 in the Binding of Cobalt Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Binding of Cobalt Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ H:Co123 b:99.6 occ:0.26 NE2 H:HIS79 2.7 67.9 1.0 CD2 H:HIS79 2.9 65.6 1.0 CE1 H:HIS79 4.0 66.3 1.0 CG H:HIS79 4.3 63.0 1.0 NZ C:LYS36 4.6 68.9 1.0 ND1 H:HIS79 4.7 66.0 1.0 OH F:TYR88 4.8 46.7 1.0

Cobalt binding site 6 out of 43 in the Binding of Cobalt Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Binding of Cobalt Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ H:Co124 b:81.2 occ:0.41 NE2 H:HIS106 1.9 65.0 1.0 CE1 H:HIS106 2.7 64.0 1.0 CD2 H:HIS106 3.0 63.1 1.0 NZ H:LYS105 3.7 66.4 1.0 ND1 H:HIS106 3.9 63.0 1.0 OE2 H:GLU102 4.0 64.2 1.0 CG H:HIS106 4.1 60.2 1.0

Cobalt binding site 7 out of 43 in the Binding of Cobalt Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Binding of Cobalt Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Co74 b:0.5 occ:0.64 N7 I:DG61 2.5 99.7 1.0 C8 I:DG61 3.3 100.0 1.0 C5 I:DG61 3.6 99.9 1.0 O6 I:DG61 3.9 0.0 1.0 N7 I:DA60 4.1 92.4 1.0 C8 I:DA60 4.1 92.6 1.0 C6 I:DG61 4.2 0.1 1.0 O6 I:DG62 4.5 0.5 1.0 N9 I:DG61 4.6 0.3 1.0 C4 I:DG61 4.7 99.9 1.0 N9 I:DA60 5.0 93.1 1.0 C5 I:DA60 5.0 92.8 1.0

Cobalt binding site 8 out of 43 in the Binding of Cobalt Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Binding of Cobalt Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Co75 b:97.3 occ:0.67 N7 I:DG48 1.9 95.8 1.0 C8 I:DG48 2.9 95.7 1.0 C5 I:DG48 3.0 96.0 1.0 O6 I:DG48 3.4 95.8 1.0 C6 I:DG48 3.5 96.0 1.0 C2' I:DT47 3.7 0.0 1.0 N9 I:DG48 4.1 95.7 1.0 C4 I:DG48 4.1 96.0 1.0 OP2 I:DG48 4.3 97.7 1.0 C3' I:DT47 4.6 0.2 1.0 O6 I:DG49 4.6 93.4 1.0 O3' I:DT47 4.7 99.9 1.0 C1' I:DT47 4.8 0.8 1.0 N1 I:DG48 4.9 95.6 1.0

Cobalt binding site 9 out of 43 in the Binding of Cobalt Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Binding of Cobalt Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Co76 b:85.0 occ:0.52 N7 I:DG27 2.1 79.3 1.0 C8 I:DG27 3.1 79.0 1.0 C5 I:DG27 3.1 79.1 1.0 O6 I:DG27 3.3 79.2 1.0 C6 I:DG27 3.6 79.3 1.0 C8 I:DA26 3.8 90.2 1.0 N7 I:DA26 3.8 90.4 1.0 N9 I:DG27 4.3 78.5 1.0 C4 I:DG27 4.3 79.0 1.0 O6 J:DG-28 4.5 0.6 1.0 N9 I:DA26 4.5 89.8 1.0 N4 I:DC28 4.7 81.1 1.0 C5 I:DA26 4.7 90.2 1.0 C2' I:DA26 4.8 88.6 1.0 N1 I:DG27 5.0 79.3 1.0 OP2 I:DA26 5.0 99.0 1.0

Cobalt binding site 10 out of 43 in the Binding of Cobalt Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Binding of Cobalt Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Co77 b:0.8 occ:0.63 N7 I:DG-3 2.3 82.5 1.0 C8 I:DG-3 3.1 82.5 1.0 C5 I:DG-3 3.3 82.7 1.0 O6 I:DG-3 3.8 82.5 1.0 C6 I:DG-3 3.9 82.5 1.0 O6 I:DG-2 4.2 89.1 1.0 N9 I:DG-3 4.3 82.3 1.0 C4 I:DG-3 4.4 82.5 1.0 C2' I:DT-4 4.5 74.6 1.0 C6 I:DT-4 4.7 75.5 1.0 C5 I:DT-4 4.9 76.2 1.0 OP2 I:DG-3 5.0 76.1 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