Chlorine in PDB 3mgq: Binding of Nickel Ions to the Nucleosome Core Particle

The structure of Binding of Nickel Ions to the Nucleosome Core Particle, PDB code: 3mgq 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)	51.00 / 2.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.129, 109.643, 183.109, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 27.6

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

Nickel

(Ni)

47 atoms

The binding sites of Chlorine atom in the Binding of Nickel Ions to the Nucleosome Core Particle (pdb code 3mgq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Binding of Nickel Ions to the Nucleosome Core Particle, PDB code: 3mgq:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Binding of Nickel Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Binding of Nickel Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl3147 b:67.3 occ:0.71 N A:LYS122 3.2 50.7 1.0 CD A:PRO121 3.3 52.8 1.0 CB A:PRO121 3.6 52.0 1.0 N A:PRO121 3.7 52.7 1.0 CG A:PRO121 3.7 52.3 1.0 CB A:LYS122 3.7 49.8 1.0 CG A:LYS122 3.8 51.7 1.0 C A:PRO121 3.9 51.4 1.0 CA A:LYS122 4.0 50.2 1.0 CA A:PRO121 4.0 51.9 1.0 CB A:MET120 4.0 53.0 1.0 C A:MET120 4.3 52.9 1.0 CD A:LYS122 4.3 51.6 1.0 CE A:LYS122 4.4 55.7 1.0 CA A:MET120 4.7 53.1 1.0 SD A:MET120 4.8 55.9 1.0 CG A:MET120 4.9 53.4 1.0 O A:MET120 5.0 53.5 1.0

Chlorine binding site 2 out of 4 in the Binding of Nickel Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Binding of Nickel Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl3146 b:72.0 occ:1.00 N C:GLY46 3.0 60.9 1.0 CA C:GLY46 3.3 60.4 1.0 N D:SER88 3.4 60.9 1.0 N C:ALA47 3.5 58.7 1.0 CB D:THR87 3.6 61.7 1.0 CA D:THR87 3.7 61.7 1.0 C C:GLY44 3.7 63.7 1.0 CA C:GLY44 3.8 64.1 1.0 N C:ALA45 3.9 63.3 1.0 C C:GLY46 3.9 59.7 1.0 C D:THR87 4.0 61.6 1.0 O C:GLY44 4.1 63.7 1.0 OP1 J:DA38 4.2 97.8 1.0 C C:ALA45 4.2 62.2 1.0 CB D:SER88 4.2 60.6 1.0 CG2 D:THR87 4.3 61.3 1.0 OG D:SER88 4.3 61.0 1.0 CA D:SER88 4.4 60.3 1.0 CA C:ALA45 4.6 62.8 1.0 CA C:ALA47 4.7 57.3 1.0 OG1 D:THR87 4.8 63.5 1.0 CB C:ALA47 4.8 57.5 1.0 N C:GLY44 4.9 65.0 1.0 O D:ILE86 5.0 61.8 1.0

Chlorine binding site 3 out of 4 in the Binding of Nickel Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Binding of Nickel Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl3148 b:65.3 occ:0.68 N E:LYS122 3.0 44.9 1.0 CD E:PRO121 3.3 47.4 1.0 N E:PRO121 3.4 47.0 1.0 CB E:PRO121 3.6 46.1 1.0 CG E:LYS122 3.7 44.5 1.0 CB E:LYS122 3.8 43.9 1.0 CG E:PRO121 3.8 46.2 1.0 CA E:PRO121 3.8 46.5 1.0 C E:PRO121 3.8 46.2 1.0 CB E:MET120 3.9 46.3 1.0 CA E:LYS122 4.0 44.2 1.0 C E:MET120 4.1 46.6 1.0 CE E:MET120 4.1 45.7 1.0 NZ E:LYS122 4.1 51.8 1.0 CA E:MET120 4.5 46.6 1.0 CD E:LYS122 4.7 47.7 1.0 CG E:MET120 4.8 46.4 1.0 O E:MET120 4.8 46.8 1.0

Chlorine binding site 4 out of 4 in the Binding of Nickel Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Binding of Nickel Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl3145 b:78.5 occ:1.00 N G:GLY46 3.0 63.6 1.0 N H:SER88 3.4 60.3 1.0 CA G:GLY46 3.5 62.9 1.0 C G:GLY44 3.5 65.3 1.0 CA H:THR87 3.5 60.4 1.0 CA G:GLY44 3.5 65.4 1.0 N G:ALA47 3.7 62.0 1.0 N G:ALA45 3.8 65.0 1.0 CB H:THR87 3.8 60.3 1.0 C H:THR87 3.9 60.6 1.0 O G:GLY44 3.9 65.5 1.0 C G:GLY46 4.1 62.8 1.0 C G:ALA45 4.1 64.4 1.0 OP1 I:DA38 4.2 0.4 1.0 CG2 H:THR87 4.4 58.7 1.0 CA G:ALA45 4.5 64.4 1.0 CB H:SER88 4.5 60.2 1.0 CA H:SER88 4.5 60.3 1.0 N G:GLY44 4.5 65.9 1.0 O H:ILE86 4.6 60.8 1.0 OG H:SER88 4.7 61.9 1.0 CA G:ALA47 4.8 61.2 1.0 CB G:ALA47 4.8 61.0 1.0 N H:THR87 4.8 60.6 1.0 O H:THR87 5.0 61.4 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