Chlorine in PDB 2cv5: Crystal Structure of Human Nucleosome Core Particle

The structure of Crystal Structure of Human Nucleosome Core Particle, PDB code: 2cv5 was solved by Y.Tsunaka, N.Kajimura, S.Tate, K.Morikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.564, 108.370, 169.425, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 27.7

The structure of Crystal Structure of Human Nucleosome Core Particle also contains other interesting chemical elements:

Manganese

(Mn)

9 atoms

The binding sites of Chlorine atom in the Crystal Structure of Human Nucleosome Core Particle (pdb code 2cv5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human Nucleosome Core Particle, PDB code: 2cv5:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Human 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 Crystal Structure of Human Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2004 b:44.6 occ:1.00 N A:LYS122 3.4 27.5 1.0 CB A:LYS122 3.4 25.5 1.0 CD A:PRO121 3.6 27.3 1.0 CB A:MET120 3.8 26.0 1.0 N A:PRO121 3.9 27.4 1.0 CB A:PRO121 4.0 27.2 1.0 CA A:LYS122 4.0 26.8 1.0 CG A:PRO121 4.2 26.3 1.0 CE A:LYS122 4.2 36.1 1.0 C A:PRO121 4.3 27.3 1.0 CA A:PRO121 4.4 27.6 1.0 C A:MET120 4.4 27.0 1.0 CG A:LYS122 4.6 31.5 1.0 CD A:LYS122 4.6 32.7 1.0 NZ A:LYS122 4.7 37.3 1.0 CA A:MET120 4.7 26.7 1.0 CD1 B:LEU49 4.8 32.6 1.0 CG A:MET120 4.9 27.6 1.0 SD A:MET120 5.0 34.4 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Human 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 Crystal Structure of Human Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl2001 b:34.5 occ:1.00 N C:GLY46 3.2 19.7 1.0 N D:SER88 3.3 22.1 1.0 CA C:GLY46 3.6 19.1 1.0 CB D:THR87 3.6 23.4 1.0 N C:ALA47 3.6 19.4 1.0 CA D:THR87 3.7 22.8 1.0 OP1 J:DT258 3.8 50.5 1.0 CA C:GLY44 3.8 25.1 1.0 C C:GLY44 3.9 25.8 1.0 N C:ALA45 3.9 24.0 1.0 OG D:SER88 4.0 29.9 1.0 C D:THR87 4.0 23.1 1.0 C C:GLY46 4.0 19.8 1.0 CB D:SER88 4.0 23.6 1.0 CG2 D:THR87 4.2 21.6 1.0 CA D:SER88 4.2 22.1 1.0 C C:ALA45 4.3 21.2 1.0 O C:GLY44 4.4 25.3 1.0 CA C:ALA45 4.7 22.9 1.0 CA C:ALA47 4.7 18.9 1.0 OG1 D:THR87 4.8 23.3 1.0 CB C:ALA47 4.8 21.1 1.0 N C:GLY44 4.9 26.2 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Human 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 Crystal Structure of Human Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl2003 b:42.7 occ:1.00 CG E:LYS122 3.2 34.1 1.0 CD E:PRO121 3.3 22.0 1.0 N E:LYS122 3.5 22.6 1.0 CB E:PRO121 3.7 22.9 1.0 N E:PRO121 3.8 22.6 1.0 CB E:MET120 3.8 25.0 1.0 CG E:PRO121 3.9 21.4 1.0 CD E:LYS122 3.9 38.3 1.0 CE E:LYS122 4.0 38.0 1.0 CB E:LYS122 4.0 26.3 1.0 CA E:PRO121 4.1 22.7 1.0 C E:PRO121 4.3 22.3 1.0 C E:MET120 4.3 23.0 1.0 CA E:LYS122 4.3 26.0 1.0 CA E:MET120 4.6 23.8 1.0 NZ E:LYS122 4.7 40.9 1.0 CG E:MET120 4.7 28.0 1.0 SD E:MET120 4.8 37.3 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Human 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 Crystal Structure of Human Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl2002 b:31.4 occ:1.00 N G:GLY46 3.0 22.9 1.0 N H:SER88 3.3 15.6 1.0 N G:ALA47 3.4 19.7 1.0 CA G:GLY46 3.5 22.1 1.0 CB H:THR87 3.6 17.6 1.0 N G:ALA45 3.6 26.6 1.0 C G:GLY44 3.6 26.4 1.0 CA H:THR87 3.6 18.0 1.0 CA G:GLY44 3.6 25.1 1.0 C G:GLY46 3.8 20.5 1.0 C H:THR87 3.9 16.6 1.0 C G:ALA45 4.0 24.2 1.0 OG H:SER88 4.0 20.6 1.0 OP1 I:DA111 4.1 49.1 1.0 O G:GLY44 4.2 27.2 1.0 CB H:SER88 4.2 17.0 1.0 CG2 H:THR87 4.3 17.1 1.0 CA G:ALA45 4.3 25.5 1.0 CA H:SER88 4.3 15.7 1.0 CA G:ALA47 4.4 18.7 1.0 CB G:ALA47 4.5 19.1 1.0 N G:GLY44 4.6 26.7 1.0 OG1 H:THR87 4.7 19.8 1.0 O G:GLY46 4.9 20.9 1.0 O H:ILE86 5.0 21.3 1.0 N H:THR87 5.0 17.7 1.0

Y.Tsunaka, N.Kajimura, S.Tate, K.Morikawa. Alteration of the Nucleosomal Dna Path in the Crystal Structure of A Human Nucleosome Core Particle Nucleic Acids Res. V. 33 3424 2005.
ISSN: ISSN 0305-1048
PubMed: 15951514
DOI: 10.1093/NAR/GKI663