Chlorine in PDB 6jr1: Crystal Structure of the Human Nucleosome Phased with 16 Selenium Atoms

The structure of Crystal Structure of the Human Nucleosome Phased with 16 Selenium Atoms, PDB code: 6jr1 was solved by M.Saotome, N.Horikoshi, K.Urano, T.Kujirai, H.Yuzurihara, H.Kurumizaka, W.Kagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.74 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.461, 108.539, 170.462, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24.3

The structure of Crystal Structure of the Human Nucleosome Phased with 16 Selenium Atoms also contains other interesting chemical elements:

Manganese

(Mn)

8 atoms

The binding sites of Chlorine atom in the Crystal Structure of the Human Nucleosome Phased with 16 Selenium Atoms (pdb code 6jr1). 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 the Human Nucleosome Phased with 16 Selenium Atoms, PDB code: 6jr1:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of the Human Nucleosome Phased with 16 Selenium Atoms


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 the Human Nucleosome Phased with 16 Selenium Atoms within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:49.7 occ:1.00 N A:LYS122 3.2 27.0 1.0 CD A:PRO121 3.5 25.9 1.0 CB A:LYS122 3.6 29.7 1.0 N A:PRO121 3.7 30.6 1.0 CG A:LYS122 3.8 30.1 1.0 CE A:LYS122 3.8 49.0 1.0 CB A:PRO121 3.8 35.0 1.0 CB A:MSE120 3.8 23.7 1.0 CA A:LYS122 4.0 31.9 1.0 CG A:PRO121 4.0 35.2 1.0 C A:PRO121 4.1 32.0 1.0 CA A:PRO121 4.1 26.1 1.0 CE A:MSE120 4.3 60.1 1.0 C A:MSE120 4.3 34.9 1.0 CD A:LYS122 4.4 39.4 1.0 CA A:MSE120 4.7 27.9 1.0 SE A:MSE120 4.9 40.6 1.0 CG A:MSE120 4.9 31.0 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of the Human Nucleosome Phased with 16 Selenium Atoms


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 the Human Nucleosome Phased with 16 Selenium Atoms within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:33.5 occ:1.00 O J:HOH430 3.1 41.2 1.0 N D:SER91 3.2 22.9 1.0 N C:GLY46 3.2 27.9 1.0 CB D:THR90 3.5 30.3 1.0 CA D:THR90 3.6 25.3 1.0 CA C:GLY46 3.6 20.9 1.0 N C:ALA47 3.6 25.4 1.0 CA C:GLY44 3.8 31.4 1.0 C C:GLY44 3.9 33.5 1.0 N C:ALA45 3.9 30.9 1.0 C D:THR90 3.9 29.0 1.0 OG D:SER91 3.9 38.3 1.0 C C:GLY46 4.0 26.1 1.0 O D:HOH228 4.1 43.3 1.0 OP1 J:DT258 4.1 52.0 1.0 CB D:SER91 4.1 22.9 1.0 CG2 D:THR90 4.2 18.5 1.0 CA D:SER91 4.3 27.8 1.0 C C:ALA45 4.4 28.9 1.0 O C:GLY44 4.5 32.4 1.0 CA C:ALA47 4.6 21.6 1.0 OG1 D:THR90 4.7 24.3 1.0 CB C:ALA47 4.7 24.9 1.0 CA C:ALA45 4.7 29.2 1.0 N C:GLY44 4.8 29.5 1.0 N D:THR90 4.9 25.2 1.0 O C:GLY46 5.0 25.3 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of the Human Nucleosome Phased with 16 Selenium Atoms


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 the Human Nucleosome Phased with 16 Selenium Atoms within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl202 b:47.3 occ:1.00 N E:LYS122 3.3 27.1 1.0 CD E:PRO121 3.5 24.0 1.0 CG E:LYS122 3.5 32.2 1.0 CB E:LYS122 3.6 29.9 1.0 CD E:LYS122 3.7 44.0 1.0 N E:PRO121 3.7 24.6 1.0 CB E:MSE120 3.8 24.5 1.0 CB E:PRO121 3.9 29.6 1.0 CG E:PRO121 4.0 28.2 1.0 CA E:LYS122 4.1 29.6 1.0 CA E:PRO121 4.1 29.0 1.0 C E:PRO121 4.2 29.4 1.0 CE E:MSE120 4.2 56.8 1.0 C E:MSE120 4.3 27.9 1.0 CA E:MSE120 4.6 29.1 1.0 SE E:MSE120 4.9 36.1 1.0 CG E:MSE120 4.9 29.2 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of the Human Nucleosome Phased with 16 Selenium Atoms


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 the Human Nucleosome Phased with 16 Selenium Atoms within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl201 b:31.5 occ:1.00 N G:GLY46 3.1 25.4 1.0 N H:SER91 3.2 22.6 1.0 O I:HOH340 3.5 47.1 1.0 CA H:THR90 3.5 20.6 1.0 N G:ALA47 3.5 22.0 1.0 CB H:THR90 3.5 26.8 1.0 CA G:GLY46 3.6 29.4 1.0 C G:GLY44 3.7 35.1 1.0 CA G:GLY44 3.7 28.1 1.0 N G:ALA45 3.8 28.4 1.0 C H:THR90 3.9 24.3 1.0 C G:GLY46 3.9 26.8 1.0 OP1 I:DA111 4.0 53.0 1.0 OG H:SER91 4.0 25.2 1.0 CG2 H:THR90 4.1 22.2 1.0 CB H:SER91 4.2 20.0 1.0 O G:GLY44 4.2 32.6 1.0 C G:ALA45 4.2 27.9 1.0 CA H:SER91 4.3 25.1 1.0 CA G:ALA47 4.5 26.9 1.0 CB G:ALA47 4.5 24.0 1.0 CA G:ALA45 4.6 32.2 1.0 N G:GLY44 4.6 27.9 1.0 OG1 H:THR90 4.7 23.8 1.0 O H:ILE89 4.8 24.8 1.0 N H:THR90 4.8 23.1 1.0 O G:GLY46 5.0 29.2 1.0

M.Saotome, N.Horikoshi, K.Urano, T.Kujirai, H.Yuzurihara, H.Kurumizaka, W.Kagawa. Structure Determination of the Nucleosome Core Particle By Selenium Sad Phasing. Acta Crystallogr D Struct V. 75 930 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 31588924
DOI: 10.1107/S2059798319012713