Chlorine in PDB 5gsu: Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B

The structure of Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B, PDB code: 5gsu was solved by T.Kumarevel, P.Sivaraman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.33 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	107.095, 109.740, 182.445, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 25.7

The structure of Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B also contains other interesting chemical elements:

Manganese

(Mn)

15 atoms

The binding sites of Chlorine atom in the Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B (pdb code 5gsu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B, PDB code: 5gsu:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B


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 Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl201 b:79.1 occ:1.00 N G:GLY48 2.9 68.0 1.0 N G:ALA47 3.2 79.4 1.0 C G:GLY46 3.5 77.2 1.0 N H:SER89 3.6 67.2 1.0 CA G:GLY48 3.6 71.3 1.0 CA G:GLY46 3.6 79.9 1.0 N G:ALA49 3.7 71.3 1.0 OP1 I:DA111 3.7 92.8 1.0 CB H:SER88 3.8 30.0 1.0 CA H:SER88 3.8 67.5 1.0 C G:ALA47 3.9 75.2 1.0 CA G:ALA47 4.0 75.3 1.0 C G:GLY48 4.1 75.9 1.0 OG H:SER89 4.1 75.9 1.0 C H:SER88 4.2 67.2 1.0 O G:GLY46 4.3 75.9 1.0 CB G:ALA47 4.4 74.6 1.0 CB H:SER89 4.5 69.2 1.0 CA H:SER89 4.6 70.2 1.0 CA G:ALA49 4.8 64.2 1.0 CB G:ALA49 4.8 67.5 1.0 N G:GLY46 4.9 73.7 1.0 O H:ILE87 4.9 75.5 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B


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 Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B within 5.0Å range: probe atom residue distance (Å) B Occ I:Cl209 b:98.4 occ:1.00 C7 I:DT120 3.2 0.9 1.0 OP2 I:DT120 3.2 0.1 1.0 MN I:MN206 3.5 0.3 1.0 C5 I:DT120 4.2 1.0 1.0 C6 I:DT120 4.3 0.6 1.0 P I:DT120 4.5 0.7 1.0 O6 I:DG121 4.9 0.7 1.0 C2' I:DT119 4.9 0.1 1.0 OP1 I:DT120 5.0 0.4 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B


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 Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B within 5.0Å range: probe atom residue distance (Å) B Occ J:Cl306 b:96.9 occ:1.00 N7 J:DG268 2.8 0.2 1.0 O6 J:DG268 3.7 0.7 1.0 C5 J:DG268 3.8 0.5 1.0 C8 J:DG268 3.8 0.4 1.0 O4 J:DT269 3.8 0.3 1.0 MN J:MN302 4.1 0.3 1.0 C6 J:DG268 4.1 0.9 1.0 N6 I:DA24 4.3 0.3 1.0 C8 J:DG267 4.5 0.9 1.0 N7 J:DG267 4.7 0.5 1.0 C4 J:DT269 4.8 0.7 1.0 C4 J:DG268 5.0 0.3 1.0 N9 J:DG268 5.0 0.8 1.0

S.Padavattan, V.Thiruselvam, T.Shinagawa, K.Hasegawa, T.Kumasaka, S.Ishii, T.Kumarevel. Structural Analyses of the Nucleosome Complexes with Human Testis-Specific Histone Variants, HTH2A and HTH2B Biophys. Chem. V. 221 41 2017.
ISSN: ISSN 1873-4200
PubMed: 27992841
DOI: 10.1016/J.BPC.2016.11.013