Chlorine in PDB 5gt3: Crystal Structure of Nucleosome Particle in the Presence of Human Testis-Specific Histone Variant, HTH2B

The structure of Crystal Structure of Nucleosome Particle in the Presence of Human Testis-Specific Histone Variant, HTH2B, PDB code: 5gt3 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)	34.70 / 2.91
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.887, 110.078, 182.811, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25.8

The structure of Crystal Structure of Nucleosome Particle in the Presence of Human Testis-Specific Histone Variant, HTH2B also contains other interesting chemical elements:

Manganese

(Mn)

12 atoms

The binding sites of Chlorine atom in the Crystal Structure of Nucleosome Particle in the Presence of Human Testis-Specific Histone Variant, HTH2B (pdb code 5gt3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Nucleosome Particle in the Presence of Human Testis-Specific Histone Variant, HTH2B, PDB code: 5gt3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Crystal Structure of Nucleosome Particle in the Presence of Human Testis-Specific Histone Variant, HTH2B


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 Particle in the Presence of Human Testis-Specific Histone Variant, HTH2B within 5.0Å range: probe atom residue distance (Å) B Occ I:Cl204 b:91.9 occ:1.00 O6 I:DG121 2.7 0.9 1.0 N7 I:DG121 2.8 0.6 1.0 C6 I:DG121 3.3 0.4 1.0 C5 I:DG121 3.3 0.8 1.0 C6 I:DT120 3.7 0.1 1.0 C7 I:DT120 3.7 0.7 1.0 C5 I:DT120 3.9 0.3 1.0 C8 I:DG121 3.9 0.2 1.0 C2' I:DT120 4.0 99.9 1.0 N1 I:DT120 4.6 0.6 1.0 C4 I:DG121 4.6 0.2 1.0 N1 I:DG121 4.7 0.3 1.0 C4 I:DT120 4.9 0.3 1.0 N9 I:DG121 4.9 0.0 1.0 C1' I:DT120 4.9 0.9 1.0

Chlorine binding site 2 out of 5 in the Crystal Structure of Nucleosome Particle in the Presence of Human Testis-Specific Histone Variant, HTH2B


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 Particle in the Presence of Human Testis-Specific Histone Variant, HTH2B within 5.0Å range: probe atom residue distance (Å) B Occ I:Cl205 b:80.7 occ:1.00 N7 I:DG100 2.7 92.7 1.0 O6 I:DG100 3.1 95.3 1.0 C5 I:DG100 3.5 88.3 1.0 C6 I:DG100 3.6 95.3 1.0 C8 I:DG100 3.8 86.4 1.0 C8 I:DA99 3.9 92.3 1.0 N7 I:DA99 4.0 93.4 1.0 OP2 I:DA99 4.1 86.6 1.0 C4 I:DG100 4.7 82.8 1.0 N9 I:DG100 4.9 83.7 1.0 N9 I:DA99 5.0 86.0 1.0

Chlorine binding site 3 out of 5 in the Crystal Structure of Nucleosome Particle in the Presence of Human Testis-Specific Histone Variant, HTH2B


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 Particle in the Presence of Human Testis-Specific Histone Variant, HTH2B within 5.0Å range: probe atom residue distance (Å) B Occ J:Cl308 b:1.0 occ:1.00 N7 J:DG283 2.8 0.6 1.0 O6 J:DG283 3.0 0.1 1.0 O6 J:DG284 3.3 0.9 1.0 C5 J:DG283 3.4 0.3 1.0 C6 J:DG283 3.5 0.0 1.0 C8 J:DG283 3.9 0.2 1.0 C6 J:DG284 4.4 0.4 1.0 N4 I:DC9 4.6 98.5 1.0 C4 J:DG283 4.6 0.8 1.0 N1 J:DG283 4.8 0.7 1.0 N9 J:DG283 4.9 1.0 1.0

Chlorine binding site 4 out of 5 in the Crystal Structure of Nucleosome Particle in the Presence of Human Testis-Specific Histone Variant, HTH2B


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 Nucleosome Particle in the Presence of Human Testis-Specific Histone Variant, HTH2B within 5.0Å range: probe atom residue distance (Å) B Occ J:Cl309 b:0.8 occ:1.00 N7 J:DG185 2.9 0.1 1.0 O6 J:DG186 2.9 0.2 1.0 OP2 J:DG185 3.1 0.6 1.0 C8 J:DG185 3.4 1.0 1.0 C6 J:DG186 3.9 0.5 1.0 C5 J:DG185 4.2 0.3 1.0 C2' J:DT184 4.4 0.2 1.0 P J:DG185 4.5 0.8 1.0 N1 J:DG186 4.5 0.7 1.0 O6 J:DG185 4.7 0.9 1.0 N9 J:DG185 4.7 0.6 1.0 C5 J:DG186 4.8 0.3 1.0 C6 J:DG185 4.9 0.6 1.0 O3' J:DT184 4.9 0.3 1.0

Chlorine binding site 5 out of 5 in the Crystal Structure of Nucleosome Particle in the Presence of Human Testis-Specific Histone Variant, HTH2B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Nucleosome Particle in the Presence of Human Testis-Specific Histone Variant, HTH2B within 5.0Å range: probe atom residue distance (Å) B Occ J:Cl310 b:0.7 occ:1.00 OP2 J:DA173 2.8 0.1 1.0 C5' J:DA173 3.3 0.3 1.0 P J:DA173 4.0 0.3 1.0 C8 J:DA173 4.1 0.5 1.0 C2' J:DA173 4.1 0.8 1.0 O5' J:DA173 4.1 0.8 1.0 C4' J:DA173 4.3 0.5 1.0 C3' J:DA173 4.3 0.8 1.0 OP1 J:DA173 4.7 0.3 1.0 O4' J:DA173 4.7 0.7 1.0 C1' J:DA173 4.8 0.7 1.0 N9 J:DA173 4.9 0.9 1.0 N7 J:DA173 5.0 0.3 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