Chlorine in PDB 5gt0: Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A

The structure of Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A, PDB code: 5gt0 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)	36.80 / 2.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.788, 108.966, 170.951, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 28

The structure of Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A also contains other interesting chemical elements:

Manganese

(Mn)

14 atoms

The binding sites of Chlorine atom in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A (pdb code 5gt0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A, PDB code: 5gt0:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A


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 Complex with Human Testis-Specific Histone Variants, TH2A within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl202 b:37.5 occ:1.00 MN E:MN201 2.2 42.1 1.0 OD1 E:ASP77 2.7 27.1 1.0 CG E:ASP77 4.0 23.3 1.0 CG E:GLN76 4.0 26.4 1.0 CD E:GLN76 4.3 37.7 1.0 OE1 E:GLN76 4.4 35.8 1.0 OD2 E:ASP77 4.6 19.2 1.0 CB E:GLN76 4.6 25.0 1.0 N E:ASP77 4.7 18.7 1.0 C E:GLN76 4.8 23.1 1.0 O E:GLU73 4.8 27.0 1.0 O E:GLN76 4.8 26.1 1.0 CA E:ASP77 4.9 19.0 1.0 NE2 E:GLN76 4.9 53.1 1.0 O F:LEU22 4.9 24.3 1.0

Chlorine binding site 2 out of 6 in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A


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 Complex with Human Testis-Specific Histone Variants, TH2A within 5.0Å range: probe atom residue distance (Å) B Occ I:Cl207 b:57.2 occ:1.00 O6 I:DG68 2.8 64.5 1.0 C6 I:DG68 4.0 58.5 1.0 N4 J:DC225 4.3 64.0 1.0 N7 J:DG224 4.5 67.7 1.0 O6 J:DG224 4.6 62.6 1.0 C5 I:DG68 4.8 54.3 1.0 N7 I:DG68 4.8 56.5 1.0 N7 I:DA67 5.0 56.6 1.0 N1 I:DG68 5.0 58.2 1.0

Chlorine binding site 3 out of 6 in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A


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 Complex with Human Testis-Specific Histone Variants, TH2A within 5.0Å range: probe atom residue distance (Å) B Occ I:Cl208 b:73.4 occ:1.00 O6 I:DG134 2.9 0.2 1.0 MN I:MN202 3.7 77.8 1.0 C6 I:DG134 4.1 97.2 1.0 N6 I:DA133 4.1 0.1 1.0 N7 I:DA133 4.1 0.8 1.0 O6 I:DG135 4.7 93.2 1.0 N4 J:DC158 4.7 96.2 1.0 N7 I:DG134 4.9 94.5 1.0 C5 I:DG134 4.9 94.2 1.0 C5 I:DA133 4.9 0.5 1.0 C6 I:DA133 5.0 0.8 1.0

Chlorine binding site 4 out of 6 in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A


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 Complex with Human Testis-Specific Histone Variants, TH2A within 5.0Å range: probe atom residue distance (Å) B Occ I:Cl209 b:61.3 occ:1.00 O4' J:DA218 4.2 47.1 1.0 C4' J:DA218 4.4 44.6 1.0 N3 I:DA77 4.4 52.7 1.0 C4' I:DG78 4.5 51.0 1.0 N2 J:DG217 4.5 48.8 1.0 C5' I:DG78 4.5 52.9 1.0 O4' I:DG78 4.6 51.9 1.0 C2 I:DA77 4.9 49.9 1.0 C5' J:DA218 4.9 42.3 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A


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 Complex with Human Testis-Specific Histone Variants, TH2A within 5.0Å range: probe atom residue distance (Å) B Occ I:Cl210 b:68.1 occ:1.00 OP1 I:DT136 3.6 85.9 1.0 C5' I:DT136 4.2 96.0 1.0 OP2 I:DG137 4.5 76.3 1.0 C4' I:DT136 4.5 95.6 1.0 P I:DT136 4.6 87.4 1.0 C3' I:DT136 4.8 96.5 1.0 O5' I:DT136 4.8 93.5 1.0

Chlorine binding site 6 out of 6 in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A within 5.0Å range: probe atom residue distance (Å) B Occ J:Cl307 b:37.6 occ:1.00 N7 J:DG217 2.6 38.7 1.0 C8 J:DG217 3.4 38.0 1.0 C5 J:DG217 3.6 40.7 1.0 O6 J:DG217 3.8 49.3 1.0 N6 J:DA218 4.0 49.0 1.0 C6 J:DG217 4.0 46.3 1.0 O J:HOH416 4.3 27.3 1.0 C2' J:DT216 4.4 41.0 1.0 OP2 J:DG217 4.6 37.8 1.0 N9 J:DG217 4.6 38.3 1.0 C4 J:DG217 4.7 41.2 1.0 C6 J:DT216 4.9 39.4 1.0 C6 J:DA218 5.0 43.9 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