Chlorine in PDB 3a6n: The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T

The structure of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T, PDB code: 3a6n was solved by H.Tachiwana, W.Kagawa, A.Osakabe, K.Koichiro, T.Shiga, H.Kimura, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.476, 109.521, 181.052, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 26.4

The structure of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T also contains other interesting chemical elements:

Manganese

(Mn)

8 atoms

The binding sites of Chlorine atom in the The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T (pdb code 3a6n). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T, PDB code: 3a6n:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:64.6 occ:1.00 N A:LYS122 3.0 38.4 1.0 CD A:PRO121 3.2 38.5 1.0 N A:PRO121 3.3 38.9 1.0 CB A:PRO121 3.4 38.2 1.0 CG A:LYS122 3.7 40.2 1.0 CA A:PRO121 3.7 38.9 1.0 CB A:LYS122 3.7 36.1 1.0 CG A:PRO121 3.8 39.0 1.0 C A:PRO121 3.8 39.4 1.0 CB A:MET120 3.8 40.7 1.0 CA A:LYS122 3.9 37.7 1.0 C A:MET120 4.1 38.6 1.0 CD A:LYS122 4.2 41.2 1.0 CA A:MET120 4.5 38.5 1.0 CG A:MET120 4.7 45.9 1.0 CE A:LYS122 4.8 43.8 1.0 O A:MET120 4.9 37.9 1.0 O A:PRO121 4.9 41.0 1.0 CD1 B:LEU49 5.0 42.1 1.0

Chlorine binding site 2 out of 4 in the The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl2001 b:48.6 occ:1.00 N D:SER91 3.1 40.6 1.0 N C:GLY46 3.2 43.1 1.0 CA C:GLY46 3.5 42.7 1.0 CB D:THR90 3.6 41.8 1.0 N C:ALA47 3.6 40.0 1.0 CA D:THR90 3.6 41.2 1.0 OG D:SER91 3.6 40.7 1.0 C D:THR90 3.8 41.0 1.0 CB D:SER91 3.9 39.7 1.0 C C:GLY46 3.9 42.8 1.0 OP1 J:DT258 4.0 84.6 1.0 CA C:GLY44 4.1 47.9 1.0 CA D:SER91 4.1 40.5 1.0 C C:GLY44 4.1 47.4 1.0 N C:ALA45 4.1 46.9 1.0 CG2 D:THR90 4.3 40.1 1.0 C C:ALA45 4.4 46.0 1.0 O C:GLY44 4.6 47.4 1.0 CA C:ALA47 4.7 36.6 1.0 OG1 D:THR90 4.7 40.8 1.0 CA C:ALA45 4.8 46.9 1.0 CB C:ALA47 4.9 36.5 1.0 O C:GLY46 4.9 43.9 1.0 N D:THR90 5.0 39.5 1.0

Chlorine binding site 3 out of 4 in the The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl201 b:57.8 occ:1.00 CB E:LYS122 3.2 37.1 1.0 N E:LYS122 3.2 35.0 1.0 CA E:LYS122 3.7 36.0 1.0 NZ E:LYS122 3.8 46.8 1.0 CD E:PRO121 3.9 37.0 1.0 CB E:MET120 4.0 40.6 1.0 N E:PRO121 4.1 37.1 1.0 CB E:PRO121 4.1 34.8 1.0 CG E:LYS122 4.3 39.7 1.0 C E:PRO121 4.3 36.0 1.0 CA E:PRO121 4.4 37.0 1.0 CG E:PRO121 4.5 35.3 1.0 CE E:LYS122 4.5 43.6 1.0 C E:MET120 4.6 36.3 1.0 SD E:MET120 4.7 52.8 1.0 CG E:MET120 4.7 45.6 1.0 CA E:MET120 4.9 37.1 1.0 CD E:LYS122 5.0 44.2 1.0

Chlorine binding site 4 out of 4 in the The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl201 b:45.8 occ:1.00 N G:GLY46 3.2 45.6 1.0 N H:SER91 3.4 44.4 1.0 CA G:GLY44 3.4 47.9 1.0 CA H:THR90 3.5 43.1 1.0 CB H:THR90 3.6 42.8 1.0 C G:GLY44 3.6 47.9 1.0 N G:ALA45 3.6 47.4 1.0 N G:ALA47 3.7 44.4 1.0 CA G:GLY46 3.8 45.3 1.0 C H:THR90 4.0 44.0 1.0 OG H:SER91 4.0 49.6 1.0 OP1 I:DA111 4.1 87.3 1.0 C G:GLY46 4.1 46.1 1.0 CG2 H:THR90 4.2 40.1 1.0 O G:GLY44 4.3 48.9 1.0 C G:ALA45 4.3 46.2 1.0 CB H:SER91 4.4 47.2 1.0 CA H:SER91 4.5 46.5 1.0 CA G:ALA45 4.5 46.5 1.0 N G:GLY44 4.6 48.9 1.0 CA G:ALA47 4.6 43.0 1.0 CB G:ALA47 4.7 43.3 1.0 OG1 H:THR90 4.7 44.5 1.0 O H:ILE89 4.8 38.2 1.0 N H:THR90 4.8 41.1 1.0

H.Tachiwana, W.Kagawa, A.Osakabe, K.Kawaguchi, T.Shiga, Y.Hayashi-Takanaka, H.Kimura, H.Kurumizaka. Structural Basis of Instability of the Nucleosome Containing A Testis-Specific Histone Variant, Human H3T Proc.Natl.Acad.Sci.Usa V. 107 10454 2010.
ISSN: ISSN 0027-8424
PubMed: 20498094
DOI: 10.1073/PNAS.1003064107