Chlorine in PDB 3x1t: Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA

The structure of Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA, PDB code: 3x1t was solved by P.Sivaraman, T.S.Kumarevel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.96 / 2.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.771, 109.597, 181.597, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 26.6

The structure of Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA also contains other interesting chemical elements:

Manganese

(Mn)

22 atoms

The binding sites of Chlorine atom in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA (pdb code 3x1t). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA, PDB code: 3x1t:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


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 Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ J:Cl308 b:89.0 occ:1.00 N7 J:DG267 3.0 0.5 1.0 O6 J:DG268 3.5 0.2 1.0 C8 J:DG267 3.7 99.9 1.0 OP2 J:DG267 4.0 86.8 1.0 C5 J:DG267 4.1 98.0 1.0 CL J:CL312 4.2 88.6 1.0 O6 J:DG267 4.4 0.2 1.0 C6 J:DG268 4.6 0.9 1.0 C6 J:DG267 4.6 99.6 1.0 N9 J:DG267 5.0 94.2 1.0

Chlorine binding site 2 out of 8 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


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 Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ J:Cl309 b:90.6 occ:1.00 N3 J:DA203 3.7 81.2 1.0 O2 I:DT91 3.9 75.7 1.0 C2 J:DA203 4.0 82.6 1.0 O4' J:DG204 4.2 84.9 1.0 O J:HOH408 4.8 83.9 1.0 C4' J:DG204 4.8 77.7 1.0 C4 J:DA203 5.0 88.7 1.0

Chlorine binding site 3 out of 8 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


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 Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ J:Cl310 b:95.2 occ:1.00 OP2 J:DG246 4.2 0.9 1.0 OP1 J:DG246 4.5 98.4 1.0 P J:DG246 4.7 97.1 1.0 O5' J:DG246 4.8 99.6 1.0

Chlorine binding site 4 out of 8 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


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 Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ J:Cl311 b:93.9 occ:1.00 O2 I:DT38 4.0 1.0 1.0 O4' J:DA257 4.5 98.4 1.0 C4' J:DA257 4.5 95.6 1.0 O4' I:DG39 4.6 98.1 1.0 C5' J:DA257 4.8 97.9 1.0 N3 I:DG39 4.8 0.7 1.0 C2 J:DA255 4.8 0.6 1.0 C4' I:DG39 4.8 97.2 1.0 N3 J:DA256 4.9 0.8 1.0

Chlorine binding site 5 out of 8 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


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 Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ J:Cl312 b:88.6 occ:1.00 N7 J:DG268 2.8 94.7 1.0 O6 J:DG268 2.9 0.2 1.0 C5 J:DG268 3.4 98.4 1.0 C6 J:DG268 3.4 0.9 1.0 O4 J:DT269 3.9 0.0 1.0 C8 J:DG268 3.9 92.8 1.0 N6 I:DA24 4.2 0.9 1.0 CL J:CL308 4.2 89.0 1.0 C4 J:DG268 4.6 91.6 1.0 C8 J:DG267 4.6 99.9 1.0 N1 J:DG268 4.7 98.4 1.0 N7 J:DG267 4.7 0.5 1.0 N9 J:DG268 4.9 87.8 1.0 C4 J:DT269 5.0 99.5 1.0

Chlorine binding site 6 out of 8 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


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 Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:69.5 occ:1.00 O A:HOH305 2.8 42.0 1.0 ND2 B:ASN64 3.9 46.0 1.0 CD1 B:PHE61 4.1 41.6 1.0 OE1 B:GLN93 4.4 53.9 1.0 CE1 B:PHE61 4.5 33.9 1.0 CA B:PHE61 4.9 34.2 1.0 CG B:ASN64 4.9 38.3 1.0 CB B:ASN64 4.9 34.3 1.0 CG B:PHE61 5.0 39.1 1.0

Chlorine binding site 7 out of 8 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl203 b:49.9 occ:1.00 N C:GLY46 3.3 35.6 1.0 N D:SER91 3.4 38.9 1.0 CA D:THR90 3.4 40.6 1.0 CB D:THR90 3.5 40.0 1.0 CA C:GLY44 3.6 44.9 1.0 C C:GLY44 3.6 46.5 1.0 CA C:GLY46 3.7 37.5 1.0 N C:ALA47 3.8 41.0 1.0 N C:ALA45 3.8 41.6 1.0 C D:THR90 3.9 42.0 1.0 OP1 J:DT258 3.9 62.9 1.0 CG2 D:THR90 4.1 36.0 1.0 C C:GLY46 4.2 41.2 1.0 O C:GLY44 4.2 43.5 1.0 OG D:SER91 4.4 40.4 1.0 C C:ALA45 4.4 42.9 1.0 CB D:SER91 4.4 41.2 1.0 CA D:SER91 4.5 36.3 1.0 CA C:ALA45 4.7 40.8 1.0 O D:ILE89 4.7 43.7 1.0 N C:GLY44 4.7 45.0 1.0 OG1 D:THR90 4.7 40.9 1.0 N D:THR90 4.7 41.1 1.0 CA C:ALA47 4.8 36.3 1.0 CB C:ALA47 4.9 41.4 1.0

Chlorine binding site 8 out of 8 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl204 b:77.3 occ:1.00 O D:SER123 4.5 62.7 1.0

S.Padavattan, T.Shinagawa, K.Hasegawa, T.Kumasaka, S.Ishii, T.Kumarevel. Structural and Functional Analyses of Nucleosome Complexes with Mouse Histone Variants TH2A and TH2B, Involved in Reprogramming Biochem.Biophys.Res.Commun. V. 464 929 2015.
ISSN: ISSN 0006-291X
PubMed: 26188507
DOI: 10.1016/J.BBRC.2015.07.070