Chlorine in PDB 5jrg: Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf)

The structure of Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf), PDB code: 5jrg was solved by A.Osakabe, Y.Arimura, N.Horikoshi, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.15 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.491, 108.773, 169.571, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.5

The structure of Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf) also contains other interesting chemical elements:

Manganese

(Mn)

15 atoms

The binding sites of Chlorine atom in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf) (pdb code 5jrg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf), PDB code: 5jrg:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf)


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 the Nucleosome Containing the Dna with Tetrahydrofuran (Thf) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:47.7 occ:1.00 CE A:LYS122 3.1 42.1 1.0 N A:LYS122 3.3 29.7 1.0 CD A:PRO121 3.4 28.0 1.0 CB A:PRO121 3.6 29.4 1.0 CB A:LYS122 3.7 27.5 1.0 N A:PRO121 3.7 31.2 1.0 CG A:PRO121 3.8 29.3 1.0 CB A:MET120 3.9 30.5 1.0 CG A:LYS122 3.9 31.0 1.0 CA A:PRO121 4.1 31.3 1.0 CA A:LYS122 4.1 29.4 1.0 NZ A:LYS122 4.1 52.5 1.0 CD A:LYS122 4.1 37.8 1.0 C A:PRO121 4.2 34.6 1.0 C A:MET120 4.4 33.7 1.0 CA A:MET120 4.7 30.2 1.0 SD A:MET120 4.7 49.6 1.0 CG A:MET120 4.9 30.4 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf)


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 the Nucleosome Containing the Dna with Tetrahydrofuran (Thf) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:35.4 occ:1.00 N C:GLY46 3.0 27.6 1.0 N D:SER91 3.1 25.5 1.0 CA C:GLY46 3.2 23.7 1.0 N C:ALA47 3.4 23.7 1.0 CB D:THR90 3.6 29.1 1.0 CA D:THR90 3.6 27.6 1.0 C C:GLY46 3.6 25.9 1.0 C C:GLY44 3.8 29.4 1.0 CA C:GLY44 3.8 27.3 1.0 C D:THR90 3.8 27.4 1.0 OG D:SER91 3.8 28.7 1.0 CB D:SER91 3.9 21.4 1.0 N C:ALA45 3.9 31.8 1.0 CA D:SER91 4.1 24.0 1.0 C C:ALA45 4.2 28.8 1.0 CG2 D:THR90 4.3 29.5 1.0 O C:GLY44 4.3 28.3 1.0 OP1 J:DA110 4.5 42.7 1.0 CA C:ALA47 4.5 24.3 1.0 CA C:ALA45 4.7 28.8 1.0 O C:GLY46 4.7 30.6 1.0 OG1 D:THR90 4.7 29.2 1.0 CB C:ALA47 4.7 21.7 1.0 N C:GLY44 4.8 32.6 1.0 O D:THR90 5.0 26.9 1.0 O D:ILE89 5.0 26.2 1.0 N D:THR90 5.0 24.7 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf)


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 the Nucleosome Containing the Dna with Tetrahydrofuran (Thf) within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl3002 b:43.7 occ:1.00 CE E:LYS122 3.2 33.5 1.0 N E:LYS122 3.3 25.6 1.0 CB E:LYS122 3.6 25.7 1.0 CD E:PRO121 3.6 27.4 1.0 CG E:LYS122 3.9 30.6 1.0 N E:PRO121 3.9 25.5 1.0 CB E:MET120 4.0 26.6 1.0 CB E:PRO121 4.0 28.4 1.0 CA E:LYS122 4.1 29.4 1.0 CD E:LYS122 4.1 31.5 1.0 CG E:PRO121 4.2 24.3 1.0 C E:PRO121 4.3 27.3 1.0 CA E:PRO121 4.3 27.2 1.0 NZ E:LYS122 4.3 37.5 1.0 C E:MET120 4.5 23.7 1.0 SD E:MET120 4.8 38.2 1.0 CA E:MET120 4.8 25.2 1.0 CG E:MET120 5.0 22.6 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf)


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 the Nucleosome Containing the Dna with Tetrahydrofuran (Thf) within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl2001 b:30.6 occ:1.00 O I:HOH337 2.8 32.3 1.0 N G:GLY46 3.0 22.2 1.0 N H:SER91 3.3 20.6 1.0 N G:ALA47 3.5 23.8 1.0 CA G:GLY46 3.5 20.2 1.0 C G:GLY44 3.5 26.5 1.0 CA G:GLY44 3.6 26.6 1.0 N G:ALA45 3.6 29.8 1.0 CB H:THR90 3.7 20.5 1.0 CA H:THR90 3.7 20.0 1.0 C G:GLY46 3.9 23.8 1.0 C H:THR90 4.0 21.8 1.0 O G:GLY44 4.0 27.3 1.0 OG H:SER91 4.1 25.0 1.0 C G:ALA45 4.1 25.4 1.0 CB H:SER91 4.2 23.1 1.0 CG2 H:THR90 4.3 19.4 1.0 CA H:SER91 4.4 23.6 1.0 CA G:ALA45 4.4 25.7 1.0 CA G:ALA47 4.5 21.8 1.0 CB G:ALA47 4.6 17.7 1.0 OP2 I:DA110 4.6 37.2 1.0 OP1 I:DA110 4.6 30.0 1.0 N G:GLY44 4.6 28.4 1.0 OG1 H:THR90 4.8 26.4 1.0 O H:ILE89 4.9 22.4 1.0

A.Osakabe, Y.Arimura, S.Matsumoto, N.Horikoshi, K.Sugasawa, H.Kurumizaka. Polymorphism of Apyrimidinic Dna Structures in the Nucleosome Sci Rep V. 7 41783 2017.
ISSN: ESSN 2045-2322
PubMed: 28139742
DOI: 10.1038/SREP41783