Chlorine in PDB 5y0d: Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant

The structure of Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant, PDB code: 5y0d was solved by H.Kurumizaka, Y.Arimura, R.Fujita, M.Noda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.58 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.992, 107.316, 167.719, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 25.2

The structure of Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant also contains other interesting chemical elements:

Manganese

(Mn)

10 atoms

The binding sites of Chlorine atom in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant (pdb code 5y0d). 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 Human Nucleosome Containing the H2B E76K Mutant, PDB code: 5y0d:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant


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 Human Nucleosome Containing the H2B E76K Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:41.4 occ:1.00 N A:LYS122 3.3 28.5 1.0 CD A:PRO121 3.6 27.1 1.0 CB A:LYS122 3.6 27.2 1.0 CG A:LYS122 3.7 28.4 1.0 N A:PRO121 3.8 28.4 1.0 CB A:PRO121 3.9 32.6 1.0 CB A:MET120 3.9 26.7 1.0 CD A:LYS122 4.0 29.9 1.0 CG A:PRO121 4.0 30.7 1.0 CA A:LYS122 4.1 33.3 1.0 C A:PRO121 4.2 33.4 1.0 CA A:PRO121 4.2 29.8 1.0 C A:MET120 4.5 30.8 1.0 CE A:LYS122 4.5 40.4 1.0 CA A:MET120 4.7 26.0 1.0 SD A:MET120 4.8 40.0 1.0 CG A:MET120 4.8 30.9 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant


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 Human Nucleosome Containing the H2B E76K Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl2001 b:32.5 occ:1.00 N C:GLY46 3.1 28.5 1.0 N D:SER91 3.2 25.2 1.0 CA C:GLY46 3.5 28.1 1.0 CB D:THR90 3.6 26.1 1.0 C C:GLY44 3.6 32.0 1.0 CA C:GLY44 3.6 31.0 1.0 CA D:THR90 3.7 24.6 1.0 N C:ALA47 3.7 26.8 1.0 N C:ALA45 3.7 38.8 1.0 C D:THR90 3.9 28.6 1.0 C C:GLY46 3.9 29.6 1.0 OP1 J:DT258 4.1 40.5 1.0 OG D:SER91 4.1 33.9 1.0 O C:GLY44 4.1 27.5 1.0 CB D:SER91 4.1 26.7 1.0 C C:ALA45 4.2 32.7 1.0 CA D:SER91 4.2 27.5 1.0 CG2 D:THR90 4.4 26.1 1.0 CA C:ALA45 4.5 36.2 1.0 OG1 D:THR90 4.6 24.9 1.0 CA C:ALA47 4.7 26.9 1.0 N C:GLY44 4.7 28.4 1.0 CB C:ALA47 4.8 27.2 1.0 OP2 J:DT258 4.9 39.8 1.0 O C:GLY46 5.0 29.1 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant


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 Human Nucleosome Containing the H2B E76K Mutant within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl201 b:39.9 occ:1.00 N E:LYS122 3.1 26.7 1.0 CD E:PRO121 3.6 21.8 1.0 N E:PRO121 3.6 22.2 1.0 CB E:PRO121 3.7 30.4 1.0 CG E:LYS122 3.7 27.4 1.0 CB E:LYS122 3.8 24.9 1.0 CB E:MET120 3.9 25.4 1.0 CA E:PRO121 4.0 25.9 1.0 C E:PRO121 4.0 27.5 1.0 CG E:PRO121 4.0 24.6 1.0 CA E:LYS122 4.0 24.1 1.0 CD E:LYS122 4.1 30.8 1.0 C E:MET120 4.3 22.7 1.0 CE E:LYS122 4.6 32.9 1.0 CA E:MET120 4.7 22.2 1.0 SD E:MET120 4.8 33.3 1.0 CG E:MET120 4.8 26.8 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant


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 Human Nucleosome Containing the H2B E76K Mutant within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl201 b:30.5 occ:1.00 N G:GLY46 3.1 27.4 1.0 N H:SER91 3.3 23.7 1.0 CA G:GLY46 3.5 28.9 1.0 O H:HOH218 3.5 38.8 1.0 CB H:THR90 3.6 25.9 1.0 N G:ALA47 3.7 28.3 1.0 CA H:THR90 3.7 25.7 1.0 C G:GLY44 3.8 30.0 1.0 OG H:SER91 3.8 32.0 1.0 CA G:GLY44 3.9 29.9 1.0 N G:ALA45 3.9 29.2 1.0 C G:GLY46 3.9 25.1 1.0 C H:THR90 4.0 24.1 1.0 CB H:SER91 4.1 30.0 1.0 OP1 I:DA111 4.1 51.5 1.0 O G:GLY44 4.2 30.2 1.0 C G:ALA45 4.3 30.4 1.0 CA H:SER91 4.3 26.0 1.0 CG2 H:THR90 4.3 26.1 1.0 CA G:ALA45 4.6 31.4 1.0 OG1 H:THR90 4.7 27.1 1.0 CA G:ALA47 4.7 24.7 1.0 CB G:ALA47 4.9 25.1 1.0 N G:GLY44 4.9 26.6 1.0 O G:GLY46 5.0 29.3 1.0

Y.Arimura, M.Ikura, R.Fujita, M.Noda, W.Kobayashi, N.Horikoshi, J.Sun, L.Shi, M.Kusakabe, M.Harata, Y.Ohkawa, S.Tashiro, H.Kimura, T.Ikura, H.Kurumizaka. Cancer-Associated Mutations of Histones H2B, H3.1 and H2A.Z.1 Affect the Structure and Stability of the Nucleosome. Nucleic Acids Res. V. 46 10007 2018.
ISSN: ESSN 1362-4962
PubMed: 30053102
DOI: 10.1093/NAR/GKY661