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Chlorine in PDB 5x7x: The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution

Protein crystallography data

The structure of The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution, PDB code: 5x7x was solved by Y.Arimura, H.Taguchi, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.60 / 2.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.887, 107.509, 167.415, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 25.6

Other elements in 5x7x:

The structure of The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution also contains other interesting chemical elements:

Manganese (Mn) 13 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution (pdb code 5x7x). 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 Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution, PDB code: 5x7x:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5x7x

Go back to Chlorine Binding Sites List in 5x7x
Chlorine binding site 1 out of 4 in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:30.8
occ:1.00
 O A:HOH327 3.0 35.9 1.0
N A:LYS122 3.3 20.6 1.0
CB A:LYS122 3.4 21.5 1.0
CD A:PRO121 3.7 20.3 1.0
CE A:MET120 3.8 26.6 1.0
CA A:LYS122 3.9 19.1 1.0
N A:PRO121 4.0 17.9 1.0
CB A:PRO121 4.0 19.5 1.0
CB A:MET120 4.0 19.5 1.0
CE A:LYS122 4.1 24.6 1.0
CG A:PRO121 4.2 16.6 1.0
C A:PRO121 4.3 19.6 1.0
CA A:PRO121 4.4 18.4 1.0
C A:MET120 4.6 19.0 1.0
CG A:LYS122 4.7 25.2 1.0
NZ A:LYS122 4.8 30.6 1.0
CD A:LYS122 4.8 25.8 1.0
CA A:MET120 4.9 15.6 1.0
CG A:MET120 5.0 19.2 1.0

Chlorine binding site 2 out of 4 in 5x7x

Go back to Chlorine Binding Sites List in 5x7x
Chlorine binding site 2 out of 4 in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:25.6
occ:1.00
 N C:GLY46 3.1 18.9 1.0
N D:SER91 3.3 19.7 1.0
CA C:GLY46 3.5 18.4 1.0
N C:ALA47 3.6 17.9 1.0
CB D:THR90 3.6 21.5 1.0
OP1 J:DT258 3.7 31.5 1.0
CA C:GLY44 3.7 22.4 1.0
C C:GLY44 3.7 20.5 1.0
CA D:THR90 3.7 19.0 1.0
N C:ALA45 3.8 18.2 1.0
C C:GLY46 3.9 17.9 1.0
OG D:SER91 4.0 26.9 1.0
C D:THR90 4.0 19.3 1.0
CB D:SER91 4.2 22.9 1.0
CG2 D:THR90 4.2 20.5 1.0
C C:ALA45 4.2 17.4 1.0
O C:GLY44 4.3 17.4 1.0
CA D:SER91 4.3 19.7 1.0
CA C:ALA45 4.6 18.5 1.0
CA C:ALA47 4.6 16.6 1.0
O D:HOH203 4.7 22.6 1.0
N C:GLY44 4.7 20.5 1.0
CB C:ALA47 4.7 17.9 1.0
OG1 D:THR90 4.8 23.7 1.0
O C:GLY46 5.0 18.3 1.0

Chlorine binding site 3 out of 4 in 5x7x

Go back to Chlorine Binding Sites List in 5x7x
Chlorine binding site 3 out of 4 in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl201

b:29.6
occ:1.00
 CG E:LYS122 3.2 22.9 1.0
N E:LYS122 3.3 17.1 1.0
CD E:PRO121 3.4 11.9 1.0
CE E:LYS122 3.5 25.7 1.0
CB E:LYS122 3.7 15.8 1.0
N E:PRO121 3.7 13.5 1.0
CD E:LYS122 3.7 23.2 1.0
CB E:MET120 3.7 15.0 1.0
CB E:PRO121 3.8 15.1 1.0
CG E:PRO121 4.0 11.3 1.0
CA E:LYS122 4.0 14.3 1.0
C E:PRO121 4.1 15.0 1.0
CA E:PRO121 4.1 14.8 1.0
C E:MET120 4.3 13.3 1.0
NZ E:LYS122 4.5 25.9 1.0
CA E:MET120 4.6 14.5 1.0
CG E:MET120 4.7 15.2 1.0
SD E:MET120 4.8 24.3 1.0

Chlorine binding site 4 out of 4 in 5x7x

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Chlorine binding site 4 out of 4 in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl2001

b:23.8
occ:1.00
 O I:HOH304 3.1 31.6 1.0
N G:GLY46 3.1 20.8 1.0
O H:HOH211 3.3 27.4 1.0
N H:SER91 3.3 14.7 1.0
CB H:THR90 3.5 13.1 1.0
CA G:GLY46 3.6 17.6 1.0
N G:ALA47 3.6 15.3 1.0
CA H:THR90 3.7 14.3 1.0
C G:GLY44 3.7 19.0 1.0
CA G:GLY44 3.7 18.0 1.0
N G:ALA45 3.8 21.2 1.0
OP1 I:DA111 3.8 39.6 1.0
OG H:SER91 4.0 21.1 1.0
C G:GLY46 4.0 17.4 1.0
C H:THR90 4.0 13.8 1.0
CG2 H:THR90 4.1 12.1 1.0
CB H:SER91 4.2 16.5 1.0
C G:ALA45 4.2 20.1 1.0
O G:GLY44 4.3 22.1 1.0
CA H:SER91 4.4 14.5 1.0
CA G:ALA45 4.6 18.9 1.0
CA G:ALA47 4.6 13.1 1.0
OG1 H:THR90 4.7 17.3 1.0
CB G:ALA47 4.7 12.1 1.0
N G:GLY44 4.8 20.6 1.0

Reference:

H.Taguchi, Y.Xie, N.Horikoshi, K.Maehara, A.Harada, J.Nogami, K.Sato, Y.Arimura, A.Osakabe, T.Kujirai, T.Iwasaki, Y.Semba, T.Tachibana, H.Kimura, Y.Ohkawa, H.Kurumizaka. Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8 Biochemistry V. 56 2184 2017.
ISSN: ISSN 1520-4995
PubMed: 28374988
DOI: 10.1021/ACS.BIOCHEM.6B01098
Page generated: Sat Jul 12 10:32:30 2025

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