Chlorine in PDB 5gtc: Crystal Structure of Complex Between Dmap-Sh Conjugated with A Kaposi'S Sarcoma Herpesvirus Lana Peptide (5-15) and Nucleosome Core Particle

The structure of Crystal Structure of Complex Between Dmap-Sh Conjugated with A Kaposi'S Sarcoma Herpesvirus Lana Peptide (5-15) and Nucleosome Core Particle, PDB code: 5gtc was solved by Y.Arimura, D.Kato, H.Suto, H.Kurumizaka, S.A.Kawashima, K.Yamatsugu, M.Kanai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.59 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	107.225, 109.017, 176.194, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 26.7

The structure of Crystal Structure of Complex Between Dmap-Sh Conjugated with A Kaposi'S Sarcoma Herpesvirus Lana Peptide (5-15) and Nucleosome Core Particle also contains other interesting chemical elements:

Manganese

(Mn)

6 atoms

The binding sites of Chlorine atom in the Crystal Structure of Complex Between Dmap-Sh Conjugated with A Kaposi'S Sarcoma Herpesvirus Lana Peptide (5-15) and Nucleosome Core Particle (pdb code 5gtc). 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 Complex Between Dmap-Sh Conjugated with A Kaposi'S Sarcoma Herpesvirus Lana Peptide (5-15) and Nucleosome Core Particle, PDB code: 5gtc:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Complex Between Dmap-Sh Conjugated with A Kaposi'S Sarcoma Herpesvirus Lana Peptide (5-15) and Nucleosome Core Particle


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 Complex Between Dmap-Sh Conjugated with A Kaposi'S Sarcoma Herpesvirus Lana Peptide (5-15) and Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1001 b:83.8 occ:1.00 N A:LYS122 3.0 65.0 1.0 CB A:LYS122 3.4 64.8 1.0 CB A:PRO121 3.6 65.4 1.0 CD A:PRO121 3.6 68.0 1.0 CA A:LYS122 3.7 61.7 1.0 N A:PRO121 3.7 68.5 1.0 C A:PRO121 3.9 66.6 1.0 CG A:PRO121 3.9 63.8 1.0 CA A:PRO121 4.0 68.2 1.0 CB A:MET120 4.0 63.9 1.0 C A:MET120 4.3 64.5 1.0 CG A:LYS122 4.5 69.7 1.0 CE A:LYS122 4.6 70.9 1.0 CD A:LYS122 4.7 74.6 1.0 CA A:MET120 4.7 62.2 1.0 O A:MET120 4.9 67.6 1.0 O A:PRO121 5.0 65.6 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Complex Between Dmap-Sh Conjugated with A Kaposi'S Sarcoma Herpesvirus Lana Peptide (5-15) and Nucleosome Core Particle


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 Complex Between Dmap-Sh Conjugated with A Kaposi'S Sarcoma Herpesvirus Lana Peptide (5-15) and Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1001 b:66.5 occ:1.00 N C:GLY46 3.1 59.9 1.0 N D:SER91 3.4 65.9 1.0 C C:GLY44 3.4 63.8 1.0 CA C:GLY44 3.5 60.8 1.0 N C:ALA45 3.5 66.3 1.0 CB D:THR90 3.5 64.2 1.0 CA C:GLY46 3.5 61.4 1.0 CA D:THR90 3.6 61.9 1.0 N C:ALA47 3.7 63.4 1.0 OP1 J:DT258 4.0 83.9 1.0 C C:GLY46 4.0 58.9 1.0 C D:THR90 4.0 63.1 1.0 O C:GLY44 4.0 67.6 1.0 CG2 D:THR90 4.1 71.3 1.0 OG D:SER91 4.1 65.5 1.0 C C:ALA45 4.2 63.8 1.0 CB D:SER91 4.2 57.2 1.0 CA D:SER91 4.4 57.6 1.0 CA C:ALA45 4.4 62.3 1.0 N C:GLY44 4.6 59.6 1.0 CA C:ALA47 4.7 50.1 1.0 CB C:ALA47 4.7 49.9 1.0 OG1 D:THR90 4.7 66.6 1.0 O D:ILE89 5.0 64.0 1.0 N D:THR90 5.0 61.0 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Complex Between Dmap-Sh Conjugated with A Kaposi'S Sarcoma Herpesvirus Lana Peptide (5-15) and Nucleosome Core Particle


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 Complex Between Dmap-Sh Conjugated with A Kaposi'S Sarcoma Herpesvirus Lana Peptide (5-15) and Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl1001 b:77.1 occ:1.00 N E:LYS122 3.0 52.7 1.0 CB E:LYS122 3.4 54.6 1.0 CB E:PRO121 3.5 53.2 1.0 CA E:LYS122 3.7 50.9 1.0 CD E:PRO121 3.8 55.9 1.0 N E:PRO121 3.8 54.6 1.0 C E:PRO121 3.8 54.9 1.0 CA E:PRO121 4.0 54.1 1.0 CG E:PRO121 4.0 57.0 1.0 CB E:MET120 4.0 54.0 1.0 C E:MET120 4.4 53.6 1.0 CE E:LYS122 4.5 65.1 1.0 CG E:LYS122 4.6 63.6 1.0 CD E:LYS122 4.7 61.3 1.0 CA E:MET120 4.9 56.8 1.0 O E:PRO121 4.9 58.7 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Complex Between Dmap-Sh Conjugated with A Kaposi'S Sarcoma Herpesvirus Lana Peptide (5-15) and Nucleosome Core Particle


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 Complex Between Dmap-Sh Conjugated with A Kaposi'S Sarcoma Herpesvirus Lana Peptide (5-15) and Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl1001 b:68.7 occ:1.00 N G:GLY46 3.3 59.1 1.0 N G:ALA45 3.5 67.5 1.0 N H:SER91 3.6 53.5 1.0 CA G:GLY44 3.6 62.8 1.0 CB H:THR90 3.6 51.6 1.0 C G:GLY44 3.7 65.2 1.0 CA H:THR90 3.8 54.4 1.0 OP1 I:DA111 3.8 85.7 1.0 CA G:GLY46 3.8 53.2 1.0 N G:ALA47 3.9 64.7 1.0 C H:THR90 4.2 54.8 1.0 CG2 H:THR90 4.2 55.1 1.0 OG H:SER91 4.2 58.6 1.0 C G:GLY46 4.3 60.3 1.0 C G:ALA45 4.3 63.9 1.0 CB H:SER91 4.4 57.5 1.0 CA G:ALA45 4.4 62.9 1.0 O G:GLY44 4.4 62.5 1.0 CA H:SER91 4.6 53.6 1.0 N G:GLY44 4.8 65.5 1.0 OG1 H:THR90 4.8 54.4 1.0 CB G:ALA47 4.9 53.8 1.0 CA G:ALA47 4.9 51.4 1.0

Y.Amamoto, Y.Aoi, N.Nagashima, H.Suto, D.Yoshidome, Y.Arimura, A.Osakabe, D.Kato, H.Kurumizaka, S.A.Kawashima, K.Yamatsugu, M.Kanai. Synthetic Posttranslational Modifications: Chemical Catalyst-Driven Regioselective Histone Acylation of Native Chromatin. J. Am. Chem. Soc. V. 139 7568 2017.
ISSN: ESSN 1520-5126
PubMed: 28534629
DOI: 10.1021/JACS.7B02138