Chlorine in PDB 5m31: Macrodomain of Thermus Aquaticus Darg

The structure of Macrodomain of Thermus Aquaticus Darg, PDB code: 5m31 was solved by A.Ariza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.16 / 1.67
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.600, 45.020, 35.540, 90.00, 101.25, 90.00
R / Rfree (%)	17.2 / 20.3

The binding sites of Chlorine atom in the Macrodomain of Thermus Aquaticus Darg (pdb code 5m31). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Macrodomain of Thermus Aquaticus Darg, PDB code: 5m31:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Macrodomain of Thermus Aquaticus Darg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Macrodomain of Thermus Aquaticus Darg within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:37.4 occ:1.00 O A:HOH402 3.0 20.8 1.0 O A:HOH355 3.0 42.0 1.0 N A:GLY28 3.3 25.8 1.0 N A:LYS29 3.6 30.1 1.0 O A:VAL26 3.7 22.4 1.0 ND2 A:ASN22 3.7 23.3 1.0 O A:HOH336 3.8 30.1 1.0 CB A:TRP83 3.9 27.2 1.0 O A:LYS29 4.0 28.9 1.0 CA A:GLY28 4.1 28.1 1.0 CA A:MET27 4.1 21.7 1.0 CG A:LYS29 4.1 42.2 1.0 O A:HOH303 4.1 26.9 1.0 C A:MET27 4.2 24.6 1.0 C A:GLY28 4.3 30.1 1.0 C A:VAL26 4.3 22.7 1.0 CB A:ALA32 4.5 21.4 1.0 CG1 A:VAL26 4.5 25.4 1.0 CA A:LYS29 4.5 33.0 1.0 N A:MET27 4.6 22.7 1.0 CB A:LYS29 4.6 39.0 1.0 C A:LYS29 4.6 31.6 1.0 CG A:TRP83 4.8 28.8 1.0 CA A:TRP83 4.9 25.2 1.0 CE A:LYS29 5.0 52.0 1.0

Chlorine binding site 2 out of 3 in the Macrodomain of Thermus Aquaticus Darg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Macrodomain of Thermus Aquaticus Darg within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:40.5 occ:1.00 O A:HOH364 3.5 46.2 1.0 O1 A:GOL202 3.8 33.2 1.0 CG A:GLN34 3.9 33.2 1.0 CB A:GLN34 3.9 29.1 1.0 CG1 A:VAL31 4.1 24.6 1.0 CB A:LEU9 4.2 20.5 1.0 CG2 A:VAL31 4.2 27.7 1.0 CD2 A:LEU9 4.3 19.7 1.0 CA A:VAL31 4.3 24.7 1.0 CG A:LEU10 4.3 32.5 1.0 CE1 A:PHE35 4.4 21.8 1.0 CB A:VAL31 4.5 25.5 1.0 O2 A:GOL202 4.5 50.4 1.0 O A:VAL31 4.5 22.3 1.0 C2 A:GOL202 4.6 51.4 1.0 CD2 A:LEU10 4.6 32.9 1.0 CD1 A:PHE35 4.7 21.7 1.0 CG A:LEU9 4.7 20.1 1.0 CD1 A:LEU10 4.8 36.6 1.0 C1 A:GOL202 4.8 42.8 1.0 OD1 A:ASN8 4.9 28.8 1.0 C A:VAL31 4.9 22.7 1.0 N A:LEU9 5.0 21.4 1.0

Chlorine binding site 3 out of 3 in the Macrodomain of Thermus Aquaticus Darg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Macrodomain of Thermus Aquaticus Darg within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl205 b:35.2 occ:1.00 NE A:ARG65 3.4 23.9 1.0 N A:ASN42 3.4 21.8 1.0 CB A:PHE39 3.7 22.8 1.0 CB A:ASP41 3.7 28.0 1.0 CD A:ARG65 3.8 22.2 1.0 CG A:ARG65 3.9 22.5 1.0 CE2 A:TYR63 3.9 24.6 1.0 CD1 A:PHE39 3.9 23.2 1.0 CA A:PHE39 3.9 23.6 1.0 N A:ASP41 3.9 25.2 1.0 C A:PHE39 4.0 23.9 1.0 CB A:ASN42 4.0 19.1 1.0 O A:PHE39 4.1 22.1 1.0 CA A:ASP41 4.1 25.9 1.0 C A:ASP41 4.2 23.7 1.0 CG A:PHE39 4.2 22.6 1.0 CD2 A:TYR63 4.2 22.6 1.0 CA A:ASN42 4.3 20.0 1.0 O A:HOH329 4.4 36.3 1.0 CZ A:ARG65 4.4 24.5 1.0 N A:PRO40 4.5 25.1 1.0 CG A:ASP41 4.6 31.4 1.0 NH1 A:ARG65 4.7 26.0 1.0 OD2 A:ASP41 4.8 32.9 1.0 C A:PRO40 4.8 25.2 1.0 CZ A:TYR63 4.9 25.6 1.0 CB A:ARG65 4.9 23.4 1.0

G.Jankevicius, A.Ariza, M.Ahel, I.Ahel. The Toxin-Antitoxin System Dartg Catalyzes Reversible Adp-Ribosylation of Dna. Mol. Cell V. 64 1109 2016.
ISSN: ISSN 1097-4164
PubMed: 27939941
DOI: 10.1016/J.MOLCEL.2016.11.014