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Chlorine in PDB 5m31: Macrodomain of Thermus Aquaticus Darg

Protein crystallography data

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

Chlorine Binding Sites:

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 5m31

Go back to Chlorine Binding Sites List in 5m31
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 5m31

Go back to Chlorine Binding Sites List in 5m31
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 5m31

Go back to Chlorine Binding Sites List in 5m31
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

Reference:

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
Page generated: Sat Dec 12 12:05:04 2020

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