Chlorine in PDB 6dt1: Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate

All present enzymatic activity of Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate:
6.5.1.1;

The structure of Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate, PDB code: 6dt1 was solved by K.Shi, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	113.02 / 2.75
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.526, 67.429, 114.635, 88.78, 80.94, 62.97
R / Rfree (%)	17 / 21.9

The structure of Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate (pdb code 6dt1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate, PDB code: 6dt1:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate


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 Ligase From Bacteriophage T4 Complexed with Dna Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl516 b:0.2 occ:1.00 O2 A:GOL514 2.9 91.3 1.0 CG A:ARG41 3.9 71.6 1.0 C2 A:GOL514 4.0 87.1 1.0 C3 A:GOL514 4.0 83.8 1.0 CA A:ARG41 4.1 45.0 1.0 NE2 A:GLN44 4.4 33.0 1.0 CB A:ARG41 4.4 59.8 1.0 CZ A:ARG111 4.4 31.4 1.0 NH2 A:ARG111 4.5 29.9 1.0 NH1 A:ARG111 4.5 27.0 1.0 N A:ARG41 4.6 33.4 1.0 O A:TYR39 4.7 46.4 1.0 NE A:ARG111 4.7 27.5 1.0 CG A:ARG111 4.7 36.9 1.0 CB A:ARG111 4.7 30.2 1.0 NH2 A:ARG41 4.8 85.4 1.0 O A:THR38 4.9 25.4 1.0 C A:SER40 5.0 37.5 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of the Ligase From Bacteriophage T4 Complexed with Dna Intermediate


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 Ligase From Bacteriophage T4 Complexed with Dna Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl502 b:88.7 occ:1.00 O E:LYS367 3.3 64.7 1.0 CG E:TYR141 4.2 59.8 1.0 CZ A:PHE296 4.3 69.6 1.0 CD2 E:TYR141 4.3 62.9 1.0 OH E:TYR335 4.3 72.0 1.0 C E:LYS367 4.4 65.2 1.0 CD1 E:TYR141 4.4 62.2 1.0 CB A:ALA295 4.5 80.5 1.0 CE1 A:PHE296 4.5 71.6 1.0 N E:LYS367 4.6 67.9 1.0 CE2 E:TYR141 4.6 64.4 1.0 CZ E:TYR335 4.6 74.3 1.0 CE1 E:TYR141 4.7 64.5 1.0 CB E:TYR141 4.7 59.8 1.0 O A:ALA295 4.7 72.2 1.0 CZ E:TYR141 4.7 67.9 1.0 CE2 E:TYR335 4.8 75.9 1.0 CA E:PHE366 5.0 66.5 1.0 CE2 A:PHE296 5.0 71.1 1.0

K.Shi, T.E.Bohl, J.Park, A.Zasada, S.Malik, S.Banerjee, V.Tran, N.Li, Z.Yin, F.Kurniawan, K.Orellana, H.Aihara. T4 Dna Ligase Structure Reveals A Prototypical Atp-Dependent Ligase with A Unique Mode of Sliding Clamp Interaction. Nucleic Acids Res. V. 46 10474 2018.
ISSN: ESSN 1362-4962
PubMed: 30169742
DOI: 10.1093/NAR/GKY776