Chlorine in PDB 7qvq: Human Telomeric Dna G-Quadruplex of A Gold(III) Complex Containing the 2,4,6-Tris (2-Pyrimidyl)-1,3,5-Triazine Ligand

The structure of Human Telomeric Dna G-Quadruplex of A Gold(III) Complex Containing the 2,4,6-Tris (2-Pyrimidyl)-1,3,5-Triazine Ligand, PDB code: 7qvq was solved by C.Bazzicalupi, U.Ryde, P.Gratteri, J.Bergmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.76 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	36.78, 71.53, 26.24, 90, 92.08, 90
R / Rfree (%)	26 / 28.7

The structure of Human Telomeric Dna G-Quadruplex of A Gold(III) Complex Containing the 2,4,6-Tris (2-Pyrimidyl)-1,3,5-Triazine Ligand also contains other interesting chemical elements:

Potassium	(K)	3 atoms
Gold	(Au)	4 atoms

The binding sites of Chlorine atom in the Human Telomeric Dna G-Quadruplex of A Gold(III) Complex Containing the 2,4,6-Tris (2-Pyrimidyl)-1,3,5-Triazine Ligand (pdb code 7qvq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Human Telomeric Dna G-Quadruplex of A Gold(III) Complex Containing the 2,4,6-Tris (2-Pyrimidyl)-1,3,5-Triazine Ligand, PDB code: 7qvq:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Human Telomeric Dna G-Quadruplex of A Gold(III) Complex Containing the 2,4,6-Tris (2-Pyrimidyl)-1,3,5-Triazine Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Telomeric Dna G-Quadruplex of A Gold(III) Complex Containing the 2,4,6-Tris (2-Pyrimidyl)-1,3,5-Triazine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl104 b:54.1 occ:0.25 CL1 A:I6K104 0.0 54.1 0.2 C10 A:I6K105 2.2 61.1 0.2 AU1 A:I6K104 2.3 64.8 0.2 N5 A:I6K106 2.8 67.0 0.2 C7 A:I6K106 3.0 67.8 0.2 C9 A:I6K105 3.2 62.7 0.2 C12 A:I6K105 3.2 60.4 0.2 C8 A:DG5 3.3 35.9 1.0 C12 A:I6K107 3.3 75.4 0.2 N7 A:DG5 3.3 31.5 1.0 N3 A:I6K104 3.4 54.7 0.2 C9 A:I6K104 3.5 54.7 0.2 N2 A:I6K104 3.6 54.5 0.2 N9 A:DG5 3.7 37.6 1.0 N4 A:I6K107 3.8 75.5 0.2 C5 A:DG5 3.8 30.7 1.0 C8 A:I6K104 3.8 54.0 0.2 O A:HOH242 4.0 50.9 1.0 C4 A:DG5 4.0 31.3 1.0 C13 A:I6K106 4.1 67.8 0.2 C2' A:DG5 4.2 44.4 1.0 N9 A:I6K106 4.3 61.2 0.2 N1 A:I6K104 4.4 53.0 0.2 C15 A:I6K106 4.4 69.4 0.2 N3 A:I6K105 4.4 62.6 0.2 N4 A:I6K105 4.5 60.8 0.2 C10 A:I6K107 4.5 75.5 0.2 C1' A:DG5 4.5 40.5 1.0 N2 A:DG23 4.5 32.3 1.0 C6 A:DG5 4.6 29.1 1.0 C3 A:I6K106 4.7 66.2 0.2 O A:HOH213 4.7 52.2 1.0 C2 A:I6K104 4.7 52.7 0.2 N6 A:I6K106 4.7 49.7 0.2 C13 A:I6K104 4.9 52.1 0.2 C10 A:I6K104 4.9 54.0 0.2 C2 A:I6K105 4.9 61.9 0.2 N3 A:DG5 5.0 27.9 1.0

Chlorine binding site 2 out of 4 in the Human Telomeric Dna G-Quadruplex of A Gold(III) Complex Containing the 2,4,6-Tris (2-Pyrimidyl)-1,3,5-Triazine Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Telomeric Dna G-Quadruplex of A Gold(III) Complex Containing the 2,4,6-Tris (2-Pyrimidyl)-1,3,5-Triazine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl105 b:60.8 occ:0.25 CL1 A:I6K105 0.0 60.8 0.2 C5 A:I6K106 0.9 57.7 0.2 C16 A:I6K106 0.9 52.6 0.2 N9 A:I6K104 0.9 46.6 0.2 C3 A:I6K104 1.0 51.0 0.2 C2 A:I6K107 1.0 76.6 0.2 N3 A:I6K107 1.1 77.7 0.2 C1 A:I6K107 1.4 77.3 0.2 N7 A:I6K106 1.5 50.4 0.2 N8 A:I6K106 1.6 61.7 0.2 N1 A:I6K107 1.7 77.4 0.2 C13 A:I6K104 1.7 52.1 0.2 N5 A:I6K104 2.0 51.7 0.2 AU1 A:I6K107 2.0 85.9 0.2 N9 A:I6K106 2.2 61.2 0.2 N6 A:I6K106 2.2 49.7 0.2 C5 A:I6K104 2.3 44.4 0.2 N4 A:I6K107 2.3 75.5 0.2 AU1 A:I6K105 2.3 71.2 0.2 N1 A:I6K104 2.3 53.0 0.2 C9 A:I6K107 2.4 76.5 0.2 N8 A:I6K107 2.7 76.5 0.2 C19 A:I6K106 2.8 48.0 0.2 C1 A:I6K106 2.8 66.9 0.2 N2 A:I6K104 3.0 54.5 0.2 C3 A:I6K107 3.0 76.5 0.2 C1 A:I6K104 3.1 51.4 0.2 C12 A:I6K107 3.1 75.4 0.2 N8 A:I6K104 3.1 48.0 0.2 C17 A:I6K106 3.2 48.6 0.2 C10 A:I6K107 3.2 75.5 0.2 C3 A:I6K106 3.2 66.2 0.2 O6 A:DG23 3.3 32.8 1.0 C16 A:I6K104 3.3 39.6 0.2 N6 A:I6K104 3.4 36.9 0.2 C6 A:DG23 3.4 31.7 1.0 C7 A:I6K104 3.4 52.2 0.2 N3 A:I6K105 3.4 62.6 0.2 C20 A:I6K106 3.5 48.2 0.2 N1 A:I6K106 3.5 68.9 0.2 C9 A:I6K105 3.6 62.7 0.2 N2 A:I6K105 3.6 61.6 0.2 C5 A:I6K107 3.7 74.0 0.2 N2 A:I6K107 3.7 78.3 0.2 N9 A:I6K107 3.8 74.7 0.2 C5 A:DG23 3.9 30.4 1.0 C13 A:I6K107 3.9 76.3 0.2 C8 A:I6K105 3.9 60.1 0.2 CL1 A:I6K107 3.9 79.1 0.2 AU1 A:I6K104 3.9 64.8 0.2 N1 A:DG23 4.0 32.1 1.0 C8 A:I6K104 4.0 54.0 0.2 C2 A:I6K106 4.1 67.0 0.2 C15 A:I6K104 4.2 53.1 0.2 N1 A:DG17 4.2 32.1 1.0 N7 A:DG23 4.3 29.5 1.0 N4 A:I6K106 4.4 65.7 0.2 O6 A:DG5 4.4 28.4 1.0 N1 A:I6K105 4.4 62.8 0.2 O6 A:DG17 4.5 32.3 1.0 C2 A:I6K104 4.5 52.7 0.2 N7 A:I6K104 4.6 37.5 0.2 C13 A:I6K106 4.6 67.8 0.2 C6 A:DG17 4.6 31.6 1.0 C4 A:DG23 4.7 29.4 1.0 C17 A:I6K104 4.7 35.3 0.2 C2 A:I6K105 4.8 61.9 0.2 C2 A:DG23 4.8 31.7 1.0 C2 A:DG17 4.9 31.6 1.0 C13 A:I6K105 4.9 60.5 0.2 C8 A:I6K107 4.9 78.6 0.2 N3 A:I6K104 5.0 54.7 0.2 C10 A:I6K105 5.0 61.1 0.2 N2 A:DG17 5.0 32.2 1.0 K A:K101 5.0 31.7 1.0

Chlorine binding site 3 out of 4 in the Human Telomeric Dna G-Quadruplex of A Gold(III) Complex Containing the 2,4,6-Tris (2-Pyrimidyl)-1,3,5-Triazine Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Telomeric Dna G-Quadruplex of A Gold(III) Complex Containing the 2,4,6-Tris (2-Pyrimidyl)-1,3,5-Triazine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl106 b:68.0 occ:0.25 CL1 A:I6K106 0.0 68.0 0.2 C20 A:I6K107 0.6 67.5 0.2 C5 A:I6K105 1.0 60.1 0.2 C16 A:I6K105 1.1 59.5 0.2 C19 A:I6K107 1.2 68.9 0.2 N8 A:I6K105 1.6 61.1 0.2 N7 A:I6K105 1.6 59.0 0.2 C17 A:I6K107 2.0 67.4 0.2 N9 A:I6K105 2.2 60.3 0.2 AU1 A:I6K106 2.3 81.1 0.2 N6 A:I6K105 2.3 60.1 0.2 N7 A:I6K107 2.4 71.3 0.2 C1 A:I6K105 2.8 62.5 0.2 C19 A:I6K105 2.9 56.4 0.2 N6 A:I6K107 2.9 69.0 0.2 C16 A:I6K107 2.9 71.7 0.2 N4 A:I6K104 3.1 51.6 0.2 C12 A:I6K104 3.2 52.7 0.2 C8 A:DG11 3.2 31.2 1.0 C3 A:I6K105 3.2 61.3 0.2 C17 A:I6K105 3.3 57.9 0.2 N7 A:DG11 3.4 28.3 1.0 N9 A:DG11 3.4 32.1 1.0 N3 A:I6K106 3.5 68.5 0.2 N1 A:I6K105 3.5 62.8 0.2 C5 A:DG11 3.5 26.8 1.0 C20 A:I6K105 3.6 56.4 0.2 C4 A:DG11 3.6 27.1 1.0 N2 A:I6K106 3.6 69.6 0.2 C9 A:I6K106 3.6 67.1 0.2 C8 A:I6K106 3.9 70.3 0.2 C2' A:DG11 4.0 42.2 1.0 C2 A:I6K105 4.1 61.9 0.2 C1' A:DG11 4.1 39.0 1.0 O A:HOH245 4.1 47.0 1.0 C2 A:I6K104 4.3 52.7 0.2 C6 A:DG11 4.3 25.5 1.0 N1 A:I6K106 4.4 68.9 0.2 N4 A:I6K105 4.4 60.8 0.2 N3 A:DG11 4.4 26.3 1.0 C5 A:I6K107 4.4 74.0 0.2 C10 A:I6K104 4.5 54.0 0.2 C13 A:I6K105 4.7 60.5 0.2 N8 A:I6K104 4.7 48.0 0.2 C2 A:I6K106 4.8 67.0 0.2 O4 A:DT6 4.8 83.7 1.0 C13 A:I6K106 4.9 67.8 0.2 N2 A:DG5 4.9 32.9 1.0 N1 A:DG11 4.9 26.9 1.0 C2 A:DG11 5.0 26.5 1.0 O6 A:DG11 5.0 25.7 1.0 C1 A:I6K104 5.0 51.4 0.2

Chlorine binding site 4 out of 4 in the Human Telomeric Dna G-Quadruplex of A Gold(III) Complex Containing the 2,4,6-Tris (2-Pyrimidyl)-1,3,5-Triazine Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human Telomeric Dna G-Quadruplex of A Gold(III) Complex Containing the 2,4,6-Tris (2-Pyrimidyl)-1,3,5-Triazine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl107 b:79.1 occ:0.25 CL1 A:I6K107 0.0 79.1 0.2 C19 A:I6K106 1.7 48.0 0.2 AU1 A:I6K107 2.3 85.9 0.2 N7 A:I6K106 2.4 50.4 0.2 C20 A:I6K106 2.8 48.2 0.2 O4 A:DT18 3.2 72.2 1.0 N5 A:I6K104 3.2 51.7 0.2 N3 A:I6K107 3.4 77.7 0.2 N7 A:DG23 3.5 29.5 1.0 C9 A:I6K107 3.5 76.5 0.2 C7 A:I6K104 3.5 52.2 0.2 C8 A:DG23 3.6 34.0 1.0 N2 A:I6K107 3.6 78.3 0.2 C16 A:I6K106 3.7 52.6 0.2 N2 A:DG17 3.8 32.2 1.0 C8 A:I6K107 3.9 78.6 0.2 CL1 A:I6K105 3.9 60.8 0.2 C17 A:I6K106 4.0 48.6 0.2 C5 A:DG23 4.3 30.4 1.0 C4 A:DT18 4.3 67.6 1.0 N9 A:I6K104 4.4 46.6 0.2 C13 A:I6K104 4.4 52.1 0.2 N1 A:I6K107 4.4 77.4 0.2 N6 A:I6K106 4.4 49.7 0.2 N9 A:DG23 4.5 34.6 1.0 C2 A:DG17 4.5 31.6 1.0 N6 A:I6K104 4.6 36.9 0.2 O A:HOH203 4.6 44.6 1.0 N3 A:DT18 4.7 63.6 1.0 C2 A:I6K107 4.7 76.6 0.2 C3 A:I6K104 4.8 51.0 0.2 C4 A:DG23 4.8 29.4 1.0 C5 A:I6K106 4.8 57.7 0.2 C10 A:I6K107 4.9 75.5 0.2 C13 A:I6K107 4.9 76.3 0.2 C15 A:I6K104 4.9 53.1 0.2 O A:HOH226 4.9 43.0 1.0 N8 A:I6K106 4.9 61.7 0.2 N1 A:DG17 5.0 32.1 1.0

C.Bazzicalupi, A.Bonardi, T.Biver, M.Ferraroni, F.Papi, M.Savastano, P.Lombardi, P.Gratteri. Probing the Efficiency of 13-Pyridylalkyl Berberine Derivatives to Human Telomeric G-Quadruplexes Binding: Spectroscopic, Solid State and in Silico Analysis. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 36430540
DOI: 10.3390/IJMS232214061