Gold 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
Chlorine	(Cl)	4 atoms

The binding sites of Gold 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 Gold atom.
In total 4 binding sites of Gold 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 Gold binding site number: 1; 2; 3; 4;

Gold 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 Gold with other atoms in the Au 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:Au104 b:64.8 occ:0.25 AU1 A:I6K104 0.0 64.8 0.2 C9 A:I6K105 1.0 62.7 0.2 C10 A:I6K105 1.3 61.1 0.2 N4 A:I6K107 1.7 75.5 0.2 N5 A:I6K106 1.8 67.0 0.2 C12 A:I6K107 2.0 75.4 0.2 N9 A:I6K106 2.0 61.2 0.2 N1 A:I6K104 2.1 53.0 0.2 N3 A:I6K104 2.2 54.7 0.2 N2 A:I6K104 2.2 54.5 0.2 CL1 A:I6K104 2.3 54.1 0.2 N3 A:I6K105 2.3 62.6 0.2 C13 A:I6K106 2.5 67.8 0.2 C3 A:I6K106 2.5 66.2 0.2 C12 A:I6K105 2.7 60.4 0.2 C2 A:I6K107 3.0 76.6 0.2 C7 A:I6K106 3.0 67.8 0.2 C2 A:I6K104 3.0 52.7 0.2 C1 A:I6K104 3.0 51.4 0.2 C3 A:I6K104 3.0 51.0 0.2 C13 A:I6K104 3.0 52.1 0.2 C9 A:I6K104 3.1 54.7 0.2 N6 A:I6K106 3.1 49.7 0.2 C8 A:I6K104 3.2 54.0 0.2 C5 A:I6K106 3.3 57.7 0.2 C2 A:I6K105 3.3 61.9 0.2 C10 A:I6K107 3.4 75.5 0.2 C5 A:DG5 3.4 30.7 1.0 N4 A:I6K105 3.4 60.8 0.2 N7 A:DG5 3.4 31.5 1.0 C6 A:DG5 3.5 29.1 1.0 O6 A:DG5 3.6 28.4 1.0 C16 A:I6K106 3.7 52.6 0.2 N8 A:I6K107 3.8 76.5 0.2 C1 A:I6K107 3.8 77.3 0.2 N1 A:I6K106 3.9 68.9 0.2 N2 A:I6K106 3.9 69.6 0.2 CL1 A:I6K105 3.9 60.8 0.2 AU1 A:I6K105 4.0 71.2 0.2 N3 A:I6K107 4.0 77.7 0.2 C8 A:DG5 4.1 35.9 1.0 C4 A:DG5 4.1 31.3 1.0 N1 A:DG23 4.2 32.1 1.0 C9 A:I6K107 4.2 76.5 0.2 C15 A:I6K106 4.2 69.4 0.2 C17 A:I6K106 4.3 48.6 0.2 N2 A:DG23 4.3 32.3 1.0 N8 A:I6K104 4.3 48.0 0.2 N4 A:I6K104 4.3 51.6 0.2 N1 A:DG5 4.3 29.9 1.0 N9 A:I6K104 4.3 46.6 0.2 N5 A:I6K104 4.3 51.7 0.2 C10 A:I6K104 4.4 54.0 0.2 N8 A:I6K106 4.4 61.7 0.2 C2 A:DG23 4.5 31.7 1.0 C15 A:I6K104 4.5 53.1 0.2 N9 A:DG5 4.5 37.6 1.0 C8 A:I6K106 4.5 70.3 0.2 C1 A:I6K106 4.6 66.9 0.2 C1 A:I6K105 4.7 62.5 0.2 C5 A:I6K104 4.8 44.4 0.2 C12 A:I6K104 4.9 52.7 0.2 C2 A:DG5 4.9 31.2 1.0 N3 A:DG5 4.9 27.9 1.0 C6 A:DG23 4.9 31.7 1.0 C7 A:I6K104 4.9 52.2 0.2 N1 A:I6K105 5.0 62.8 0.2

Gold 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 Gold with other atoms in the Au 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:Au105 b:71.2 occ:0.25 AU1 A:I6K105 0.0 71.2 0.2 N8 A:I6K107 0.5 76.5 0.2 C1 A:I6K106 0.7 66.9 0.2 N8 A:I6K104 0.8 48.0 0.2 C5 A:I6K104 0.9 44.4 0.2 C1 A:I6K107 0.9 77.3 0.2 N8 A:I6K106 1.1 61.7 0.2 N1 A:I6K106 1.3 68.9 0.2 C5 A:I6K107 1.4 74.0 0.2 C1 A:I6K104 1.4 51.4 0.2 N9 A:I6K104 1.6 46.6 0.2 C5 A:I6K106 1.7 57.7 0.2 N1 A:I6K107 1.8 77.4 0.2 C3 A:I6K106 1.9 66.2 0.2 N1 A:I6K104 1.9 53.0 0.2 C3 A:I6K104 2.0 51.0 0.2 N9 A:I6K106 2.0 61.2 0.2 N1 A:I6K105 2.1 62.8 0.2 C2 A:I6K106 2.2 67.0 0.2 N9 A:I6K107 2.2 74.7 0.2 N3 A:I6K105 2.2 62.6 0.2 N2 A:I6K105 2.2 61.6 0.2 C3 A:I6K107 2.2 76.5 0.2 CL1 A:I6K105 2.3 60.8 0.2 C16 A:I6K104 2.3 39.6 0.2 C2 A:I6K107 2.3 76.6 0.2 C16 A:I6K107 2.8 71.7 0.2 C2 A:I6K104 2.9 52.7 0.2 N4 A:I6K107 3.0 75.5 0.2 C3 A:I6K105 3.0 61.3 0.2 N7 A:I6K104 3.0 37.5 0.2 N4 A:I6K106 3.0 65.7 0.2 C1 A:I6K105 3.0 62.5 0.2 C2 A:I6K105 3.1 61.9 0.2 C13 A:I6K105 3.1 60.5 0.2 N3 A:I6K106 3.1 68.5 0.2 C16 A:I6K106 3.1 52.6 0.2 C9 A:I6K105 3.2 62.7 0.2 C8 A:I6K105 3.2 60.1 0.2 N6 A:I6K104 3.3 36.9 0.2 N7 A:I6K107 3.3 71.3 0.2 AU1 A:I6K106 3.3 81.1 0.2 C13 A:I6K106 3.3 67.8 0.2 N3 A:I6K107 3.4 77.7 0.2 C13 A:I6K104 3.5 52.1 0.2 N4 A:I6K104 3.6 51.6 0.2 C13 A:I6K107 3.7 76.3 0.2 AU1 A:I6K107 3.7 85.9 0.2 N7 A:I6K106 3.7 50.4 0.2 O6 A:DG17 3.8 32.3 1.0 N6 A:I6K107 3.8 69.0 0.2 O6 A:DG11 3.8 25.7 1.0 N2 A:I6K106 3.9 69.6 0.2 N3 A:I6K104 3.9 54.7 0.2 AU1 A:I6K104 4.0 64.8 0.2 O6 A:DG5 4.0 28.4 1.0 N6 A:I6K106 4.0 49.7 0.2 O6 A:DG23 4.0 32.8 1.0 N5 A:I6K104 4.3 51.7 0.2 N2 A:I6K107 4.3 78.3 0.2 N2 A:I6K104 4.3 54.5 0.2 C6 A:DG11 4.3 25.5 1.0 N5 A:I6K106 4.3 67.0 0.2 N9 A:I6K105 4.3 60.3 0.2 N8 A:I6K105 4.3 61.1 0.2 C12 A:I6K106 4.3 65.3 0.2 C9 A:I6K106 4.3 67.1 0.2 C19 A:I6K104 4.3 36.3 0.2 C12 A:I6K107 4.3 75.4 0.2 N4 A:I6K105 4.3 60.8 0.2 C6 A:DG17 4.3 31.6 1.0 N5 A:I6K105 4.4 58.7 0.2 N1 A:DG11 4.4 26.9 1.0 C10 A:I6K105 4.5 61.1 0.2 C17 A:I6K104 4.5 35.3 0.2 K A:K101 4.5 31.7 1.0 C15 A:I6K105 4.5 58.4 0.2 C9 A:I6K107 4.6 76.5 0.2 N5 A:I6K107 4.6 75.1 0.2 C19 A:I6K107 4.6 68.9 0.2 C6 A:DG5 4.6 29.1 1.0 N1 A:DG17 4.6 32.1 1.0 C6 A:DG23 4.7 31.7 1.0 C5 A:I6K105 4.8 60.1 0.2 N1 A:DG5 4.8 29.9 1.0 C10 A:I6K106 4.9 65.7 0.2 C12 A:I6K105 4.9 60.4 0.2 C12 A:I6K104 4.9 52.7 0.2 C20 A:I6K104 5.0 35.6 0.2 C7 A:I6K105 5.0 57.7 0.2 C17 A:I6K107 5.0 67.4 0.2

Gold 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 Gold with other atoms in the Au 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:Au106 b:81.1 occ:0.25 AU1 A:I6K106 0.0 81.1 0.2 N7 A:I6K107 0.2 71.3 0.2 C1 A:I6K105 0.7 62.5 0.2 N8 A:I6K105 1.1 61.1 0.2 C16 A:I6K107 1.2 71.7 0.2 C19 A:I6K107 1.3 68.9 0.2 N1 A:I6K105 1.3 62.8 0.2 N4 A:I6K104 1.5 51.6 0.2 C5 A:I6K105 1.7 60.1 0.2 C3 A:I6K105 1.9 61.3 0.2 N9 A:I6K105 2.1 60.3 0.2 N1 A:I6K106 2.1 68.9 0.2 N3 A:I6K106 2.2 68.5 0.2 N2 A:I6K106 2.2 69.6 0.2 C2 A:I6K105 2.2 61.9 0.2 N6 A:I6K107 2.2 69.0 0.2 C20 A:I6K107 2.2 67.5 0.2 CL1 A:I6K106 2.3 68.0 0.2 C5 A:I6K107 2.4 74.0 0.2 C2 A:I6K104 2.4 52.7 0.2 N8 A:I6K104 2.5 48.0 0.2 C17 A:I6K107 2.5 67.4 0.2 C12 A:I6K104 2.6 52.7 0.2 C1 A:I6K104 2.7 51.4 0.2 N8 A:I6K107 2.8 76.5 0.2 C3 A:I6K106 3.0 66.2 0.2 C13 A:I6K106 3.0 67.8 0.2 C1 A:I6K106 3.1 66.9 0.2 C2 A:I6K106 3.1 67.0 0.2 N3 A:I6K105 3.1 62.6 0.2 N4 A:I6K105 3.1 60.8 0.2 C16 A:I6K105 3.1 59.5 0.2 C9 A:I6K106 3.2 67.1 0.2 C8 A:I6K106 3.2 70.3 0.2 C6 A:DG11 3.3 25.5 1.0 C5 A:DG11 3.3 26.8 1.0 AU1 A:I6K105 3.3 71.2 0.2 C13 A:I6K105 3.3 60.5 0.2 O6 A:DG11 3.5 25.7 1.0 N9 A:I6K107 3.5 74.7 0.2 N7 A:DG11 3.5 28.3 1.0 N3 A:I6K104 3.7 54.7 0.2 C5 A:I6K104 3.8 44.4 0.2 N7 A:I6K105 3.8 59.0 0.2 C10 A:I6K104 3.9 54.0 0.2 N2 A:I6K105 3.9 61.6 0.2 N1 A:DG11 3.9 26.9 1.0 C4 A:DG11 3.9 27.1 1.0 N7 A:I6K104 4.0 37.5 0.2 N6 A:I6K105 4.1 60.1 0.2 N1 A:I6K104 4.1 53.0 0.2 C1 A:I6K107 4.2 77.3 0.2 C8 A:DG11 4.2 31.2 1.0 C9 A:I6K104 4.3 54.7 0.2 N9 A:I6K106 4.3 61.2 0.2 N8 A:I6K106 4.3 61.7 0.2 N1 A:DG5 4.3 29.9 1.0 N5 A:I6K105 4.3 58.7 0.2 N5 A:I6K106 4.3 67.0 0.2 C9 A:I6K105 4.3 62.7 0.2 N4 A:I6K106 4.3 65.7 0.2 C12 A:I6K105 4.3 60.4 0.2 C16 A:I6K104 4.4 39.6 0.2 N9 A:DG11 4.4 32.1 1.0 N2 A:DG5 4.4 32.9 1.0 C10 A:I6K106 4.5 65.7 0.2 C2 A:DG11 4.5 26.5 1.0 C15 A:I6K106 4.5 69.4 0.2 N3 A:DG11 4.6 26.3 1.0 C3 A:I6K107 4.6 76.5 0.2 C2 A:DG5 4.7 31.2 1.0 C5 A:I6K106 4.8 57.7 0.2 N9 A:I6K104 4.9 46.6 0.2 C10 A:I6K105 4.9 61.1 0.2 C12 A:I6K106 4.9 65.3 0.2 N1 A:I6K107 4.9 77.4 0.2 C7 A:I6K106 4.9 67.8 0.2 C3 A:I6K104 5.0 51.0 0.2

Gold 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 Gold with other atoms in the Au 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:Au107 b:85.9 occ:0.25 AU1 A:I6K107 0.0 85.9 0.2 N7 A:I6K106 1.2 50.4 0.2 CL1 A:I6K105 2.0 60.8 0.2 N1 A:I6K107 2.1 77.4 0.2 C19 A:I6K106 2.1 48.0 0.2 N3 A:I6K107 2.1 77.7 0.2 N9 A:I6K104 2.2 46.6 0.2 N2 A:I6K107 2.2 78.3 0.2 CL1 A:I6K107 2.3 79.1 0.2 C16 A:I6K106 2.3 52.6 0.2 N6 A:I6K104 2.6 36.9 0.2 N5 A:I6K104 2.6 51.7 0.2 N8 A:I6K106 2.7 61.7 0.2 C5 A:I6K106 2.9 57.7 0.2 C1 A:I6K107 3.0 77.3 0.2 C3 A:I6K107 3.0 76.5 0.2 C2 A:I6K107 3.0 76.6 0.2 C3 A:I6K104 3.0 51.0 0.2 C13 A:I6K107 3.0 76.3 0.2 C9 A:I6K107 3.1 76.5 0.2 C5 A:I6K104 3.2 44.4 0.2 C8 A:I6K107 3.2 78.6 0.2 C13 A:I6K104 3.2 52.1 0.2 C20 A:I6K106 3.4 48.2 0.2 C16 A:I6K104 3.4 39.6 0.2 C8 A:I6K105 3.5 60.1 0.2 N6 A:I6K106 3.6 49.7 0.2 N1 A:DG17 3.6 32.1 1.0 C17 A:I6K104 3.6 35.3 0.2 N2 A:DG17 3.7 32.2 1.0 AU1 A:I6K105 3.7 71.2 0.2 C2 A:DG17 3.7 31.6 1.0 N7 A:DG23 3.7 29.5 1.0 C7 A:I6K104 3.8 52.2 0.2 O6 A:DG23 3.9 32.8 1.0 C17 A:I6K106 3.9 48.6 0.2 C1 A:I6K106 3.9 66.9 0.2 N2 A:I6K105 3.9 61.6 0.2 C5 A:DG23 4.0 30.4 1.0 C6 A:DG23 4.1 31.7 1.0 N9 A:I6K106 4.2 61.2 0.2 N8 A:I6K107 4.2 76.5 0.2 N4 A:I6K107 4.3 75.5 0.2 N9 A:I6K107 4.3 74.7 0.2 N1 A:I6K104 4.3 53.0 0.2 N5 A:I6K107 4.3 75.1 0.2 C6 A:DG17 4.3 31.6 1.0 N4 A:I6K106 4.3 65.7 0.2 C10 A:I6K107 4.4 75.5 0.2 N8 A:I6K104 4.5 48.0 0.2 N3 A:DG17 4.5 28.8 1.0 C15 A:I6K107 4.5 78.0 0.2 C8 A:DG23 4.5 34.0 1.0 C15 A:I6K105 4.6 58.4 0.2 N2 A:I6K104 4.6 54.5 0.2 C2 A:I6K106 4.7 67.0 0.2 C5 A:I6K107 4.7 74.0 0.2 N7 A:I6K104 4.7 37.5 0.2 O6 A:DG17 4.8 32.3 1.0 C12 A:I6K107 4.8 75.4 0.2 C1 A:I6K104 4.9 51.4 0.2 C7 A:I6K107 4.9 76.6 0.2 C20 A:I6K104 5.0 35.6 0.2 O A:HOH203 5.0 44.6 1.0 C4 A:DG23 5.0 29.4 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