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Gold in PDB 6h5r: Structure of the Complex of A Human Telomeric Dna with Bis(1-Butyl-3- Methyl-Imidazole-2-Ylidene) Gold(I)

Protein crystallography data

The structure of Structure of the Complex of A Human Telomeric Dna with Bis(1-Butyl-3- Methyl-Imidazole-2-Ylidene) Gold(I), PDB code: 6h5r was solved by C.Bazzicalupi, P.Gratteri, F.Papi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.69 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 36.600, 71.370, 27.050, 90.00, 92.42, 90.00
R / Rfree (%) 22.8 / 25.3

Other elements in 6h5r:

The structure of Structure of the Complex of A Human Telomeric Dna with Bis(1-Butyl-3- Methyl-Imidazole-2-Ylidene) Gold(I) also contains other interesting chemical elements:

Strontium (Sr) 1 atom
Potassium (K) 2 atoms

Gold Binding Sites:

The binding sites of Gold atom in the Structure of the Complex of A Human Telomeric Dna with Bis(1-Butyl-3- Methyl-Imidazole-2-Ylidene) Gold(I) (pdb code 6h5r). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 4 binding sites of Gold where determined in the Structure of the Complex of A Human Telomeric Dna with Bis(1-Butyl-3- Methyl-Imidazole-2-Ylidene) Gold(I), PDB code: 6h5r:
Jump to Gold binding site number: 1; 2; 3; 4;

Gold binding site 1 out of 4 in 6h5r

Go back to Gold Binding Sites List in 6h5r
Gold binding site 1 out of 4 in the Structure of the Complex of A Human Telomeric Dna with Bis(1-Butyl-3- Methyl-Imidazole-2-Ylidene) Gold(I)


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Structure of the Complex of A Human Telomeric Dna with Bis(1-Butyl-3- Methyl-Imidazole-2-Ylidene) Gold(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au104

b:66.5
occ:0.25
AU A:FTQ104 0.0 66.5 0.2
C16 A:FTQ106 0.3 37.7 0.2
N6 A:FTQ107 1.0 42.1 0.2
C14 A:FTQ107 1.0 41.7 0.2
C17 A:FTQ106 1.3 37.0 0.2
C12 A:FTQ107 1.6 41.7 0.2
C15 A:FTQ106 1.7 37.9 0.2
C15 A:FTQ107 2.0 41.5 0.2
C11 A:FTQ105 2.0 57.2 0.2
C10 A:FTQ104 2.0 65.9 0.2
C1 A:FTQ104 2.0 64.2 0.2
C16 A:FTQ107 2.2 41.6 0.2
C13 A:FTQ107 2.3 42.1 0.2
C10 A:FTQ107 2.3 42.0 0.2
N5 A:FTQ107 2.8 42.4 0.2
C12 A:FTQ106 2.8 38.1 0.2
N6 A:FTQ104 2.9 65.8 0.2
N2 A:FTQ104 3.0 64.0 0.2
N1 A:FTQ104 3.0 63.8 0.2
N5 A:FTQ104 3.0 65.4 0.2
C2 A:FTQ105 3.1 54.9 0.2
N5 A:FTQ105 3.2 57.5 0.2
C12 A:FTQ104 3.2 66.4 0.2
C2 A:FTQ104 3.4 63.5 0.2
C3 A:FTQ104 3.4 62.8 0.2
C11 A:FTQ104 3.5 65.4 0.2
C17 A:FTQ107 3.6 42.0 0.2
C6 A:DG23 3.6 28.2 1.0
N1 A:DG23 3.7 27.2 1.0
C10 A:FTQ105 3.8 57.4 0.2
O6 A:DG23 3.9 27.5 1.0
C15 A:FTQ104 3.9 67.0 0.2
AU A:FTQ107 3.9 42.8 0.2
AU A:FTQ105 3.9 58.8 0.2
C18 A:FTQ104 4.0 63.0 0.2
C5 A:DG23 4.0 28.4 1.0
N6 A:FTQ106 4.1 39.6 0.2
C14 A:FTQ104 4.1 65.7 0.2
C4 A:FTQ104 4.2 63.5 0.2
C13 A:FTQ104 4.2 65.3 0.2
C5 A:FTQ104 4.2 63.2 0.2
C2 A:DG23 4.2 28.4 1.0
C11 A:FTQ107 4.2 42.2 0.2
N1 A:FTQ105 4.4 55.8 0.2
C13 A:FTQ105 4.4 57.3 0.2
C4 A:DG23 4.4 29.6 1.0
O6 A:DG5 4.5 28.7 1.0
N3 A:DG23 4.6 28.1 1.0
C14 A:FTQ106 4.6 39.3 0.2
C1 A:FTQ105 4.7 56.8 0.2
N7 A:DG23 4.7 29.2 1.0
C7 A:DT24 4.8 60.3 1.0
N2 A:DG23 4.8 28.6 1.0
C3 A:FTQ106 4.9 39.9 0.2
C19 A:FTQ106 5.0 39.3 0.2

Gold binding site 2 out of 4 in 6h5r

Go back to Gold Binding Sites List in 6h5r
Gold binding site 2 out of 4 in the Structure of the Complex of A Human Telomeric Dna with Bis(1-Butyl-3- Methyl-Imidazole-2-Ylidene) Gold(I)


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Structure of the Complex of A Human Telomeric Dna with Bis(1-Butyl-3- Methyl-Imidazole-2-Ylidene) Gold(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au105

b:58.8
occ:0.25
AU A:FTQ105 0.0 58.8 0.2
C3 A:FTQ106 1.0 39.9 0.2
N2 A:FTQ104 1.0 64.0 0.2
C5 A:FTQ104 1.2 63.2 0.2
C3 A:FTQ104 1.5 62.8 0.2
C18 A:FTQ106 1.8 39.3 0.2
C10 A:FTQ105 2.0 57.4 0.2
C1 A:FTQ105 2.0 56.8 0.2
C18 A:FTQ104 2.1 63.0 0.2
C19 A:FTQ104 2.2 62.8 0.2
C15 A:FTQ107 2.3 41.5 0.2
C1 A:FTQ104 2.3 64.2 0.2
C19 A:FTQ106 2.3 39.3 0.2
N2 A:FTQ106 2.4 40.1 0.2
C4 A:FTQ104 2.4 63.5 0.2
C12 A:FTQ107 2.7 41.7 0.2
N1 A:FTQ104 2.9 63.8 0.2
C20 A:FTQ104 2.9 62.9 0.2
C16 A:FTQ107 2.9 41.6 0.2
N1 A:FTQ105 3.0 55.8 0.2
N6 A:FTQ105 3.0 57.3 0.2
N5 A:FTQ105 3.0 57.5 0.2
N2 A:FTQ105 3.0 57.0 0.2
C1 A:FTQ106 3.2 40.8 0.2
C12 A:FTQ106 3.2 38.1 0.2
C2 A:FTQ105 3.2 54.9 0.2
C11 A:FTQ105 3.5 57.2 0.2
C17 A:FTQ107 3.5 42.0 0.2
C3 A:FTQ105 3.5 57.3 0.2
C5 A:FTQ106 3.5 40.1 0.2
C20 A:FTQ106 3.6 39.0 0.2
AU A:FTQ106 3.6 43.0 0.2
C12 A:FTQ105 3.7 0.5 0.0
C16 A:FTQ106 3.7 37.7 0.2
N1 A:DG5 3.7 28.9 1.0
C6 A:DG5 3.8 29.4 1.0
AU A:FTQ104 3.9 66.5 0.2
O6 A:DG5 3.9 28.7 1.0
N6 A:FTQ107 4.1 42.1 0.2
C15 A:FTQ106 4.1 37.9 0.2
C4 A:FTQ105 4.1 56.1 0.2
C14 A:FTQ105 4.1 56.8 0.2
C13 A:FTQ105 4.2 57.3 0.2
C5 A:FTQ105 4.2 56.0 0.2
O6 A:DG11 4.2 27.6 1.0
C2 A:DG5 4.3 29.2 1.0
C2 A:FTQ104 4.3 63.5 0.2
N6 A:FTQ106 4.3 39.6 0.2
C5 A:DG5 4.4 30.3 1.0
N1 A:FTQ106 4.4 40.4 0.2
C19 A:FTQ107 4.5 41.0 0.2
C10 A:FTQ106 4.6 40.0 0.2
C4 A:FTQ106 4.6 40.0 0.2
C18 A:FTQ105 4.7 57.7 0.2
N2 A:DG5 4.8 29.3 1.0
C6 A:DG11 4.8 27.3 1.0
C15 A:FTQ105 4.8 0.5 0.0
C4 A:DG5 4.8 30.5 1.0
N3 A:DG5 4.8 29.4 1.0
C14 A:FTQ107 4.9 41.7 0.2

Gold binding site 3 out of 4 in 6h5r

Go back to Gold Binding Sites List in 6h5r
Gold binding site 3 out of 4 in the Structure of the Complex of A Human Telomeric Dna with Bis(1-Butyl-3- Methyl-Imidazole-2-Ylidene) Gold(I)


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of Structure of the Complex of A Human Telomeric Dna with Bis(1-Butyl-3- Methyl-Imidazole-2-Ylidene) Gold(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au106

b:43.0
occ:0.25
AU A:FTQ106 0.0 43.0 0.2
C5 A:FTQ105 0.8 56.0 0.2
C4 A:FTQ105 1.0 56.1 0.2
N2 A:FTQ105 1.2 57.0 0.2
C19 A:FTQ107 1.4 41.0 0.2
N1 A:FTQ105 1.4 55.8 0.2
C1 A:FTQ105 1.5 56.8 0.2
C18 A:FTQ107 1.9 41.5 0.2
C20 A:FTQ104 1.9 62.9 0.2
C3 A:FTQ107 1.9 41.5 0.2
C10 A:FTQ106 2.0 40.0 0.2
C1 A:FTQ106 2.0 40.8 0.2
C18 A:FTQ104 2.1 63.0 0.2
C19 A:FTQ104 2.3 62.8 0.2
C3 A:FTQ105 2.6 57.3 0.2
C3 A:FTQ104 2.8 62.8 0.2
C20 A:FTQ107 2.9 41.3 0.2
C2 A:FTQ105 2.9 54.9 0.2
N6 A:FTQ106 3.0 39.6 0.2
N2 A:FTQ106 3.0 40.1 0.2
N1 A:FTQ106 3.0 40.4 0.2
N5 A:FTQ106 3.1 39.9 0.2
C12 A:FTQ106 3.2 38.1 0.2
C18 A:FTQ105 3.3 57.7 0.2
N2 A:FTQ107 3.3 41.8 0.2
C3 A:FTQ106 3.3 39.9 0.2
C2 A:FTQ106 3.4 40.3 0.2
N1 A:DG11 3.5 26.2 1.0
C6 A:DG11 3.5 27.3 1.0
C11 A:FTQ106 3.5 39.6 0.2
AU A:FTQ105 3.6 58.8 0.2
C16 A:FTQ104 3.6 67.0 0.2
C17 A:FTQ104 3.7 67.1 0.2
C19 A:FTQ105 3.7 0.5 0.0
C2 A:DG11 3.9 27.2 1.0
O6 A:DG11 3.9 27.6 1.0
C5 A:DG11 3.9 27.8 1.0
C1 A:FTQ107 4.1 41.9 0.2
N2 A:FTQ104 4.1 64.0 0.2
C5 A:FTQ106 4.1 40.1 0.2
C14 A:FTQ106 4.1 39.3 0.2
C4 A:DG11 4.2 28.2 1.0
C4 A:FTQ106 4.2 40.0 0.2
C12 A:FTQ107 4.2 41.7 0.2
C13 A:FTQ106 4.2 39.7 0.2
N3 A:DG11 4.2 27.2 1.0
C5 A:FTQ107 4.3 41.5 0.2
AU A:FTQ107 4.3 42.8 0.2
C15 A:FTQ104 4.4 67.0 0.2
N2 A:DG11 4.5 27.1 1.0
O6 A:DG17 4.6 27.0 1.0
N7 A:DG11 4.6 29.1 1.0
C5 A:FTQ104 4.7 63.2 0.2
C15 A:FTQ106 4.7 37.9 0.2
C18 A:FTQ106 4.9 39.3 0.2
C12 A:FTQ104 4.9 66.4 0.2
C7 A:DT12 5.0 53.2 1.0
N9 A:DG11 5.0 30.1 1.0

Gold binding site 4 out of 4 in 6h5r

Go back to Gold Binding Sites List in 6h5r
Gold binding site 4 out of 4 in the Structure of the Complex of A Human Telomeric Dna with Bis(1-Butyl-3- Methyl-Imidazole-2-Ylidene) Gold(I)


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of Structure of the Complex of A Human Telomeric Dna with Bis(1-Butyl-3- Methyl-Imidazole-2-Ylidene) Gold(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au107

b:42.8
occ:0.25
AU A:FTQ107 0.0 42.8 0.2
C14 A:FTQ106 0.8 39.3 0.2
C12 A:FTQ104 0.9 66.4 0.2
C15 A:FTQ104 1.2 67.0 0.2
N6 A:FTQ106 1.4 39.6 0.2
C16 A:FTQ104 1.6 67.0 0.2
C1 A:FTQ107 2.0 41.9 0.2
C10 A:FTQ107 2.0 42.0 0.2
C13 A:FTQ106 2.1 39.7 0.2
C2 A:FTQ105 2.1 54.9 0.2
C12 A:FTQ106 2.1 38.1 0.2
C15 A:FTQ106 2.2 37.9 0.2
N6 A:FTQ104 2.3 65.8 0.2
C10 A:FTQ106 2.6 40.0 0.2
N5 A:FTQ106 2.8 39.9 0.2
N1 A:FTQ107 3.0 41.7 0.2
N6 A:FTQ107 3.0 42.1 0.2
N2 A:FTQ107 3.0 41.8 0.2
N5 A:FTQ107 3.0 42.4 0.2
C17 A:FTQ104 3.0 67.1 0.2
N1 A:FTQ105 3.2 55.8 0.2
C2 A:FTQ107 3.3 41.7 0.2
C14 A:FTQ104 3.3 65.7 0.2
C12 A:FTQ107 3.3 41.7 0.2
C10 A:FTQ104 3.4 65.9 0.2
C3 A:FTQ107 3.4 41.5 0.2
N1 A:DG17 3.5 25.8 1.0
C11 A:FTQ107 3.5 42.2 0.2
C6 A:DG17 3.5 26.1 1.0
C4 A:FTQ105 3.6 56.1 0.2
C16 A:FTQ106 3.7 37.7 0.2
C18 A:FTQ104 3.9 63.0 0.2
O6 A:DG17 3.9 27.0 1.0
C2 A:DG17 3.9 27.0 1.0
AU A:FTQ104 3.9 66.5 0.2
C5 A:DG17 4.0 27.9 1.0
C3 A:FTQ104 4.0 62.8 0.2
C4 A:FTQ107 4.1 41.6 0.2
C5 A:FTQ107 4.1 41.5 0.2
C14 A:FTQ107 4.2 41.7 0.2
C13 A:FTQ107 4.2 42.1 0.2
C4 A:DG17 4.3 27.9 1.0
C11 A:FTQ106 4.3 39.6 0.2
N3 A:DG17 4.3 27.0 1.0
AU A:FTQ106 4.3 43.0 0.2
C1 A:FTQ105 4.4 56.8 0.2
C13 A:FTQ104 4.5 65.3 0.2
N5 A:FTQ104 4.5 65.4 0.2
N2 A:DG17 4.5 26.3 1.0
O6 A:DG23 4.5 27.5 1.0
C17 A:FTQ106 4.5 37.0 0.2
C18 A:FTQ107 4.6 41.5 0.2
N7 A:DG17 4.7 27.9 1.0
C15 A:FTQ107 4.8 41.5 0.2
C5 A:FTQ105 4.9 56.0 0.2
N2 A:FTQ104 5.0 64.0 0.2

Reference:

F.Guarra, T.Marzo, M.Ferraroni, F.Papi, C.Bazzicalupi, P.Gratteri, G.Pescitelli, L.Messori, T.Biver, C.Gabbiani. Interaction of A Gold(I) Dicarbene Anticancer Drug with Human Telomeric Dna G-Quadruplex: Solution and Computationally Aided X-Ray Diffraction Analysis. Dalton Trans V. 47 16132 2018.
ISSN: ESSN 1477-9234
PubMed: 30378627
DOI: 10.1039/C8DT03607A
Page generated: Sat Dec 12 01:54:33 2020

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