Gold in PDB 7edu: Rna Duplex Containing C-Au-C Base Pair

The structure of Rna Duplex Containing C-Au-C Base Pair, PDB code: 7edu was solved by J.Kondo, E.Iwase, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.18 / 2.30
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	29.216, 29.216, 257.794, 90, 90, 120
R / Rfree (%)	17.7 / 22.9

The binding sites of Gold atom in the Rna Duplex Containing C-Au-C Base Pair (pdb code 7edu). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 4 binding sites of Gold where determined in the Rna Duplex Containing C-Au-C Base Pair, PDB code: 7edu:
Jump to Gold binding site number: 1; 2; 3; 4;

Gold binding site 1 out of 4 in the Rna Duplex Containing C-Au-C Base Pair


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Rna Duplex Containing C-Au-C Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ B:Au101 b:47.0 occ:1.00 N3 B:C9 2.1 35.5 1.0 N3 A:C4 2.2 26.8 1.0 C2 B:C9 2.9 34.4 1.0 O2 B:C9 2.9 34.0 1.0 C2 A:C4 3.0 23.9 1.0 O2 A:C4 3.0 25.1 1.0 C4 B:C9 3.1 29.7 1.0 C4 A:C4 3.2 27.1 1.0 N4 A:C4 3.2 26.4 1.0 N4 B:C9 3.3 26.9 1.0 O4 B:U10 3.4 39.9 1.0 C4 B:U10 3.4 36.3 1.0 N6 B:A8 3.5 33.0 1.0 N6 A:A3 3.6 27.6 1.0 O4 A:U5 3.6 32.3 1.0 N3 B:U10 3.6 32.9 1.0 C4 A:U5 3.7 28.3 1.0 N3 A:U5 3.7 31.5 1.0 O A:HOH101 3.7 37.0 1.0 N1 B:A8 3.9 28.0 1.0 C6 B:A8 3.9 32.1 1.0 C6 A:A3 4.0 28.3 1.0 N1 A:A3 4.0 27.8 1.0 C5 B:U10 4.1 38.2 1.0 O B:HOH202 4.1 26.9 1.0 N1 B:C9 4.2 37.0 1.0 C2 B:U10 4.3 37.5 1.0 N1 A:C4 4.4 36.2 1.0 C2 A:U5 4.4 32.4 1.0 C5 A:U5 4.4 23.9 1.0 C5 B:C9 4.5 36.5 1.0 C5 A:C4 4.5 27.0 1.0 C6 B:U10 4.7 39.2 1.0 N1 B:U10 4.8 35.2 1.0 C6 B:C9 4.9 34.9 1.0 O2 A:U5 4.9 29.5 1.0 C2 B:A8 4.9 30.3 1.0 N1 A:U5 4.9 29.5 1.0 O2 B:U10 4.9 42.1 1.0 C6 A:U5 4.9 28.6 1.0 C6 A:C4 4.9 32.7 1.0 C5 B:A8 5.0 31.9 1.0 C2 A:A3 5.0 29.8 1.0

Gold binding site 2 out of 4 in the Rna Duplex Containing C-Au-C Base Pair


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Rna Duplex Containing C-Au-C Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ B:Au102 b:45.3 occ:1.00 N3 B:C4 2.2 29.9 1.0 N3 A:C9 2.2 28.0 1.0 C2 B:C4 3.0 30.6 1.0 O2 B:C4 3.0 30.8 1.0 O2 A:C9 3.0 22.6 1.0 C2 A:C9 3.0 22.8 1.0 C4 B:C4 3.1 27.2 1.0 C4 A:C9 3.1 32.4 1.0 N4 B:C4 3.2 24.4 1.0 N4 A:C9 3.2 31.0 1.0 N6 B:A3 3.4 33.2 1.0 N3 B:U5 3.6 29.3 1.0 O4 B:U5 3.7 29.5 1.0 N3 A:U10 3.7 31.3 1.0 N6 A:A8 3.7 35.0 1.0 C4 B:U5 3.8 32.2 1.0 C6 B:A3 3.8 28.8 1.0 C4 A:U10 3.9 36.6 1.0 N1 B:A3 3.9 27.3 1.0 N1 A:A8 3.9 31.9 1.0 O4 A:U10 4.0 41.8 1.0 C6 A:A8 4.0 32.3 1.0 C2 A:U10 4.2 33.7 1.0 C2 B:U5 4.3 36.9 1.0 N1 B:C4 4.3 32.8 1.0 N1 A:C9 4.3 35.6 1.0 C5 B:C4 4.4 31.0 1.0 C5 A:C9 4.5 33.7 1.0 C5 A:U10 4.6 36.6 1.0 C5 B:U5 4.6 37.1 1.0 O2 A:U10 4.7 36.8 1.0 O2 B:U5 4.7 38.2 1.0 C2 B:A3 4.8 31.9 1.0 C2 A:A8 4.8 32.5 1.0 C5 B:A3 4.8 32.5 1.0 N1 A:U10 4.9 38.4 1.0 C6 B:C4 4.9 30.6 1.0 C6 A:C9 4.9 32.3 1.0 C6 A:U10 5.0 34.8 1.0 C5 A:A8 5.0 32.7 1.0

Gold binding site 3 out of 4 in the Rna Duplex Containing C-Au-C Base Pair


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of Rna Duplex Containing C-Au-C Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ C:Au101 b:44.0 occ:1.00 N3 C:C4 2.1 34.4 1.0 N3 D:C9 2.1 38.0 1.0 O2 D:C9 2.9 24.4 1.0 C2 D:C9 2.9 28.1 1.0 C4 C:C4 2.9 30.6 1.0 N4 C:C4 3.0 29.2 1.0 C2 C:C4 3.0 35.2 1.0 C4 D:C9 3.1 36.5 1.0 O2 C:C4 3.2 37.4 1.0 N4 D:C9 3.3 37.4 1.0 O4 C:U5 3.4 37.4 1.0 N3 D:U10 3.5 32.7 1.0 C4 C:U5 3.5 36.2 1.0 N3 C:U5 3.5 33.1 1.0 N6 D:A8 3.6 32.9 1.0 N6 C:A3 3.7 31.2 1.0 O4 D:U10 3.7 32.4 1.0 C4 D:U10 3.7 32.8 1.0 N1 C:A3 3.8 32.6 1.0 N1 D:A8 3.9 30.9 1.0 C6 D:A8 4.0 33.1 1.0 C6 C:A3 4.0 32.3 1.0 C2 D:U10 4.2 32.2 1.0 N1 D:C9 4.2 36.8 1.0 C5 C:C4 4.3 38.9 1.0 N1 C:C4 4.3 34.8 1.0 C5 C:U5 4.3 36.1 1.0 C2 C:U5 4.4 41.0 1.0 C5 D:C9 4.4 33.4 1.0 O2 D:U10 4.6 31.9 1.0 C5 D:U10 4.6 33.7 1.0 C2 C:A3 4.7 32.8 1.0 C6 D:C9 4.8 33.5 1.0 C6 C:C4 4.8 40.5 1.0 C2 D:A8 4.9 33.2 1.0 O2 C:U5 4.9 43.7 1.0 N1 D:U10 4.9 32.0 1.0 C5 D:A8 5.0 37.2 1.0 C6 C:U5 5.0 38.8 1.0

Gold binding site 4 out of 4 in the Rna Duplex Containing C-Au-C Base Pair


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of Rna Duplex Containing C-Au-C Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ C:Au102 b:45.3 occ:1.00 N3 C:C9 2.0 36.7 1.0 N3 D:C4 2.2 32.5 1.0 C4 C:C9 2.9 32.4 1.0 N4 C:C9 2.9 34.4 1.0 C2 C:C9 3.0 38.1 1.0 C2 D:C4 3.0 30.5 1.0 O2 D:C4 3.0 28.6 1.0 O2 C:C9 3.2 34.6 1.0 C4 D:C4 3.2 29.4 1.0 N4 D:C4 3.4 32.5 1.0 N6 D:A3 3.4 23.4 1.0 N6 C:A8 3.4 39.4 1.0 O4 C:U10 3.6 29.8 1.0 N3 D:U5 3.6 39.4 1.0 C4 C:U10 3.7 33.6 1.0 N1 D:A3 3.8 29.0 1.0 O4 D:U5 3.8 38.4 1.0 N3 C:U10 3.8 30.5 1.0 C4 D:U5 3.8 37.1 1.0 C6 D:A3 3.8 28.7 1.0 C6 C:A8 3.8 36.6 1.0 N1 C:A8 3.9 40.4 1.0 C5 C:C9 4.2 35.7 1.0 N1 C:C9 4.3 36.2 1.0 C2 D:U5 4.3 39.2 1.0 N1 D:C4 4.3 37.4 1.0 C5 C:U10 4.5 34.7 1.0 C2 C:U10 4.5 31.7 1.0 C5 D:C4 4.5 31.1 1.0 C5 D:U5 4.6 34.1 1.0 C2 D:A3 4.7 32.7 1.0 C6 C:C9 4.7 38.2 1.0 O2 D:U5 4.7 40.3 1.0 C2 C:A8 4.8 37.5 1.0 C5 D:A3 4.8 30.9 1.0 C5 C:A8 4.8 35.7 1.0 C6 D:C4 4.9 33.4 1.0

J.Kondo, E.Iwase. Rna Duplex Containing C-Au-C Base Pair To Be Published.