Atomistry » Gold » PDB 5jjo-7pvj » 7edu
Atomistry »
  Gold »
    PDB 5jjo-7pvj »
      7edu »

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

Protein crystallography data

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

Gold Binding Sites:

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 7edu

Go back to Gold Binding Sites List in 7edu
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 7edu

Go back to Gold Binding Sites List in 7edu
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 7edu

Go back to Gold Binding Sites List in 7edu
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 7edu

Go back to Gold Binding Sites List in 7edu
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

Reference:

J.Kondo, E.Iwase. Rna Duplex Containing C-Au-C Base Pair To Be Published.
Page generated: Mon Jul 7 01:41:26 2025

Last articles

Ca in 6AL6
Ca in 6AJC
Ca in 6AK9
Ca in 6AJA
Ca in 6AK8
Ca in 6AJB
Ca in 6AIJ
Ca in 6AID
Ca in 6AJ8
Ca in 6AI0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy