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

Br in 5EFH
Br in 5EV2
Br in 5EV1
Br in 5EUS
Br in 5ETV
Br in 5EAI
Br in 5E0I
Br in 5ETP
Br in 5EQH
Br in 5CYQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy