Cadmium in PDB 8aml: Crystal Structure of Auguggcau Duplex with Cadmium Ions

The structure of Crystal Structure of Auguggcau Duplex with Cadmium Ions, PDB code: 8aml was solved by A.Kiliszek, W.Rypniewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.52 / 2.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.193, 90.6, 139.623, 90, 91.5, 90
R / Rfree (%)	21.9 / 26.7

The binding sites of Cadmium atom in the Crystal Structure of Auguggcau Duplex with Cadmium Ions (pdb code 8aml). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of Auguggcau Duplex with Cadmium Ions, PDB code: 8aml:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Crystal Structure of Auguggcau Duplex with Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Auguggcau Duplex with Cadmium Ions within 5.0Å range: probe atom residue distance (Å) B Occ F:Cd101 b:207.0 occ:1.00 O6 F:G5 2.8 78.2 1.0 O6 E:G5 3.1 84.1 1.0 O4 F:U4 3.5 62.6 1.0 O4 E:U4 3.8 87.8 1.0 C6 E:G5 3.8 85.0 1.0 N1 E:G5 3.8 86.9 1.0 C6 F:G5 3.9 72.0 1.0 O6 E:G6 4.1 62.8 1.0 N1 F:G5 4.4 75.6 1.0 C4 F:U4 4.6 55.8 1.0 C4 E:U4 4.6 86.4 1.0 O6 F:G6 4.9 83.0 1.0 N3 F:U4 5.0 56.7 1.0

Cadmium binding site 2 out of 3 in the Crystal Structure of Auguggcau Duplex with Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Auguggcau Duplex with Cadmium Ions within 5.0Å range: probe atom residue distance (Å) B Occ G:Cd101 b:182.9 occ:1.00 O6 H:G5 2.8 79.7 1.0 O6 G:G5 2.8 76.2 1.0 O4 G:U4 3.2 80.1 1.0 O4 H:U4 3.3 64.7 1.0 C6 G:G5 3.8 71.8 1.0 C6 H:G5 3.8 70.2 1.0 O6 G:G6 3.9 66.5 1.0 N1 G:G5 4.0 74.8 1.0 C4 G:U4 4.2 81.0 1.0 N1 H:G5 4.3 70.5 1.0 C4 H:U4 4.3 60.3 1.0 N3 H:U4 4.6 66.6 1.0 O6 H:G3 4.8 63.2 1.0 C6 G:G6 4.9 64.3 1.0 N3 G:U4 4.9 77.9 1.0 O6 H:G6 5.0 74.0 1.0

Cadmium binding site 3 out of 3 in the Crystal Structure of Auguggcau Duplex with Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Auguggcau Duplex with Cadmium Ions within 5.0Å range: probe atom residue distance (Å) B Occ K:Cd101 b:174.7 occ:0.70 O6 L:G5 2.7 76.8 1.0 O4 K:U4 2.9 89.4 1.0 O4 L:U4 3.1 64.6 1.0 O6 K:G5 3.4 82.8 1.0 C6 L:G5 3.9 69.3 1.0 C4 K:U4 4.0 79.1 1.0 C4 L:U4 4.2 54.9 1.0 C6 K:G5 4.4 82.5 1.0 O6 L:G6 4.6 79.2 1.0 N1 K:G5 4.6 84.3 1.0 N3 K:U4 4.7 78.1 1.0 N1 L:G5 4.7 70.0 1.0 N3 L:U4 4.9 58.1 1.0 O6 K:G6 5.0 63.3 1.0 C5 L:G5 5.0 61.3 1.0

A.Kiliszek, M.Pluta, M.Bejger, W.Rypniewski. Structure and Thermodynamics of A Ugg Motif Interacting with BA2+ and Other Metal Ions: Accommodating Changes in the Rna Structure and the Presence of A G(Syn)-G(Syn) Pair. Rna 2022.
ISSN: ESSN 1469-9001
PubMed: 36319090
DOI: 10.1261/RNA.079414.122