Cadmium in PDB 8gzj: Crystal Structure of CD2+-Bound Dna Aptamer

The structure of Crystal Structure of CD2+-Bound Dna Aptamer, PDB code: 8gzj was solved by J.H.Gan, H.H.Liu, Y.Q.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.45 / 2.09
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.474, 41.932, 73.247, 90, 106.2, 90
R / Rfree (%)	23.2 / 27.4

The structure of Crystal Structure of CD2+-Bound Dna Aptamer also contains other interesting chemical elements:

Barium

(Ba)

4 atoms

The binding sites of Cadmium atom in the Crystal Structure of CD2+-Bound Dna Aptamer (pdb code 8gzj). 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 CD2+-Bound Dna Aptamer, PDB code: 8gzj:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Crystal Structure of CD2+-Bound Dna Aptamer


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 CD2+-Bound Dna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd101 b:20.2 occ:1.00 N7 A:DG9 2.3 11.3 1.0 O A:HOH201 2.4 12.3 1.0 N3 A:DC12 2.4 14.5 1.0 O2 A:DC12 2.5 14.5 1.0 N7 A:DG16 2.5 13.8 1.0 O A:HOH212 2.5 21.0 1.0 C2 A:DC12 2.8 17.7 1.0 C8 A:DG9 3.2 11.0 1.0 C5 A:DG9 3.2 17.0 1.0 C8 A:DG16 3.3 14.0 1.0 C5 A:DG16 3.5 13.3 1.0 O6 A:DG9 3.5 14.1 1.0 C4 A:DC12 3.6 15.3 1.0 C6 A:DG9 3.7 16.4 1.0 O6 A:DG16 3.9 21.9 1.0 N4 A:DC12 4.0 23.2 1.0 C6 A:DG16 4.0 12.9 1.0 N1 A:DC12 4.2 14.9 1.0 N9 A:DG9 4.4 15.4 1.0 C4 A:DG9 4.4 10.1 1.0 N9 A:DG16 4.4 16.5 1.0 C4 A:DG16 4.5 13.3 1.0 N3 A:DA15 4.7 10.7 1.0 C2 A:DA15 4.8 11.0 1.0 C5 A:DC12 4.8 15.0 1.0

Cadmium binding site 2 out of 3 in the Crystal Structure of CD2+-Bound Dna Aptamer


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 CD2+-Bound Dna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd101 b:37.6 occ:1.00 N7 B:DG9 2.3 30.9 1.0 O B:HOH202 2.4 30.0 1.0 N3 B:DC12 2.4 29.4 1.0 N7 B:DG16 2.4 28.5 1.0 O2 B:DC12 2.6 34.6 1.0 C2 B:DC12 2.9 30.6 1.0 C8 B:DG9 3.1 28.6 1.0 C8 B:DG16 3.3 28.6 1.0 C5 B:DG9 3.3 29.1 1.0 C5 B:DG16 3.4 30.6 1.0 C4 B:DC12 3.5 42.0 1.0 O6 B:DG9 3.7 43.2 1.0 O6 B:DG16 3.7 28.1 1.0 N4 B:DC12 3.8 30.5 1.0 C6 B:DG9 3.9 28.5 1.0 C6 B:DG16 3.9 28.0 1.0 N1 B:DC12 4.3 30.4 1.0 N9 B:DG9 4.3 32.3 1.0 N9 B:DG16 4.4 32.1 1.0 C4 B:DG9 4.4 28.3 1.0 C4 B:DG16 4.5 36.0 1.0 C2 B:DA15 4.5 32.6 1.0 N3 B:DA15 4.5 29.3 1.0 C5 B:DC12 4.8 29.8 1.0

Cadmium binding site 3 out of 3 in the Crystal Structure of CD2+-Bound Dna Aptamer


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 CD2+-Bound Dna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd101 b:58.4 occ:1.00 N7 C:DG16 2.4 47.3 1.0 N3 C:DC12 2.5 64.9 1.0 N7 C:DG9 2.6 81.9 1.0 O2 C:DC12 2.9 68.8 1.0 C2 C:DC12 3.1 68.9 1.0 C8 C:DG16 3.3 49.7 1.0 C5 C:DG16 3.4 55.7 1.0 C5 C:DG9 3.4 77.5 1.0 O6 C:DG9 3.5 55.0 1.0 C8 C:DG9 3.5 72.8 1.0 O6 C:DG16 3.6 58.8 1.0 C4 C:DC12 3.6 51.8 1.0 C6 C:DG9 3.8 66.4 1.0 C6 C:DG16 3.8 53.3 1.0 N4 C:DC12 3.9 46.6 1.0 N9 C:DG16 4.4 42.1 1.0 N1 C:DC12 4.5 70.8 1.0 C4 C:DG16 4.5 40.9 1.0 C4 C:DG9 4.6 72.0 1.0 N9 C:DG9 4.6 74.1 1.0 N2 C:DG8 4.7 52.5 1.0 N3 C:DA15 4.8 53.3 1.0 C5 C:DC12 4.9 52.2 1.0

H.Liu, Y.Gao, J.Mathivanan, Z.Armour-Garb, Z.Shao, Y.Zhang, X.Zhao, Q.Shao, W.Zhang, J.Yang, C.Cao, H.Li, J.Sheng, J.Gan. Crystal Structures and Identification of Novel CD2+-Specific Dna Aptamer. Nucleic Acids Res. V. 51 4625 2023.
ISSN: ESSN 1362-4962
PubMed: 37013991
DOI: 10.1093/NAR/GKAD239