Cadmium in PDB 8gzk: Crystal Structure of CD2+-Bound Dna Aptamer T10A Mutant

The structure of Crystal Structure of CD2+-Bound Dna Aptamer T10A Mutant, PDB code: 8gzk 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)	28.08 / 2.94
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	28.708, 136.379, 51.133, 90, 104.39, 90
R / Rfree (%)	23.3 / 28.9

The structure of Crystal Structure of CD2+-Bound Dna Aptamer T10A Mutant also contains other interesting chemical elements:

Barium

(Ba)

5 atoms

The binding sites of Cadmium atom in the Crystal Structure of CD2+-Bound Dna Aptamer T10A Mutant (pdb code 8gzk). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of CD2+-Bound Dna Aptamer T10A Mutant, PDB code: 8gzk:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Crystal Structure of CD2+-Bound Dna Aptamer T10A Mutant


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 T10A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd101 b:50.5 occ:1.00 N7 A:DG9 2.3 18.8 1.0 O A:HOH201 2.4 22.5 1.0 N3 A:DC12 2.5 20.8 1.0 N7 A:DG16 2.5 21.9 1.0 O2 A:DC12 2.6 19.9 1.0 C2 A:DC12 2.9 20.1 1.0 C8 A:DG16 3.2 22.1 1.0 C8 A:DG9 3.3 18.5 1.0 C5 A:DG9 3.3 18.2 1.0 O6 A:DG9 3.4 18.8 1.0 C5 A:DG16 3.5 21.6 1.0 C4 A:DC12 3.7 20.9 1.0 C6 A:DG9 3.8 18.2 1.0 O6 A:DG16 3.8 22.7 1.0 C6 A:DG16 4.0 21.6 1.0 N4 A:DC12 4.1 21.6 1.0 N1 A:DC12 4.3 19.6 1.0 N9 A:DG16 4.4 22.0 1.0 N9 A:DG9 4.5 19.5 1.0 C4 A:DG16 4.5 21.7 1.0 C4 A:DG9 4.5 19.0 1.0 N3 A:DA15 4.6 17.0 1.0 C2 A:DA15 4.6 15.7 1.0 N2 A:DG8 4.8 25.3 1.0 C5 A:DC12 4.8 20.5 1.0

Cadmium binding site 2 out of 2 in the Crystal Structure of CD2+-Bound Dna Aptamer T10A Mutant


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 T10A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd101 b:79.6 occ:1.00 N7 B:DG16 2.5 79.4 1.0 N3 B:DC12 2.5 78.7 1.0 O B:HOH201 2.6 80.1 1.0 N7 B:DG9 2.6 82.0 1.0 O2 B:DC12 2.6 79.0 1.0 O6 B:DG16 2.9 79.9 1.0 C2 B:DC12 2.9 78.8 1.0 C5 B:DG16 3.1 80.2 1.0 C6 B:DG16 3.3 80.4 1.0 O6 B:DG9 3.4 82.6 1.0 C8 B:DG16 3.5 79.6 1.0 C5 B:DG9 3.5 83.2 1.0 C8 B:DG9 3.6 82.4 1.0 C4 B:DC12 3.7 78.5 1.0 C6 B:DG9 3.8 83.4 1.0 N4 B:DC12 4.0 78.4 1.0 N1 B:DC12 4.3 78.8 1.0 C4 B:DG16 4.3 80.9 1.0 N9 B:DG16 4.5 80.5 1.0 N3 B:DA15 4.6 83.8 1.0 N1 B:DG16 4.6 81.3 1.0 N2 B:DG8 4.6 76.3 1.0 C2 B:DA15 4.6 83.9 1.0 C4 B:DG9 4.7 84.2 1.0 N9 B:DG9 4.8 83.7 1.0 C5 B:DC12 4.9 78.5 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