Cadmium in PDB 8gzm: Crystal Structure of CD2+-Bound Dna Aptamer T22C Mutant

The structure of Crystal Structure of CD2+-Bound Dna Aptamer T22C Mutant, PDB code: 8gzm 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)	22.67 / 2.55
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	46.388, 46.388, 107.301, 90, 90, 90
R / Rfree (%)	19.4 / 20.5

The structure of Crystal Structure of CD2+-Bound Dna Aptamer T22C Mutant also contains other interesting chemical elements:

Barium

(Ba)

3 atoms

The binding sites of Cadmium atom in the Crystal Structure of CD2+-Bound Dna Aptamer T22C Mutant (pdb code 8gzm). 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 T22C Mutant, PDB code: 8gzm:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Crystal Structure of CD2+-Bound Dna Aptamer T22C 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 T22C Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd101 b:39.2 occ:1.00 O A:HOH202 2.3 30.0 1.0 N7 A:DG16 2.3 31.0 1.0 O A:HOH201 2.4 33.9 1.0 N7 A:DG9 2.4 37.1 1.0 N3 A:DC12 2.5 35.1 1.0 O2 A:DC12 2.6 35.8 1.0 C2 A:DC12 2.9 36.1 1.0 C8 A:DG16 3.1 37.8 1.0 O6 A:DG9 3.2 40.4 1.0 C5 A:DG9 3.2 44.0 1.0 C5 A:DG16 3.3 44.1 1.0 C8 A:DG9 3.4 53.2 1.0 C6 A:DG9 3.6 47.1 1.0 C4 A:DC12 3.6 50.0 1.0 O6 A:DG16 3.8 40.8 1.0 C6 A:DG16 3.9 42.1 1.0 N4 A:DC12 4.0 35.1 1.0 N1 A:DC12 4.2 49.5 1.0 N9 A:DG16 4.3 46.3 1.0 C4 A:DG16 4.4 43.9 1.0 C4 A:DG9 4.5 41.3 1.0 N9 A:DG9 4.5 46.1 1.0 N3 A:DA15 4.7 41.2 1.0 C5 A:DC12 4.8 52.0 1.0 C2 A:DA15 4.9 44.8 1.0 O2 A:DT11 4.9 53.9 1.0 N1 A:DG9 4.9 41.4 1.0

Cadmium binding site 2 out of 2 in the Crystal Structure of CD2+-Bound Dna Aptamer T22C 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 T22C Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd102 b:63.8 occ:1.00 N3 A:DT10 2.3 51.4 1.0 O4 A:DT10 3.1 47.8 1.0 O A:HOH205 3.1 20.2 1.0 C4 A:DT10 3.1 53.8 1.0 C2 A:DT10 3.3 53.4 1.0 O2 A:DT10 3.4 57.9 1.0 O A:HOH204 4.4 44.1 1.0 C5 A:DT10 4.5 53.3 1.0 N1 A:DT10 4.5 56.8 1.0 C6 A:DT10 5.0 59.4 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