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

The structure of Crystal Structure of CD2+-Bound Dna Aptamer, PDB code: 8gzl 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)	29.37 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	26.8, 45.69, 147.02, 90, 92.87, 90
R / Rfree (%)	23.3 / 28.4

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

Barium

(Ba)

2 atoms

The binding sites of Cadmium atom in the Crystal Structure of CD2+-Bound Dna Aptamer (pdb code 8gzl). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Crystal Structure of CD2+-Bound Dna Aptamer, PDB code: 8gzl:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 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:67.5 occ:1.00 O A:HOH201 2.3 30.0 1.0 N3 A:DC12 2.6 63.1 1.0 N7 A:DG9 2.7 72.2 1.0 N7 A:DG16 2.7 66.0 1.0 O6 A:DG9 2.8 67.0 1.0 O2 A:DC12 2.9 91.7 1.0 C2 A:DC12 3.1 77.1 1.0 C5 A:DG9 3.3 71.5 1.0 C6 A:DG9 3.3 67.2 1.0 C8 A:DG16 3.5 66.6 1.0 C5 A:DG16 3.5 67.0 1.0 C4 A:DC12 3.7 66.1 1.0 O6 A:DG16 3.8 78.1 1.0 C8 A:DG9 3.8 74.8 1.0 C6 A:DG16 4.0 70.7 1.0 N4 A:DC12 4.0 72.2 1.0 N2 A:DG15 4.3 68.2 1.0 N3 A:DG15 4.5 73.1 1.0 N1 A:DC12 4.5 82.0 1.0 N9 A:DG16 4.5 67.4 1.0 C4 A:DG16 4.6 67.2 1.0 C4 A:DG9 4.6 69.0 1.0 C2 A:DG15 4.6 69.5 1.0 N1 A:DG9 4.7 66.5 1.0 N9 A:DG9 4.9 72.2 1.0 C5 A:DC12 5.0 75.1 1.0

Cadmium binding site 2 out of 5 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 A:Cd102 b:71.9 occ:1.00 OP2 A:DC11 2.5 75.6 1.0 N6 A:DA13 2.9 72.0 1.0 N7 A:DA13 3.6 67.0 1.0 P A:DC11 3.7 87.4 1.0 C6 A:DA13 3.8 73.1 1.0 OP1 A:DC11 4.0 75.6 1.0 C5 A:DA13 4.0 69.2 1.0 O5' A:DC11 4.4 75.6 1.0 C5 A:DC11 4.5 75.8 1.0 C6 A:DC11 4.6 83.4 1.0 C8 A:DA13 4.8 75.3 1.0 C4' A:DT10 4.9 64.1 1.0 O3' A:DT10 5.0 65.1 1.0

Cadmium binding site 3 out of 5 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 B:Cd101 b:79.1 occ:1.00 N3 B:DC12 2.6 72.9 1.0 N7 B:DG9 2.7 80.4 1.0 N7 B:DG16 2.7 85.0 1.0 O6 B:DG9 2.8 84.9 1.0 O2 B:DC12 2.9 81.6 1.0 C2 B:DC12 3.1 81.1 1.0 C5 B:DG9 3.3 83.0 1.0 C6 B:DG9 3.4 83.7 1.0 C8 B:DG16 3.5 88.0 1.0 C5 B:DG16 3.5 82.1 1.0 C4 B:DC12 3.7 72.2 1.0 O6 B:DG16 3.7 79.7 1.0 C8 B:DG9 3.8 82.5 1.0 C6 B:DG16 3.9 79.2 1.0 N4 B:DC12 4.0 73.7 1.0 N2 B:DG15 4.3 81.5 1.0 N1 B:DC12 4.4 80.5 1.0 N3 B:DG15 4.5 79.0 1.0 N9 B:DG16 4.5 87.7 1.0 C4 B:DG16 4.5 82.2 1.0 C4 B:DG9 4.6 82.5 1.0 C2 B:DG15 4.6 80.0 1.0 N1 B:DG9 4.7 83.9 1.0 N9 B:DG9 4.8 77.6 1.0 C5 B:DC12 4.9 70.3 1.0

Cadmium binding site 4 out of 5 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 4 of Crystal Structure of CD2+-Bound Dna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd101 b:66.5 occ:1.00 O C:HOH202 2.3 30.0 1.0 N7 C:DG9 2.5 66.4 1.0 N3 C:DC12 2.5 63.3 1.0 N7 C:DG16 2.7 68.6 1.0 O6 C:DG9 2.8 66.8 1.0 O2 C:DC12 3.1 85.1 1.0 C5 C:DG9 3.1 66.7 1.0 C2 C:DC12 3.2 77.0 1.0 C6 C:DG9 3.3 66.0 1.0 O6 C:DG16 3.3 73.8 1.0 C5 C:DG16 3.4 67.8 1.0 C4 C:DC12 3.5 69.0 1.0 C8 C:DG9 3.6 71.7 1.0 C6 C:DG16 3.6 73.1 1.0 C8 C:DG16 3.7 71.0 1.0 N4 C:DC12 3.7 71.4 1.0 N2 C:DG15 4.2 70.8 1.0 C4 C:DG9 4.4 67.5 1.0 C4 C:DG16 4.5 66.7 1.0 N1 C:DC12 4.5 84.1 1.0 N3 C:DG15 4.5 64.4 1.0 C2 C:DG15 4.6 64.2 1.0 N9 C:DG16 4.6 68.0 1.0 N9 C:DG9 4.6 69.5 1.0 N1 C:DG9 4.7 65.1 1.0 C5 C:DC12 4.8 77.2 1.0 N1 C:DG16 4.9 75.1 1.0

Cadmium binding site 5 out of 5 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 5 of Crystal Structure of CD2+-Bound Dna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd101 b:96.2 occ:1.00 N3 D:DC12 2.7 99.4 1.0 N7 D:DG16 2.7 106.0 1.0 O6 D:DG9 2.7 92.7 1.0 N7 D:DG9 2.8 99.4 1.0 O2 D:DC12 2.9 101.1 1.0 C2 D:DC12 3.2 103.1 1.0 C6 D:DG9 3.3 95.0 1.0 C5 D:DG9 3.4 96.0 1.0 C8 D:DG16 3.5 105.7 1.0 C5 D:DG16 3.6 104.0 1.0 C4 D:DC12 3.8 106.6 1.0 O6 D:DG16 3.9 108.9 1.0 C8 D:DG9 4.0 106.3 1.0 C6 D:DG16 4.1 104.1 1.0 N4 D:DC12 4.1 110.3 1.0 N9 D:DG16 4.5 103.2 1.0 N1 D:DC12 4.5 108.7 1.0 N2 D:DG15 4.5 94.9 1.0 C4 D:DG16 4.6 102.9 1.0 N3 D:DG15 4.6 85.4 1.0 C4 D:DG9 4.7 93.8 1.0 N1 D:DG9 4.7 94.0 1.0 C2 D:DG15 4.8 91.3 1.0 N9 D:DG9 5.0 103.6 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