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

Protein crystallography data

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

Other elements in 8gzl:

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

Cadmium (Cd) 5 atoms

Barium Binding Sites:

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

Barium binding site 1 out of 2 in 8gzl

Go back to Barium Binding Sites List in 8gzl
Barium binding site 1 out of 2 in the Crystal Structure of CD2+-Bound Dna Aptamer


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of CD2+-Bound Dna Aptamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba103

b:160.6
occ:1.00
N7 A:DG1 2.8 95.1 1.0
C8 A:DG1 3.6 98.0 1.0
C5 A:DG1 3.9 95.6 1.0
O6 A:DG1 4.2 98.4 1.0
C6 A:DG1 4.5 97.1 1.0
N9 A:DG1 4.9 102.8 1.0
N4 B:DC25 4.9 101.7 1.0

Barium binding site 2 out of 2 in 8gzl

Go back to Barium Binding Sites List in 8gzl
Barium binding site 2 out of 2 in the Crystal Structure of CD2+-Bound Dna Aptamer


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of CD2+-Bound Dna Aptamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba102

b:188.0
occ:1.00
N7 B:DG1 2.9 112.9 1.0
C8 B:DG1 3.8 113.1 1.0
C5 B:DG1 3.9 107.2 1.0
O6 B:DG1 3.9 104.2 1.0
C6 B:DG1 4.3 101.7 1.0
N4 A:DC25 4.6 103.8 1.0

Reference:

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
Page generated: Wed Jul 10 16:13:40 2024

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