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

Protein crystallography data

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

Other elements in 8gzj:

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

Cadmium (Cd) 3 atoms

Barium Binding Sites:

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

Barium binding site 1 out of 4 in 8gzj

Go back to Barium Binding Sites List in 8gzj
Barium binding site 1 out of 4 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:Ba102

b:114.8
occ:1.00
N7 A:DG1 2.9 34.8 1.0
C8 A:DG1 3.8 29.7 1.0
C5 A:DG1 3.9 24.8 1.0
O6 A:DG1 3.9 24.8 1.0
BA B:BA102 4.1 180.9 1.0
N7 B:DG23 4.2 38.2 1.0
C6 A:DG1 4.3 25.9 1.0
C8 B:DG23 4.3 37.0 1.0
N6 A:DA2 4.4 24.8 1.0
N1 A:DA2 4.4 50.4 1.0
C6 A:DA2 4.8 23.4 1.0
C5 B:DG23 5.0 25.3 1.0

Barium binding site 2 out of 4 in 8gzj

Go back to Barium Binding Sites List in 8gzj
Barium binding site 2 out of 4 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
A:Ba103

b:116.8
occ:1.00
N7 A:DG7 2.7 29.2 1.0
C8 A:DG7 3.5 17.4 1.0
O6 A:DG8 3.7 22.1 1.0
C5 A:DG7 3.8 16.3 1.0
O6 A:DG7 4.0 16.6 1.0
C6 A:DG7 4.3 18.4 1.0
C6 A:DG8 4.5 14.0 1.0
C6 A:DC6 4.6 18.1 1.0
N7 A:DG8 4.6 19.8 1.0
C5 A:DC6 4.6 17.9 1.0
N9 A:DG7 4.7 21.1 1.0
N4 A:DC18 4.8 15.0 1.0
C5 A:DG8 4.9 13.7 1.0
C4 A:DG7 4.9 24.9 1.0

Barium binding site 3 out of 4 in 8gzj

Go back to Barium Binding Sites List in 8gzj
Barium binding site 3 out of 4 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 3 of Crystal Structure of CD2+-Bound Dna Aptamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba102

b:180.9
occ:1.00
N7 B:DG23 3.3 38.2 1.0
BA A:BA102 4.1 114.8 1.0
O6 B:DG23 4.1 36.1 1.0
C6 B:DT22 4.2 26.8 1.0
C8 B:DG23 4.2 37.0 1.0
C5 B:DG23 4.3 25.3 1.0
O6 A:DG1 4.3 24.8 1.0
C5 B:DT22 4.3 36.2 1.0
C7 B:DT22 4.4 38.6 1.0
C2' B:DT22 4.5 31.8 1.0
C6 B:DG23 4.6 25.4 1.0
N1 B:DT22 4.8 28.6 1.0

Barium binding site 4 out of 4 in 8gzj

Go back to Barium Binding Sites List in 8gzj
Barium binding site 4 out of 4 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 4 of Crystal Structure of CD2+-Bound Dna Aptamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba102

b:176.9
occ:1.00
N7 C:DG7 3.8 59.9 1.0
C8 C:DG7 4.6 59.6 1.0
O6 C:DG7 4.8 57.2 1.0
C5 C:DG7 4.9 66.4 1.0
C5 C:DC6 4.9 59.4 1.0
C6 C:DC6 4.9 61.7 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 16:13:08 2024

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