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

Protein crystallography data

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

Other elements in 8gzk:

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

Cadmium (Cd) 2 atoms

Barium Binding Sites:

The binding sites of Barium 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 Barium atom.
In total 5 binding sites of Barium where determined in the Crystal Structure of CD2+-Bound Dna Aptamer T10A Mutant, PDB code: 8gzk:
Jump to Barium binding site number: 1; 2; 3; 4; 5;

Barium binding site 1 out of 5 in 8gzk

Go back to Barium Binding Sites List in 8gzk
Barium binding site 1 out of 5 in the Crystal Structure of CD2+-Bound Dna Aptamer T10A Mutant


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 T10A Mutant within 5.0Å range:

Barium binding site 2 out of 5 in 8gzk

Go back to Barium Binding Sites List in 8gzk
Barium binding site 2 out of 5 in the Crystal Structure of CD2+-Bound Dna Aptamer T10A Mutant


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 T10A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba103

b:101.2
occ:1.00
N7 A:DG1 2.8 62.8 1.0
O6 A:DG1 3.4 57.6 1.0
C5 A:DG1 3.7 57.2 1.0
C8 A:DG1 3.8 65.0 1.0
C6 A:DG1 3.9 54.7 1.0
N4 B:DC25 4.3 59.7 1.0
C4 A:DG1 4.9 56.1 1.0
N9 A:DG1 5.0 60.5 1.0

Barium binding site 3 out of 5 in 8gzk

Go back to Barium Binding Sites List in 8gzk
Barium binding site 3 out of 5 in the Crystal Structure of CD2+-Bound Dna Aptamer T10A Mutant


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 T10A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba104

b:111.4
occ:1.00
N7 A:DG7 3.2 30.9 1.0
C8 A:DG7 4.1 29.2 1.0
O6 A:DG7 4.1 30.1 1.0
C5 A:DG7 4.2 29.8 1.0
C6 A:DG7 4.6 29.5 1.0
C2' A:DC6 5.0 31.8 1.0

Barium binding site 4 out of 5 in 8gzk

Go back to Barium Binding Sites List in 8gzk
Barium binding site 4 out of 5 in the Crystal Structure of CD2+-Bound Dna Aptamer T10A Mutant


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 T10A Mutant within 5.0Å range:

Barium binding site 5 out of 5 in 8gzk

Go back to Barium Binding Sites List in 8gzk
Barium binding site 5 out of 5 in the Crystal Structure of CD2+-Bound Dna Aptamer T10A Mutant


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Crystal Structure of CD2+-Bound Dna Aptamer T10A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba103

b:98.5
occ:1.00
N7 B:DG1 2.5 58.5 1.0
C8 B:DG1 3.3 58.3 1.0
C5 B:DG1 3.7 56.2 1.0
O6 B:DG1 4.0 53.9 1.0
C6 B:DG1 4.3 55.0 1.0
N4 A:DC25 4.3 57.0 1.0
N9 B:DG1 4.6 56.5 1.0
C4 B:DG1 4.8 56.1 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 16:13:34 2024

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