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

Protein crystallography data

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

Other elements in 8gzm:

The structure of Crystal Structure of CD2+-Bound Dna Aptamer T22C 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 T22C Mutant (pdb code 8gzm). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 3 binding sites of Barium where determined in the Crystal Structure of CD2+-Bound Dna Aptamer T22C Mutant, PDB code: 8gzm:
Jump to Barium binding site number: 1; 2; 3;

Barium binding site 1 out of 3 in 8gzm

Go back to Barium Binding Sites List in 8gzm
Barium binding site 1 out of 3 in the Crystal Structure of CD2+-Bound Dna Aptamer T22C 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 T22C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba103

b:122.8
occ:1.00
N7 A:DG4 3.2 57.8 1.0
C8 A:DG4 4.0 53.8 1.0
O6 A:DG4 4.2 51.5 1.0
C5 A:DG4 4.2 56.4 1.0
C6 A:DG4 4.6 55.0 1.0
C6 A:DC3 4.6 53.9 1.0
C5 A:DC3 4.7 55.0 1.0
O4 A:DT21 4.8 49.6 1.0
OP2 A:DC3 4.9 56.4 1.0

Barium binding site 2 out of 3 in 8gzm

Go back to Barium Binding Sites List in 8gzm
Barium binding site 2 out of 3 in the Crystal Structure of CD2+-Bound Dna Aptamer T22C 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 T22C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba104

b:124.8
occ:1.00
N7 A:DG7 3.0 43.6 1.0
C8 A:DG7 3.7 40.5 1.0
C5 A:DG7 4.0 44.2 1.0
O6 A:DG7 4.2 38.5 1.0
O6 A:DG8 4.5 40.5 1.0
C6 A:DG7 4.5 39.7 1.0
N4 A:DC18 4.8 39.1 1.0
N9 A:DG7 5.0 47.3 1.0

Barium binding site 3 out of 3 in 8gzm

Go back to Barium Binding Sites List in 8gzm
Barium binding site 3 out of 3 in the Crystal Structure of CD2+-Bound Dna Aptamer T22C 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 T22C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba105

b:156.9
occ:1.00
N7 A:DG23 3.1 66.6 1.0
O6 A:DG24 3.5 63.0 1.0
O6 A:DG23 3.9 48.1 1.0
C5 A:DG23 4.1 60.6 1.0
C8 A:DG23 4.1 63.8 1.0
C6 A:DG23 4.4 55.0 1.0
O6 A:DG1 4.5 64.3 1.0
C6 A:DG24 4.5 62.5 1.0
N4 A:DC2 4.6 50.1 1.0
N7 A:DG24 4.7 56.6 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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