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Barium in PDB 1nta: 2.9 A Crystal Structure of Streptomycin Rna-Aptamer

Protein crystallography data

The structure of 2.9 A Crystal Structure of Streptomycin Rna-Aptamer, PDB code: 1nta was solved by V.Tereshko, E.Skripkin, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.90
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 83.097, 83.097, 49.472, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 28.2

Other elements in 1nta:

The structure of 2.9 A Crystal Structure of Streptomycin Rna-Aptamer also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Barium Binding Sites:

The binding sites of Barium atom in the 2.9 A Crystal Structure of Streptomycin Rna-Aptamer (pdb code 1nta). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 3 binding sites of Barium where determined in the 2.9 A Crystal Structure of Streptomycin Rna-Aptamer, PDB code: 1nta:
Jump to Barium binding site number: 1; 2; 3;

Barium binding site 1 out of 3 in 1nta

Go back to Barium Binding Sites List in 1nta
Barium binding site 1 out of 3 in the 2.9 A Crystal Structure of Streptomycin Rna-Aptamer


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of 2.9 A Crystal Structure of Streptomycin Rna-Aptamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba23

b:32.5
occ:0.75
O6 A:G6 2.7 46.2 1.0
N7 A:G6 3.1 49.0 1.0
C6 A:G6 3.5 48.0 1.0
C5 A:G6 3.7 48.2 1.0
N4 A:C7 4.0 58.5 1.0
C8 A:G6 4.4 50.1 1.0
OP2 B:G111 4.5 37.1 1.0
O4 B:U112 4.7 49.1 1.0
O6 B:G114 4.7 65.8 1.0
OP2 B:U112 4.7 45.8 1.0
N4 B:C113 4.8 57.1 1.0
C5 B:U112 4.8 50.0 1.0
N1 A:G6 4.9 46.6 1.0

Barium binding site 2 out of 3 in 1nta

Go back to Barium Binding Sites List in 1nta
Barium binding site 2 out of 3 in the 2.9 A Crystal Structure of Streptomycin Rna-Aptamer


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of 2.9 A Crystal Structure of Streptomycin Rna-Aptamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba1

b:40.6
occ:1.00
O4 A:U11 2.7 46.3 1.0
O2 A:U10 3.0 39.5 1.0
O5' B:C109 3.0 40.9 1.0
OP2 B:C109 3.3 42.0 1.0
O4' B:C109 3.5 41.6 1.0
P B:C109 3.7 41.4 1.0
C4 A:U11 3.7 49.1 1.0
C2 A:U10 3.9 42.2 1.0
C5' B:C109 4.1 40.2 1.0
C4' B:C109 4.1 40.6 1.0
C5 A:U11 4.2 48.6 1.0
N3 A:U10 4.3 43.6 1.0
C3' B:A108 4.5 47.3 1.0
C1' B:C109 4.5 43.0 1.0
O3' B:A108 4.6 43.0 1.0
OP1 B:C109 4.8 44.5 1.0
N3 A:U11 5.0 49.5 1.0

Barium binding site 3 out of 3 in 1nta

Go back to Barium Binding Sites List in 1nta
Barium binding site 3 out of 3 in the 2.9 A Crystal Structure of Streptomycin Rna-Aptamer


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of 2.9 A Crystal Structure of Streptomycin Rna-Aptamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba3

b:60.0
occ:0.50
O6 B:G115 3.0 71.5 1.0
O6 B:G114 3.3 65.8 1.0
N7 B:G114 3.9 62.7 1.0
C6 B:G115 4.0 71.5 1.0
C6 B:G114 4.1 64.0 1.0
N7 B:G115 4.1 69.9 1.0
C5 B:G114 4.3 63.1 1.0
C5 B:G115 4.4 70.9 1.0
OP2 B:C113 4.9 49.7 1.0

Reference:

V.Tereshko, E.Skripkin, D.J.Patel. Encapsulating Streptomycin Within A Small 40-Mer Rna Chem.Biol. V. 10 175 2003.
ISSN: ISSN 1074-5521
PubMed: 12618190
DOI: 10.1016/S1074-5521(03)00024-3
Page generated: Sat Dec 12 01:54:59 2020

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