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Thallium in PDB 6dme: Ppgpp Riboswitch Bound to Ppgpp, Thallium Acetate Structure

Protein crystallography data

The structure of Ppgpp Riboswitch Bound to Ppgpp, Thallium Acetate Structure, PDB code: 6dme was solved by A.Peselis, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.52 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.184, 51.816, 77.862, 90.00, 128.10, 90.00
R / Rfree (%) 19.9 / 24.3

Other elements in 6dme:

The structure of Ppgpp Riboswitch Bound to Ppgpp, Thallium Acetate Structure also contains other interesting chemical elements:

Magnesium (Mg) 13 atoms

Thallium Binding Sites:

The binding sites of Thallium atom in the Ppgpp Riboswitch Bound to Ppgpp, Thallium Acetate Structure (pdb code 6dme). This binding sites where shown within 5.0 Angstroms radius around Thallium atom.
In total only one binding site of Thallium was determined in the Ppgpp Riboswitch Bound to Ppgpp, Thallium Acetate Structure, PDB code: 6dme:

Thallium binding site 1 out of 1 in 6dme

Go back to Thallium Binding Sites List in 6dme
Thallium binding site 1 out of 1 in the Ppgpp Riboswitch Bound to Ppgpp, Thallium Acetate Structure


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 1 of Ppgpp Riboswitch Bound to Ppgpp, Thallium Acetate Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl215

b:51.1
occ:1.00
N7 A:G37 2.8 16.0 1.0
N1 A:A17 2.9 19.8 1.0
O6 A:G37 2.9 19.8 1.0
O6 A:G36 3.2 19.2 1.0
N3 A:A35 3.2 16.2 1.0
N6 A:A38 3.3 13.2 1.0
N7 A:G36 3.3 23.6 1.0
C6 A:G36 3.5 17.1 1.0
C5 A:G37 3.5 17.3 1.0
C6 A:G37 3.5 19.5 1.0
C5 A:G36 3.5 15.7 1.0
O2' A:A35 3.5 36.6 1.0
C2 A:A17 3.6 18.7 1.0
C6 A:A38 3.7 14.5 1.0
C2 A:A35 3.8 14.1 1.0
C6 A:A17 3.8 14.8 1.0
N6 A:A17 3.9 19.3 1.0
C8 A:G37 4.0 18.0 1.0
C4 A:A35 4.0 16.8 1.0
C1' A:A35 4.2 26.1 1.0
C8 A:G36 4.2 25.6 1.0
N1 A:A38 4.3 16.5 1.0
C5 A:A38 4.3 15.4 1.0
N9 A:A35 4.4 24.5 1.0
C2' A:A35 4.5 27.7 1.0
N1 A:G36 4.5 17.7 1.0
C4 A:G36 4.5 16.9 1.0
O6 A:G16 4.6 15.3 1.0
N7 A:A38 4.7 17.6 1.0
C4 A:G37 4.8 16.7 1.0
N1 A:G37 4.8 17.7 1.0
N3 A:A17 4.9 19.9 1.0
N1 A:A35 4.9 14.7 1.0
N9 A:G36 4.9 20.2 1.0
O3' A:A35 5.0 32.1 1.0

Reference:

A.Peselis, A.Serganov. Ykkc Riboswitches Employ An Add-on Helix to Adjust Specificity For Polyanionic Ligands. Nat. Chem. Biol. V. 14 887 2018.
ISSN: ESSN 1552-4469
PubMed: 30120360
DOI: 10.1038/S41589-018-0114-4
Page generated: Wed Dec 16 02:29:11 2020

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