Potassium in PDB 8tg5: Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with Branched 2'-PO4 Rna

The structure of Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with Branched 2'-PO4 Rna, PDB code: 8tg5 was solved by A.Jacewicz, S.Dantuluri, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.64 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.291, 45.344, 125.239, 90, 90, 90
R / Rfree (%)	19.4 / 24.3

The structure of Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with Branched 2'-PO4 Rna also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Potassium atom in the Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with Branched 2'-PO4 Rna (pdb code 8tg5). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with Branched 2'-PO4 Rna, PDB code: 8tg5:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with Branched 2'-PO4 Rna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with Branched 2'-PO4 Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:K202 b:37.5 occ:0.58 O A:GLY28 2.7 40.2 1.0 N A:ALA72 2.9 32.7 1.0 O A:LEU13 3.0 33.5 1.0 NE2 A:HIS76 3.1 38.2 1.0 CD2 A:HIS76 3.4 39.4 1.0 CB A:ARG71 3.5 35.5 1.0 CA A:ARG71 3.5 33.9 1.0 OH A:TYR78 3.6 35.9 1.0 CB A:LEU13 3.6 25.1 1.0 C A:GLY28 3.6 35.9 1.0 C A:ARG71 3.7 30.9 1.0 C A:LEU13 3.7 31.5 1.0 O A:ALA72 3.8 32.4 1.0 CB A:ALA72 3.8 31.4 1.0 CA A:ALA72 3.8 31.9 1.0 CA A:GLY28 3.9 36.1 1.0 CA A:LEU13 4.0 26.9 1.0 C A:ALA72 4.3 31.2 1.0 CD2 A:LEU13 4.3 28.6 1.0 CE1 A:HIS76 4.3 37.1 1.0 CG A:LEU13 4.5 32.0 1.0 CG A:ARG71 4.6 32.1 1.0 CG A:HIS76 4.7 41.0 1.0 N A:ARG14 4.7 29.3 1.0 CZ A:TYR78 4.7 40.6 1.0 N A:PHE29 4.8 41.5 1.0 N A:ARG71 4.9 29.1 1.0 O A:ARG71 4.9 27.2 1.0 O A:ILE70 4.9 29.9 1.0

Potassium binding site 2 out of 2 in the Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with Branched 2'-PO4 Rna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with Branched 2'-PO4 Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:K203 b:48.6 occ:0.48 OE2 A:GLU86 2.7 53.6 1.0 N A:ILE155 2.8 43.8 1.0 O A:ASP87 3.0 45.5 1.0 CG A:GLU86 3.1 52.4 1.0 O A:ILE155 3.3 42.9 1.0 CD A:GLU86 3.3 70.1 1.0 NE A:ARG149 3.4 49.7 1.0 CG A:ARG149 3.6 50.2 1.0 CA A:ILE155 3.6 40.7 1.0 CD A:ARG149 3.6 51.6 1.0 CB A:ILE155 3.7 38.5 1.0 C A:LYS154 3.7 44.7 1.0 CA A:LYS154 3.7 51.5 1.0 C A:ILE155 3.8 43.0 1.0 C A:ASP87 3.9 51.5 1.0 CG1 A:ILE155 4.1 42.7 1.0 O A:TYR153 4.2 49.2 1.0 N A:ASP87 4.4 45.2 1.0 CD1 A:ILE155 4.4 40.5 1.0 CB A:LYS154 4.5 55.9 1.0 CB A:GLU86 4.5 47.4 1.0 OE1 A:GLU86 4.5 59.7 1.0 CZ A:ARG149 4.6 49.5 1.0 N A:LYS88 4.7 51.1 1.0 CA A:LYS88 4.7 54.3 1.0 CA A:ASP87 4.7 45.2 1.0 CD A:LYS154 4.8 66.8 1.0 N A:LYS154 4.8 47.5 1.0 CG A:LYS88 4.8 58.5 1.0 CG A:LYS154 4.8 60.5 1.0 O A:LYS154 4.9 43.4 1.0 CB A:ARG149 4.9 53.1 1.0 NH2 A:ARG149 4.9 51.5 1.0 C A:TYR153 4.9 49.2 1.0

A.Jacewicz, S.Dantuluri, S.Shuman. Structural Basis For TPT1-Catalyzed 2'-Po 4 Transfer From Rna and Nadp(H) to Nad. Proc.Natl.Acad.Sci.Usa V. 120 99120 2023.
ISSN: ESSN 1091-6490
PubMed: 37883434
DOI: 10.1073/PNAS.2312999120