Potassium in PDB 8tg4: Trna 2'-Phosphotransferase (TPT1) From Aeropyrum Pernix in Complex with Adp-Ribose-2"-Phosphate and 2'-Oh Rna

The structure of Trna 2'-Phosphotransferase (TPT1) From Aeropyrum Pernix in Complex with Adp-Ribose-2"-Phosphate and 2'-Oh Rna, PDB code: 8tg4 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)	41.86 / 1.37
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.844, 55.701, 42.249, 90, 97.79, 90
R / Rfree (%)	14.9 / 17.5

The structure of Trna 2'-Phosphotransferase (TPT1) From Aeropyrum Pernix in Complex with Adp-Ribose-2"-Phosphate and 2'-Oh Rna also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Potassium atom in the Trna 2'-Phosphotransferase (TPT1) From Aeropyrum Pernix in Complex with Adp-Ribose-2"-Phosphate and 2'-Oh Rna (pdb code 8tg4). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Trna 2'-Phosphotransferase (TPT1) From Aeropyrum Pernix in Complex with Adp-Ribose-2"-Phosphate and 2'-Oh Rna, PDB code: 8tg4:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Trna 2'-Phosphotransferase (TPT1) From Aeropyrum Pernix in Complex with Adp-Ribose-2"-Phosphate and 2'-Oh 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 Aeropyrum Pernix in Complex with Adp-Ribose-2"-Phosphate and 2'-Oh Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:K204 b:41.7 occ:0.60 O A:ARG23 2.7 29.2 1.0 OE1 A:GLU34 2.8 31.6 1.0 N A:ARG31 2.8 18.7 1.0 CD A:GLU34 3.1 32.2 1.0 OE2 A:GLU34 3.2 38.6 1.0 CA A:ALA30 3.5 14.9 1.0 CG A:ARG31 3.6 29.6 1.0 CB A:ARG31 3.6 23.5 1.0 C A:ALA30 3.6 16.0 1.0 C A:ARG23 3.7 23.9 1.0 CA A:ARG31 3.8 18.9 1.0 O A:HOH319 3.8 35.0 1.0 N A:ARG23 3.9 22.4 1.0 O A:HOH373 3.9 52.5 1.0 CG1 A:VAL22 4.0 20.9 1.0 CB A:ALA30 4.0 16.4 1.0 CG A:GLU34 4.1 26.4 1.0 CB A:GLU34 4.2 23.1 1.0 O A:ARG31 4.3 17.9 1.0 CA A:ARG23 4.4 23.9 1.0 O A:TRP29 4.5 18.0 1.0 C A:ARG31 4.6 17.3 1.0 O A:HOH430 4.6 42.1 1.0 O A:HOH410 4.7 32.8 1.0 N A:ALA30 4.7 16.4 1.0 CA A:VAL22 4.8 19.6 1.0 N A:LEU24 4.8 19.4 1.0 C A:VAL22 4.8 20.3 1.0 O A:ALA30 4.8 16.7 1.0 CB A:ARG23 4.8 30.8 1.0 CB A:VAL22 4.9 20.0 1.0 CD A:ARG31 4.9 39.5 1.0

Potassium binding site 2 out of 4 in the Trna 2'-Phosphotransferase (TPT1) From Aeropyrum Pernix in Complex with Adp-Ribose-2"-Phosphate and 2'-Oh 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 Aeropyrum Pernix in Complex with Adp-Ribose-2"-Phosphate and 2'-Oh Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:K205 b:42.8 occ:0.69 OE1 A:GLU157 2.8 30.9 1.0 OG1 A:THR165 2.9 19.2 1.0 NZ A:LYS118 2.9 29.6 1.0 O A:THR165 2.9 18.1 1.0 C A:THR165 3.3 16.2 1.0 CE A:LYS118 3.4 27.5 1.0 CG A:GLU157 3.5 22.8 1.0 CD A:GLU157 3.5 27.9 1.0 CB A:GLU157 3.6 20.3 1.0 CD A:LYS118 3.6 24.4 1.0 O A:LYS155 3.6 19.9 1.0 CB A:THR165 3.7 15.8 1.0 N A:VAL166 3.8 15.1 1.0 CA A:VAL166 3.9 14.9 1.0 O A:HOH345 3.9 26.1 1.0 N A:GLU157 4.0 16.4 1.0 CA A:THR165 4.1 15.4 1.0 O A:HOH377 4.2 23.5 1.0 CA A:GLU157 4.4 16.1 1.0 C A:LYS155 4.5 17.6 1.0 C A:VAL166 4.6 14.8 1.0 O A:HOH370 4.6 33.2 1.0 CG A:LYS118 4.7 20.2 1.0 OE2 A:GLU157 4.7 31.4 1.0 N A:THR165 4.7 15.2 1.0 N A:ASP167 4.8 16.6 1.0 C A:VAL156 4.9 16.2 1.0 CB A:LYS155 4.9 21.5 1.0 CA A:VAL156 5.0 15.4 1.0

Potassium binding site 3 out of 4 in the Trna 2'-Phosphotransferase (TPT1) From Aeropyrum Pernix in Complex with Adp-Ribose-2"-Phosphate and 2'-Oh Rna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Trna 2'-Phosphotransferase (TPT1) From Aeropyrum Pernix in Complex with Adp-Ribose-2"-Phosphate and 2'-Oh Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:K206 b:20.1 occ:0.56 O A:ARG63 2.8 15.0 1.0 NH2 A:ARG14 2.9 16.2 1.0 O A:TYR75 3.1 14.4 1.0 N A:TYR75 3.2 13.7 1.0 CE2 A:TYR75 3.4 15.6 1.0 CD2 A:TYR75 3.4 15.1 1.0 CZ A:TYR75 3.4 14.4 1.0 N A:ARG74 3.4 13.5 1.0 CG A:TYR75 3.5 14.6 1.0 CE1 A:TYR75 3.5 15.1 1.0 CD1 A:TYR75 3.5 14.3 1.0 C A:ARG63 3.5 15.1 1.0 CA A:ARG63 3.6 15.1 1.0 NE A:ARG14 3.6 14.5 1.0 CZ A:ARG14 3.7 14.9 1.0 C A:TYR75 3.8 13.4 1.0 CB A:ARG63 3.8 16.3 1.0 CB A:ALA73 3.9 14.0 1.0 CA A:TYR75 3.9 13.6 1.0 C A:ARG74 4.1 14.0 1.0 C A:ALA73 4.1 13.9 1.0 CA A:ARG74 4.1 14.6 1.0 OH A:TYR75 4.2 16.7 1.0 CA A:ALA73 4.2 13.4 1.0 CG A:ARG63 4.3 16.1 1.0 CB A:ARG74 4.3 16.4 1.0 CB A:TYR75 4.3 14.1 1.0 O28 A:9SO203 4.8 24.8 1.0 N A:TYR64 4.8 14.4 1.0 N A:GLY76 4.8 13.7 1.0 CD A:ARG14 4.9 15.2 1.0 N A:ARG63 5.0 15.5 1.0 NH1 A:ARG14 5.0 15.5 1.0

Potassium binding site 4 out of 4 in the Trna 2'-Phosphotransferase (TPT1) From Aeropyrum Pernix in Complex with Adp-Ribose-2"-Phosphate and 2'-Oh Rna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Trna 2'-Phosphotransferase (TPT1) From Aeropyrum Pernix in Complex with Adp-Ribose-2"-Phosphate and 2'-Oh Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:K207 b:26.6 occ:0.52 O A:HOH350 2.7 23.0 1.0 O18 A:9SO203 2.8 18.3 1.0 N A:HIS120 2.9 14.9 1.0 ND1 A:HIS120 3.3 16.8 1.0 O A:HOH355 3.3 19.7 1.0 O15 A:9SO203 3.5 17.9 1.0 CB A:HIS120 3.5 15.9 1.0 CA A:VAL119 3.7 14.3 1.0 P16 A:9SO203 3.7 18.5 1.0 C A:VAL119 3.7 13.6 1.0 O A:LYS118 3.7 16.1 1.0 CA A:HIS120 3.8 14.1 1.0 C20 A:9SO203 3.8 22.2 1.0 CG A:HIS120 3.9 14.9 1.0 CE1 A:HIS96 4.1 16.5 1.0 O A:HIS120 4.1 15.0 1.0 O A:HOH331 4.1 17.9 1.0 O19 A:9SO203 4.2 22.2 1.0 C A:HIS120 4.4 14.3 1.0 CG1 A:VAL119 4.5 15.7 1.0 CE1 A:HIS120 4.5 16.9 1.0 C A:LYS118 4.6 14.8 1.0 CB A:VAL119 4.6 15.4 1.0 N A:VAL119 4.6 14.7 1.0 ND1 A:HIS96 4.6 15.9 1.0 O14 A:9SO203 4.7 19.5 1.0 P12 A:9SO203 4.8 17.7 1.0 O A:VAL119 4.9 14.9 1.0 CD A:ARG116 5.0 17.6 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