Potassium in PDB 8tfx: Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 2',5'-Adp

The structure of Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 2',5'-Adp, PDB code: 8tfx 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)	42.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.554, 44.626, 124.397, 90, 90, 90
R / Rfree (%)	17.6 / 20.3

The structure of Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 2',5'-Adp also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Potassium atom in the Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 2',5'-Adp (pdb code 8tfx). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 2',5'-Adp, PDB code: 8tfx:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in the Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 2',5'-Adp


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 2',5'-Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:K211 b:21.3 occ:0.43 O A:GLY28 2.6 20.4 1.0 O A:LEU13 2.8 20.1 1.0 N A:ALA72 3.0 16.1 1.0 NE2 A:HIS76 3.1 23.5 1.0 CD2 A:HIS76 3.4 21.6 1.0 OH A:TYR78 3.5 20.3 1.0 CB A:ARG71 3.5 18.6 1.0 C A:GLY28 3.6 20.4 1.0 CA A:ARG71 3.6 17.7 1.0 C A:LEU13 3.7 17.3 1.0 CB A:LEU13 3.7 15.4 1.0 O A:ALA72 3.8 21.3 1.0 C A:ARG71 3.8 16.7 1.0 CB A:ALA72 3.8 17.5 1.0 CA A:ALA72 3.9 17.3 1.0 CA A:GLY28 3.9 18.3 1.0 CA A:LEU13 4.0 17.1 1.0 C A:ALA72 4.3 18.7 1.0 CE1 A:HIS76 4.3 22.2 1.0 CD2 A:LEU13 4.4 20.6 1.0 CG A:LEU13 4.6 17.0 1.0 CZ A:TYR78 4.6 22.3 1.0 CG A:ARG71 4.7 17.7 1.0 N A:ARG14 4.7 18.2 1.0 CG A:HIS76 4.8 20.1 1.0 N A:PHE29 4.8 22.8 1.0 N A:ARG71 5.0 19.4 1.0 O A:ARG71 5.0 17.9 1.0

Potassium binding site 2 out of 6 in the Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 2',5'-Adp


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 2',5'-Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:K212 b:35.7 occ:0.47 OE2 A:GLU86 2.7 49.7 1.0 N A:ILE155 2.9 26.4 1.0 O A:ASP87 3.0 31.6 1.0 NE A:ARG149 3.2 33.1 1.0 CG A:GLU86 3.2 41.7 1.0 CD A:GLU86 3.3 49.6 1.0 O A:ILE155 3.4 28.5 1.0 CD A:ARG149 3.5 34.6 1.0 CB A:ILE155 3.6 21.3 1.0 CA A:ILE155 3.6 23.6 1.0 CG A:ARG149 3.7 48.8 1.0 C A:LYS154 3.8 31.0 1.0 CA A:LYS154 3.9 34.3 1.0 C A:ILE155 3.9 28.6 1.0 CG1 A:ILE155 4.0 25.8 1.0 C A:ASP87 4.0 37.4 1.0 CD A:LYS154 4.1 68.5 1.0 O A:TYR153 4.2 45.2 1.0 CZ A:ARG149 4.3 35.0 1.0 CD1 A:ILE155 4.4 28.2 1.0 NZ A:LYS154 4.4 57.7 1.0 N A:ASP87 4.5 30.6 1.0 OE1 A:GLU86 4.5 51.9 1.0 NH2 A:ARG149 4.6 32.9 1.0 CE A:LYS154 4.6 71.8 1.0 CB A:GLU86 4.6 36.1 1.0 CB A:LYS154 4.6 37.1 1.0 CA A:LYS88 4.8 33.7 1.0 N A:LYS88 4.8 38.3 1.0 CA A:ASP87 4.8 35.8 1.0 CB A:ARG149 4.8 43.5 1.0 N A:LYS154 4.9 32.9 1.0 CG A:LYS154 5.0 58.3 1.0 O A:LYS154 5.0 32.9 1.0 CG2 A:ILE155 5.0 21.5 1.0

Potassium binding site 3 out of 6 in the Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 2',5'-Adp


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 Pyrococcus Horikoshii in Complex with 2',5'-Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:K213 b:42.0 occ:0.74 CL A:CL210 2.5 49.8 0.7 O A:HOH339 2.8 46.7 1.0 N A:GLY96 3.1 22.2 1.0 CA A:ALA127 3.7 23.0 1.0 CA A:HIS95 3.8 17.5 1.0 CB A:ALA127 3.8 22.6 1.0 CB A:THR130 3.9 35.9 1.0 C A:HIS95 3.9 22.1 1.0 O A:HIS119 3.9 27.2 1.0 O A:TYR94 3.9 20.9 1.0 CA A:GLY96 4.0 24.9 1.0 OG1 A:THR130 4.1 47.9 1.0 CG2 A:THR130 4.1 42.1 1.0 O A:ALA127 4.2 23.4 1.0 ND1 A:HIS95 4.2 25.1 1.0 O A:GLY96 4.3 27.6 1.0 C A:ALA127 4.4 26.9 1.0 CA A:LEU120 4.5 19.6 1.0 C A:HIS119 4.6 24.6 1.0 C A:LEU120 4.6 24.8 1.0 N A:SER121 4.6 22.7 1.0 N A:HIS95 4.6 20.2 1.0 C A:TYR94 4.6 22.8 1.0 C A:GLY96 4.7 27.9 1.0 CG A:HIS95 4.7 22.0 1.0 CB A:HIS95 4.8 21.4 1.0 CB A:SER121 4.8 27.3 1.0 N A:ALA127 4.8 24.1 1.0 N A:LEU120 4.8 22.2 1.0 CE1 A:HIS95 4.9 27.1 1.0

Potassium binding site 4 out of 6 in the Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 2',5'-Adp


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 Pyrococcus Horikoshii in Complex with 2',5'-Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:K214 b:32.5 occ:0.57 N A:GLU49 3.0 21.8 1.0 O A:HOH336 3.3 31.1 1.0 CB A:GLU49 3.4 26.1 1.0 N A:GLU48 3.5 22.1 1.0 CB A:THR47 3.6 23.4 1.0 CA A:GLU49 3.7 21.1 1.0 CB A:GLU48 3.8 21.0 1.0 C A:GLU48 3.9 20.8 1.0 CA A:GLU48 3.9 21.8 1.0 OG1 A:THR47 4.0 24.9 1.0 C A:THR47 4.3 18.2 1.0 OE1 A:GLU49 4.4 48.4 1.0 CA A:THR47 4.5 19.5 1.0 CG2 A:THR47 4.6 23.6 1.0 CG A:GLU49 4.7 41.3 1.0 O A:HOH308 4.8 45.2 1.0 O A:HOH338 4.9 25.1 1.0 CG A:GLU48 5.0 23.9 1.0

Potassium binding site 5 out of 6 in the Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 2',5'-Adp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 2',5'-Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:K215 b:69.5 occ:1.00 N A:SER31 3.1 22.7 1.0 OE1 A:GLU34 3.1 52.5 1.0 O A:HOH390 3.2 55.9 1.0 O A:HOH352 3.4 40.4 1.0 O A:HOH398 3.6 49.5 1.0 CA A:VAL30 3.6 21.9 1.0 CB A:VAL30 3.7 21.7 1.0 C A:VAL30 3.8 21.9 1.0 O A:GLU23 3.9 30.4 1.0 CB A:SER31 3.9 26.3 1.0 CA A:SER31 4.1 21.7 1.0 CD A:GLU34 4.1 71.2 1.0 N A:GLU23 4.2 26.4 1.0 CG1 A:VAL30 4.3 23.5 1.0 C A:GLU23 4.5 34.3 1.0 CB A:GLU34 4.7 24.9 1.0 O A:HOH394 4.8 48.0 1.0 CG A:GLU34 4.8 25.8 1.0 CA A:GLU23 4.9 27.1 1.0 CD2 A:LEU22 4.9 27.0 1.0 CB A:LEU22 4.9 23.0 1.0 OE2 A:GLU34 4.9 68.0 1.0 CG2 A:VAL30 4.9 20.6 1.0 CA A:LEU22 4.9 24.3 1.0 O A:SER31 4.9 19.3 1.0

Potassium binding site 6 out of 6 in the Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 2',5'-Adp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 2',5'-Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:K216 b:28.7 occ:0.47 OD2 A:ASP58 2.5 22.8 1.0 O A:HOH361 2.7 30.8 1.0 O A:HOH348 2.9 24.3 1.0 OG A:SER6 2.9 19.7 1.0 CB A:SER6 3.4 17.0 1.0 CG A:ASP58 3.5 24.7 1.0 CB A:ASP58 3.7 21.1 1.0 CG2 A:ILE54 3.8 20.2 1.0 CA A:ASP58 4.0 23.1 1.0 NH1 A:ARG62 4.0 25.7 1.0 OE2 A:GLU59 4.1 44.5 1.0 CE2 A:TYR63 4.2 18.7 1.0 O A:ILE54 4.2 20.0 1.0 N1 A:A2P201 4.5 18.6 0.9 N6 A:A2P201 4.5 24.4 1.0 OD1 A:ASP58 4.6 24.8 1.0 N A:ASP58 4.7 22.3 1.0 CA A:SER6 4.9 17.7 1.0 C A:ILE54 4.9 20.3 1.0 CD2 A:TYR63 4.9 19.2 1.0 CB A:ILE54 4.9 17.5 1.0 O A:ARG2 5.0 21.0 1.0 C6 A:A2P201 5.0 19.9 0.7

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