Chlorine 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:

Potassium

(K)

2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Trna 2'-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with Branched 2'-PO4 Rna, PDB code: 8tg5:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 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 Chlorine with other atoms in the Cl 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:Cl204 b:67.8 occ:0.92 OE2 A:GLU19 2.9 47.6 1.0 CG A:GLU19 3.4 46.0 1.0 CD A:GLU19 3.6 43.6 1.0 CZ A:PHE20 3.6 41.2 1.0 CE2 A:PHE20 3.9 42.4 1.0 CE1 A:PHE20 3.9 45.5 1.0 O A:GLU19 4.2 41.2 1.0 CD2 A:PHE20 4.4 47.4 1.0 CD1 A:PHE20 4.4 40.6 1.0 O A:HOH337 4.6 43.4 1.0 CG A:PHE20 4.6 46.6 1.0 C A:GLU19 4.8 53.0 1.0 OE1 A:GLU19 4.8 46.9 1.0 CB A:GLU19 4.8 43.8 1.0

Chlorine binding site 2 out of 3 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 Chlorine with other atoms in the Cl 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:Cl205 b:61.9 occ:1.00 N A:GLY75 3.0 35.9 1.0 NE2 A:HIS119 3.1 45.3 1.0 OE1 A:GLN116 3.6 100.5 1.0 CA A:TYR74 3.8 40.5 1.0 CA A:GLY75 3.8 39.6 1.0 CE1 A:HIS119 3.9 50.4 1.0 C A:TYR74 3.9 37.9 1.0 CB A:TYR74 4.1 37.6 1.0 CD2 A:HIS119 4.1 47.1 1.0 N A:HIS76 4.2 38.5 1.0 CD1 A:LEU82 4.4 46.7 1.0 CD1 A:TYR117 4.4 54.4 1.0 C A:GLY75 4.4 45.1 1.0 ND1 A:HIS76 4.6 37.5 1.0 CD A:GLN116 4.7 93.1 1.0 CG2 A:ILE164 4.7 36.9 1.0 CB A:TYR117 5.0 48.0 1.0

Chlorine binding site 3 out of 3 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl206 b:55.4 occ:0.66 O A:HOH323 3.1 63.2 1.0 N A:ARG100 3.2 54.0 1.0 NH1 A:ARG100 3.3 110.2 1.0 N A:ARG99 3.3 51.6 1.0 CB A:ASP137 3.5 60.0 1.0 O A:ASP137 3.6 53.7 1.0 CB A:ARG99 3.7 45.7 1.0 CA A:ARG99 3.8 57.2 1.0 CB A:VAL98 3.8 53.7 1.0 CD A:ARG100 3.9 79.5 1.0 CB A:ARG100 3.9 60.4 1.0 CZ A:ARG100 4.0 98.4 1.0 C A:ARG99 4.0 49.5 1.0 CG A:ARG100 4.1 68.7 1.0 C A:VAL98 4.1 44.0 1.0 OD1 A:ASP137 4.1 60.5 1.0 CA A:ARG100 4.2 59.6 1.0 CG A:ASP137 4.2 68.5 1.0 NE A:ARG100 4.2 95.3 1.0 CA A:ASP137 4.3 55.2 1.0 C A:ASP137 4.4 53.8 1.0 CG2 A:VAL98 4.4 55.7 1.0 CA A:VAL98 4.4 50.8 1.0 N A:ASP137 4.6 58.3 1.0 O A:HOH360 4.7 44.8 1.0 CG1 A:VAL98 4.8 61.3 1.0 O A:VAL98 5.0 41.0 1.0 NH2 A:ARG100 5.0 88.7 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