Phosphorus in PDB 1ady: Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate

All present enzymatic activity of Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate:
6.1.1.21;

The structure of Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate, PDB code: 1ady was solved by S.Cusack, A.Aberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	171.300, 214.700, 49.300, 90.00, 90.00, 90.00
R / Rfree (%)	26 / 30

The binding sites of Phosphorus atom in the Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate (pdb code 1ady). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 4 binding sites of Phosphorus where determined in the Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate, PDB code: 1ady:
Jump to Phosphorus binding site number: 1; 2; 3; 4;

Phosphorus binding site 1 out of 4 in the Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate within 5.0Å range: probe atom residue distance (Å) B Occ A:P423 b:28.1 occ:1.00 P A:HAM423 0.0 28.1 1.0 O1P A:HAM423 1.5 29.8 1.0 O2P A:HAM423 1.5 30.4 1.0 O5' A:HAM423 1.6 32.0 1.0 O3P A:HAM423 1.6 23.0 1.0 C5' A:HAM423 2.6 35.3 1.0 C A:HAM423 2.8 20.9 1.0 O A:HAM423 3.2 27.6 1.0 NH2 A:ARG259 3.6 44.2 1.0 C4' A:HAM423 3.9 37.2 1.0 NH2 A:ARG112 4.0 40.0 1.0 CD1 A:LEU261 4.1 25.5 1.0 CA A:HAM423 4.1 21.1 1.0 CZ A:ARG259 4.3 41.2 1.0 O4' A:HAM423 4.3 37.2 1.0 C3' A:HAM423 4.4 37.1 1.0 NH1 A:ARG259 4.4 38.5 1.0 C8 A:HAM423 4.7 35.7 1.0 CB A:HAM423 4.8 22.4 1.0 NH1 A:ARG112 4.8 39.8 1.0 CZ A:ARG112 4.9 41.3 1.0

Phosphorus binding site 2 out of 4 in the Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate within 5.0Å range: probe atom residue distance (Å) B Occ B:P423 b:28.4 occ:1.00 P B:HAM423 0.0 28.4 1.0 O2P B:HAM423 1.5 31.2 1.0 O1P B:HAM423 1.5 30.2 1.0 O5' B:HAM423 1.6 29.6 1.0 O3P B:HAM423 1.6 21.6 1.0 C5' B:HAM423 2.6 28.6 1.0 C B:HAM423 2.8 22.6 1.0 O B:HAM423 3.2 25.0 1.0 C4' B:HAM423 3.9 26.9 1.0 CA B:HAM423 4.1 24.6 1.0 NH2 B:ARG112 4.2 35.2 1.0 CD1 B:LEU261 4.2 45.0 1.0 NH2 B:ARG259 4.3 36.3 1.0 C3' B:HAM423 4.3 26.9 1.0 O4' B:HAM423 4.3 25.8 1.0 NH1 B:ARG259 4.3 32.8 1.0 CB B:HAM423 4.6 27.9 1.0 C8 B:HAM423 4.7 28.0 1.0 CZ B:ARG259 4.8 38.9 1.0

Phosphorus binding site 3 out of 4 in the Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate within 5.0Å range: probe atom residue distance (Å) B Occ C:P423 b:34.3 occ:1.00 P C:HAM423 0.0 34.3 1.0 O1P C:HAM423 1.5 26.9 1.0 O2P C:HAM423 1.5 34.2 1.0 O3P C:HAM423 1.6 27.2 1.0 O5' C:HAM423 1.6 39.0 1.0 C5' C:HAM423 2.6 38.7 1.0 C C:HAM423 2.8 28.1 1.0 O C:HAM423 3.3 30.7 1.0 C4' C:HAM423 3.9 37.5 1.0 CA C:HAM423 4.0 24.0 1.0 NH2 C:ARG112 4.2 38.4 1.0 O4' C:HAM423 4.2 38.3 1.0 NH2 C:ARG259 4.3 76.0 1.0 C3' C:HAM423 4.3 36.7 1.0 NH1 C:ARG259 4.3 72.9 1.0 CD1 C:LEU261 4.5 37.3 1.0 CB C:HAM423 4.6 20.3 1.0 C8 C:HAM423 4.7 37.7 1.0 CZ C:ARG259 4.8 74.5 1.0 OE1 C:GLN126 4.9 20.9 1.0 NH1 C:ARG112 4.9 39.5 1.0

Phosphorus binding site 4 out of 4 in the Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Histidyl-Trna Synthetase in Complex with Histidyl-Adenylate within 5.0Å range: probe atom residue distance (Å) B Occ D:P423 b:39.4 occ:1.00 P D:HAM423 0.0 39.4 1.0 O2P D:HAM423 1.5 40.8 1.0 O1P D:HAM423 1.5 42.5 1.0 O5' D:HAM423 1.6 37.8 1.0 O3P D:HAM423 1.6 39.4 1.0 C5' D:HAM423 2.6 36.3 1.0 C D:HAM423 2.8 43.3 1.0 O D:HAM423 3.2 49.4 1.0 NH2 D:ARG259 3.8 35.2 1.0 C4' D:HAM423 3.9 39.4 1.0 NH2 D:ARG112 4.1 35.7 1.0 CD1 D:LEU261 4.2 54.6 1.0 CA D:HAM423 4.2 44.5 1.0 C3' D:HAM423 4.2 39.3 1.0 O4' D:HAM423 4.3 38.4 1.0 CB D:HAM423 4.6 45.6 1.0 C8 D:HAM423 4.7 45.8 1.0 NH1 D:ARG112 4.8 37.5 1.0 O3' D:HAM423 4.9 36.4 1.0 CZ D:ARG259 4.9 38.2 1.0 CZ D:ARG112 5.0 36.8 1.0

A.Aberg, A.Yaremchuk, M.Tukalo, B.Rasmussen, S.Cusack. Crystal Structure Analysis of the Activation of Histidine By Thermus Thermophilus Histidyl-Trna Synthetase. Biochemistry V. 36 3084 1997.
ISSN: ISSN 0006-2960
PubMed: 9115984
DOI: 10.1021/BI9618373