Sodium in PDB 3p0j: Leishmania Major Tyrosyl-Trna Synthetase in Complex with Tyrosinol, Triclinic Crystal Form 1

All present enzymatic activity of Leishmania Major Tyrosyl-Trna Synthetase in Complex with Tyrosinol, Triclinic Crystal Form 1:
6.1.1.1;

The structure of Leishmania Major Tyrosyl-Trna Synthetase in Complex with Tyrosinol, Triclinic Crystal Form 1, PDB code: 3p0j was solved by E.T.Larson, E.A.Merritt, Medical Structural Genomics Of Pathogenicprotozoa (Msgpp), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.89
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57.519, 111.934, 141.043, 74.47, 80.83, 77.13
R / Rfree (%)	24.4 / 29.3

The binding sites of Sodium atom in the Leishmania Major Tyrosyl-Trna Synthetase in Complex with Tyrosinol, Triclinic Crystal Form 1 (pdb code 3p0j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Leishmania Major Tyrosyl-Trna Synthetase in Complex with Tyrosinol, Triclinic Crystal Form 1, PDB code: 3p0j:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Leishmania Major Tyrosyl-Trna Synthetase in Complex with Tyrosinol, Triclinic Crystal Form 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Leishmania Major Tyrosyl-Trna Synthetase in Complex with Tyrosinol, Triclinic Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na711 b:68.2 occ:1.00 O A:VAL110 2.5 60.0 1.0 O A:MET107 2.5 60.0 1.0 O B:MET107 2.8 60.0 1.0 O B:VAL110 2.9 60.0 1.0 C A:VAL110 3.6 60.0 1.0 C A:MET107 3.7 60.0 1.0 C B:MET107 4.0 60.0 1.0 N A:VAL110 4.1 60.0 1.0 C B:VAL110 4.1 60.0 1.0 CB A:MET107 4.3 60.0 1.0 CA A:VAL110 4.3 60.0 1.0 O A:ASP108 4.3 60.0 1.0 CA A:MET107 4.5 60.0 1.0 C A:ASP108 4.5 60.0 1.0 CB B:MET107 4.6 60.0 1.0 N B:VAL110 4.6 60.0 1.0 N A:LEU111 4.6 60.0 1.0 N A:ASP108 4.7 60.0 1.0 CB A:VAL110 4.7 60.0 1.0 CA B:MET107 4.8 60.0 1.0 CA A:LEU111 4.8 60.0 1.0 CA A:ASP108 4.9 60.0 1.0 CA B:VAL110 4.9 60.0 1.0 C B:ASP108 4.9 60.0 1.0 O B:ASP108 4.9 60.0 1.0 CA B:LEU111 5.0 60.0 1.0 N B:LEU111 5.0 60.0 1.0

Sodium binding site 2 out of 2 in the Leishmania Major Tyrosyl-Trna Synthetase in Complex with Tyrosinol, Triclinic Crystal Form 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Leishmania Major Tyrosyl-Trna Synthetase in Complex with Tyrosinol, Triclinic Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na711 b:0.8 occ:1.00 O C:VAL110 2.2 60.0 1.0 O D:MET107 2.6 60.0 1.0 O D:VAL110 2.8 60.0 1.0 O C:MET107 3.1 60.0 1.0 C C:VAL110 3.4 60.0 1.0 C D:MET107 3.8 60.0 1.0 C D:VAL110 3.9 60.0 1.0 C C:MET107 4.2 60.0 1.0 N D:VAL110 4.2 60.0 1.0 N C:VAL110 4.2 60.0 1.0 CA C:VAL110 4.3 60.0 1.0 CB D:MET107 4.3 60.0 1.0 N C:LEU111 4.3 60.0 1.0 CA C:LEU111 4.5 60.0 1.0 CA D:MET107 4.5 60.0 1.0 CB C:MET107 4.5 60.0 1.0 CA D:VAL110 4.6 60.0 1.0 C D:ASP108 4.7 60.0 1.0 O D:ASP108 4.7 60.0 1.0 CA C:MET107 4.8 60.0 1.0 CB C:VAL110 4.8 60.0 1.0 N D:ASP108 4.8 60.0 1.0 N D:LEU111 4.9 60.0 1.0 N D:LYS109 4.9 60.0 1.0

E.T.Larson, J.E.Kim, L.J.Castaneda, A.J.Napuli, Z.Zhang, E.Fan, F.H.Zucker, C.L.Verlinde, F.S.Buckner, W.C.Van Voorhis, W.G.Hol, E.A.Merritt. The Double-Length Tyrosyl-Trna Synthetase From the Eukaryote Leishmania Major Forms An Intrinsically Asymmetric Pseudo-Dimer. J.Mol.Biol. V. 409 159 2011.
ISSN: ISSN 0022-2836
PubMed: 21420975
DOI: 10.1016/J.JMB.2011.03.026