Sodium in PDB 5h3q: Crystal Structure of Trka Kinase with Ligand

All present enzymatic activity of Crystal Structure of Trka Kinase with Ligand:
2.7.10.1;

The structure of Crystal Structure of Trka Kinase with Ligand, PDB code: 5h3q was solved by F.Noritaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.81 / 2.10
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	140.845, 157.195, 52.306, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 21.5

The structure of Crystal Structure of Trka Kinase with Ligand also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Trka Kinase with Ligand (pdb code 5h3q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Trka Kinase with Ligand, PDB code: 5h3q:

Sodium binding site 1 out of 1 in the Crystal Structure of Trka Kinase with Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Trka Kinase with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1004 b:47.2 occ:1.00 O A:HOH1142 2.7 36.2 1.0 OD1 A:ASP709 2.8 34.4 1.0 OG A:SER708 2.9 35.5 1.0 N A:ASP709 3.3 30.3 1.0 O A:HOH1132 3.4 25.6 1.0 C A:SER708 3.4 33.7 1.0 CB A:SER708 3.5 36.5 1.0 CA A:ARG649 3.5 29.5 1.0 CD1 A:PHE704 3.6 34.0 1.0 CG A:ASP709 3.7 33.9 1.0 O A:SER708 3.8 36.1 1.0 CA A:ASP709 3.8 34.4 1.0 N A:ARG649 3.9 29.5 1.0 CA A:SER708 4.0 36.6 1.0 O A:THR705 4.2 32.9 1.0 CB A:ASP709 4.3 34.3 1.0 CB A:ARG649 4.3 30.8 1.0 CG1 A:VAL647 4.3 39.7 1.0 CE1 A:PHE704 4.4 42.1 1.0 C A:ARG649 4.4 36.5 1.0 CG A:ARG649 4.4 34.0 1.0 OG A:SER712 4.5 33.1 1.0 CB A:PHE704 4.5 36.1 1.0 CG A:PHE704 4.6 38.2 1.0 O A:ARG649 4.6 29.7 1.0 O A:HOH1141 4.7 38.1 1.0 OD2 A:ASP709 4.7 33.0 1.0 CA A:PHE704 4.8 37.9 1.0 OG A:SER698 4.8 35.0 1.0 N A:SER708 4.8 37.9 1.0 N A:THR705 4.9 38.3 1.0

N.Furuya, T.Momose, K.Katsuno, N.Fushimi, H.Muranaka, C.Handa, T.Ozawa, T.Kinoshita. The Juxtamembrane Region of Trka Kinase Is Critical For Inhibitor Selectivity Bioorg. Med. Chem. Lett. V. 27 1233 2017.
ISSN: ESSN 1464-3405
PubMed: 28159414
DOI: 10.1016/J.BMCL.2017.01.056