Zinc in PDB 6pme: Trk-A in Complex with Ligand

All present enzymatic activity of Trk-A in Complex with Ligand:
2.7.10.1;

The structure of Trk-A in Complex with Ligand, PDB code: 6pme was solved by G.Subramanian, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.51 / 3.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.444, 152.085, 156.398, 90.00, 90.00, 90.00
R / Rfree (%)	25.8 / 31.5

The binding sites of Zinc atom in the Trk-A in Complex with Ligand (pdb code 6pme). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Trk-A in Complex with Ligand, PDB code: 6pme:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Trk-A in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Trk-A in Complex with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:46.9 occ:1.00 NE2 A:HIS504 1.9 46.3 1.0 OE1 A:GLU581 2.0 57.1 1.0 SG B:CYS501 2.3 47.8 1.0 SG A:CYS579 2.3 53.9 1.0 CB A:GLU581 2.7 55.4 1.0 CE1 A:HIS504 2.8 45.7 1.0 CD2 A:HIS504 2.8 43.7 1.0 CD A:GLU581 2.8 64.0 1.0 CG A:GLU581 3.0 60.4 1.0 CB A:CYS579 3.4 44.5 1.0 CB B:CYS501 3.4 42.2 1.0 ND1 A:HIS504 3.8 44.4 1.0 CG A:HIS504 3.8 42.1 1.0 O A:ILE505 3.9 45.8 1.0 CA A:GLU581 3.9 51.1 1.0 N A:GLU581 3.9 48.7 1.0 CA A:CYS579 4.1 39.0 1.0 OE2 A:GLU581 4.1 66.6 1.0 C A:CYS579 4.6 36.6 1.0 N A:THR580 4.6 38.4 1.0 CA B:CYS501 4.7 41.7 1.0 CA A:LYS506 4.8 34.7 1.0 C A:ILE505 4.8 42.4 1.0

Zinc binding site 2 out of 3 in the Trk-A in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Trk-A in Complex with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:49.3 occ:1.00 NE2 B:HIS504 2.0 47.8 1.0 OE1 B:GLU581 2.0 55.3 1.0 SG C:CYS501 2.2 51.4 1.0 SG B:CYS579 2.2 48.4 1.0 CB B:GLU581 2.9 56.4 1.0 CE1 B:HIS504 2.9 49.8 1.0 CD2 B:HIS504 3.0 45.5 1.0 CD B:GLU581 3.0 60.1 1.0 CB B:CYS579 3.3 41.6 1.0 CB C:CYS501 3.3 46.9 1.0 CG B:GLU581 3.4 54.6 1.0 O B:ILE505 3.7 52.1 1.0 N B:GLU581 3.8 50.4 1.0 CA B:GLU581 3.9 52.6 1.0 ND1 B:HIS504 3.9 48.4 1.0 CA B:CYS579 4.0 38.8 1.0 CG B:HIS504 4.0 44.5 1.0 OE2 B:GLU581 4.2 67.8 1.0 N B:THR580 4.5 42.3 1.0 C B:CYS579 4.5 38.0 1.0 CA C:CYS501 4.6 44.8 1.0 O B:GLU581 4.7 41.9 1.0 CA B:LYS506 4.8 41.0 1.0 C B:ILE505 4.8 46.7 1.0 C B:GLU581 4.8 48.0 1.0 C B:THR580 5.0 46.1 1.0

Zinc binding site 3 out of 3 in the Trk-A in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Trk-A in Complex with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn801 b:48.7 occ:1.00 NE2 C:HIS504 1.9 41.0 1.0 OE1 C:GLU581 2.0 55.0 1.0 SG C:CYS579 2.2 43.9 1.0 CB C:GLU581 2.8 49.0 1.0 CE1 C:HIS504 2.8 41.9 1.0 CD2 C:HIS504 2.9 40.6 1.0 CD C:GLU581 3.0 54.4 1.0 CG C:GLU581 3.2 49.5 1.0 CB C:CYS579 3.4 37.3 1.0 O C:ILE505 3.7 45.1 1.0 ND1 C:HIS504 3.8 40.7 1.0 N C:GLU581 3.9 42.7 1.0 CG C:HIS504 3.9 39.2 1.0 CA C:GLU581 3.9 47.2 1.0 CA C:CYS579 4.1 33.5 1.0 OE2 C:GLU581 4.2 59.3 1.0 N C:THR580 4.6 36.5 1.0 CA C:LYS506 4.7 38.0 1.0 C C:CYS579 4.7 33.0 1.0 C C:ILE505 4.7 41.8 1.0 N C:ARG507 4.8 34.3 1.0 C C:GLU581 4.9 47.2 1.0 O C:GLU581 4.9 43.3 1.0

G.Subramanian, S.J.Bowen, Y.Zhu, N.Roush, T.Zachary, C.Javens, T.Williams, A.Janssen, A.Gonzales. Synthetic Inhibitor Leads of Human Tropomyosin Receptor Kinase A (Htrka) Rsc Med Chem 2020.
DOI: 10.1039/C9MD00554D