Sodium in PDB 8yks: Pathil in Complex with Amp-Pnp

All present enzymatic activity of Pathil in Complex with Amp-Pnp:
2.7.4.16;

The structure of Pathil in Complex with Amp-Pnp, PDB code: 8yks was solved by J.Q.Lin, Z.Chung, J.Lescar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.54 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	113.19, 115.46, 132.62, 90, 90, 90
R / Rfree (%)	18.2 / 19.8

The structure of Pathil in Complex with Amp-Pnp also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Sodium atom in the Pathil in Complex with Amp-Pnp (pdb code 8yks). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Pathil in Complex with Amp-Pnp, PDB code: 8yks:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Pathil in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pathil in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:30.1 occ:1.00 O B:HOH555 2.4 31.1 1.0 OD1 B:ASP47 2.5 27.0 1.0 O1G B:ANP406 2.5 31.5 1.0 O B:HOH617 2.6 34.6 1.0 O2G B:ANP406 3.0 39.6 1.0 PG B:ANP406 3.2 26.9 1.0 MG B:MG403 3.4 64.9 1.0 CG B:ASP47 3.6 24.6 1.0 O B:HOH656 3.8 38.6 1.0 O B:HOH501 3.9 28.1 1.0 O3G B:ANP406 4.0 33.0 1.0 CB B:ASP47 4.0 20.7 1.0 O B:HOH616 4.2 37.6 1.0 CA B:ASP47 4.4 18.7 1.0 O B:THR48 4.4 20.5 1.0 MG B:MG402 4.4 25.6 1.0 N B:THR48 4.4 17.0 1.0 O1B B:ANP406 4.6 44.8 1.0 OD2 B:ASP47 4.7 26.0 1.0 N3B B:ANP406 4.7 31.3 1.0 O B:HOH559 4.7 27.3 1.0 O2A B:ANP406 4.8 44.8 1.0 O B:HOH534 4.8 27.9 1.0 O B:HOH618 4.9 26.0 1.0 C B:ASP47 4.9 17.8 1.0

Sodium binding site 2 out of 4 in the Pathil in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pathil in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:25.1 occ:1.00 O B:HOH559 2.2 27.3 1.0 O B:HOH696 2.3 28.6 1.0 OG B:SER45 2.4 16.1 1.0 O B:HOH654 2.6 19.6 1.0 OD2 B:ASP75 3.0 21.1 1.0 CG B:ASP75 3.4 20.8 1.0 CB B:SER45 3.4 18.3 1.0 O B:HOH534 3.5 27.9 1.0 MG B:MG402 3.7 25.6 1.0 OD1 B:ASP75 3.9 20.9 1.0 CB B:ASP75 4.0 16.7 1.0 O B:THR46 4.1 17.4 1.0 O B:HOH566 4.1 22.1 1.0 CA B:SER45 4.1 15.4 1.0 N B:THR46 4.2 14.8 1.0 O3G B:ANP406 4.3 33.0 1.0 OD2 B:ASP47 4.4 26.0 1.0 O B:HOH502 4.4 22.0 1.0 O B:HOH643 4.5 19.2 1.0 O2' B:ANP406 4.5 16.8 1.0 C B:SER45 4.6 16.4 1.0 C2' B:ANP406 4.8 17.6 1.0 C B:THR46 4.9 19.4 1.0

Sodium binding site 3 out of 4 in the Pathil in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Pathil in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:24.4 occ:1.00 O A:HOH527 2.4 29.2 1.0 OD2 A:ASP47 2.4 20.6 1.0 O1G A:ANP406 2.6 23.0 1.0 O3G A:ANP406 2.6 23.1 1.0 O A:HOH613 2.6 26.3 1.0 PG A:ANP406 3.1 23.8 1.0 MG A:MG403 3.4 29.8 1.0 CG A:ASP47 3.5 18.8 1.0 O A:HOH505 3.8 24.6 1.0 O2G A:ANP406 3.9 21.2 1.0 CB A:ASP47 3.9 20.2 1.0 O A:HOH693 4.0 42.5 1.0 MG A:MG401 4.1 19.7 1.0 O A:HOH548 4.1 42.0 1.0 CA A:ASP47 4.2 18.7 1.0 N A:THR48 4.4 18.3 1.0 O A:THR48 4.5 19.1 1.0 O A:HOH554 4.5 17.9 1.0 N3B A:ANP406 4.6 24.7 1.0 OD1 A:ASP47 4.6 20.4 1.0 O1B A:ANP406 4.6 29.3 1.0 C A:ASP47 4.8 19.1 1.0 O A:HOH564 4.8 20.7 1.0 O2A A:ANP406 5.0 23.6 1.0

Sodium binding site 4 out of 4 in the Pathil in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Pathil in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:19.5 occ:1.00 OG A:SER45 2.3 18.9 1.0 O A:HOH554 2.3 17.9 1.0 O A:HOH628 2.6 19.7 1.0 OD2 A:ASP75 2.7 19.0 1.0 CG A:ASP75 3.3 20.4 1.0 CB A:SER45 3.4 16.8 1.0 MG A:MG401 3.5 19.7 1.0 CB A:ASP75 3.9 17.7 1.0 OD1 A:ASP75 3.9 20.4 1.0 CA A:SER45 4.1 19.0 1.0 O A:HOH542 4.2 20.5 1.0 O A:THR46 4.2 16.2 1.0 N A:THR46 4.2 16.5 1.0 O2G A:ANP406 4.3 21.2 1.0 O A:HOH625 4.4 18.1 1.0 OD1 A:ASP47 4.5 20.4 1.0 O2' A:ANP406 4.5 17.2 1.0 O A:HOH512 4.6 17.9 1.0 C A:SER45 4.6 16.6 1.0 C2' A:ANP406 4.8 16.7 1.0 C A:THR46 5.0 16.6 1.0

J.Q.Lin, J.Lescar. Thil in Complex with Amp-Pnp To Be Published.