Magnesium in PDB 6fd3: Thiophosphorylated PAK3 Kinase Domain

All present enzymatic activity of Thiophosphorylated PAK3 Kinase Domain:
2.7.11.1;

The structure of Thiophosphorylated PAK3 Kinase Domain, PDB code: 6fd3 was solved by F.J.Sorrell, D.Wang, F.Von Delft, C.Bountra, A.M.Edwards, J.M.Elkins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.41 / 1.52
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	108.825, 108.825, 57.934, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 19

The binding sites of Magnesium atom in the Thiophosphorylated PAK3 Kinase Domain (pdb code 6fd3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Thiophosphorylated PAK3 Kinase Domain, PDB code: 6fd3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Thiophosphorylated PAK3 Kinase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thiophosphorylated PAK3 Kinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:16.5 occ:1.00 O2A A:ADP603 2.0 17.4 1.0 O A:HOH853 2.1 19.8 1.0 O2B A:ADP603 2.1 17.7 1.0 O A:HOH728 2.1 18.6 1.0 OD2 A:ASP420 2.1 17.6 1.0 OD1 A:ASN407 2.2 16.2 1.0 CG A:ASP420 3.1 19.4 1.0 CG A:ASN407 3.1 17.5 1.0 PB A:ADP603 3.2 17.2 1.0 PA A:ADP603 3.3 16.9 1.0 ND2 A:ASN407 3.5 17.3 1.0 O3A A:ADP603 3.6 17.9 1.0 CB A:ASP420 3.6 15.5 1.0 O3B A:ADP603 3.7 18.9 1.0 O A:HOH851 3.8 19.6 1.0 MG A:MG602 3.8 19.6 1.0 OD2 A:ASP406 3.9 33.0 0.6 O A:HOH895 4.1 26.8 1.0 OD1 A:ASP420 4.1 19.4 1.0 O5' A:ADP603 4.2 18.6 1.0 O A:HOH900 4.3 45.0 1.0 O3' A:ADP603 4.3 21.5 1.0 C5' A:ADP603 4.4 20.1 1.0 O1A A:ADP603 4.4 17.9 1.0 OD2 A:ASP402 4.5 17.1 1.0 O1B A:ADP603 4.5 20.6 1.0 CB A:ASN407 4.5 14.7 1.0 O A:ASP406 4.6 19.3 0.6 O A:HOH759 4.7 20.5 1.0 CE A:LYS404 4.8 24.3 1.0 O A:HOH775 4.8 22.9 1.0 C3' A:ADP603 4.8 19.3 1.0 CA A:ASN407 4.9 14.5 1.0 CA A:GLY292 4.9 26.1 1.0 CB A:ASP406 4.9 25.5 0.4 C A:ASP406 5.0 18.2 0.6

Magnesium binding site 2 out of 2 in the Thiophosphorylated PAK3 Kinase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thiophosphorylated PAK3 Kinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:19.6 occ:1.00 OD1 A:ASP420 2.0 19.4 1.0 O A:HOH851 2.0 19.6 1.0 O3B A:ADP603 2.1 18.9 1.0 O A:HOH722 2.1 18.4 1.0 OD2 A:ASP420 2.2 17.6 1.0 O A:HOH759 2.2 20.5 1.0 CG A:ASP420 2.4 19.4 1.0 PB A:ADP603 3.2 17.2 1.0 O2B A:ADP603 3.3 17.7 1.0 MG A:MG601 3.8 16.5 1.0 CB A:ASP420 3.9 15.5 1.0 OG A:SER294 3.9 29.2 0.3 O A:HOH853 4.0 19.8 1.0 NZ A:LYS312 4.0 20.9 1.0 O A:HOH708 4.1 32.2 1.0 CB A:SER294 4.1 24.7 0.3 OD2 A:ASP402 4.1 17.1 1.0 O1B A:ADP603 4.2 20.6 1.0 CB A:SER294 4.3 26.6 0.7 O3A A:ADP603 4.3 17.9 1.0 O A:HOH775 4.4 22.9 1.0 N A:GLY422 4.6 18.2 1.0 O2A A:ADP603 4.6 17.4 1.0 CA A:ASP420 4.6 19.1 1.0 CA A:GLY422 4.7 19.0 1.0 O A:ASP420 4.7 17.9 1.0 C A:ASP420 4.8 14.6 1.0 CE1 A:PHE423 4.8 32.0 1.0 CD1 A:PHE423 4.9 27.7 1.0 PA A:ADP603 4.9 16.9 1.0 N A:SER294 4.9 26.0 0.7 N A:SER294 5.0 26.0 0.3 CZ A:PHE423 5.0 27.4 1.0

F.J.Sorrell, L.M.Kilian, J.M.Elkins. Solution Structures and Biophysical Analysis of Full-Length Group A Paks Reveal They Are Monomeric and Auto-Inhibited Incis. Biochem.J. V. 476 1037 2019.
ISSN: ESSN 1470-8728
PubMed: 30858169
DOI: 10.1042/BCJ20180867