Magnesium in PDB 4jdi: Crystal Structure of Serine/Threonine-Protein Kinase Pak 4 in Complex with Paktide S Peptide Substrate

All present enzymatic activity of Crystal Structure of Serine/Threonine-Protein Kinase Pak 4 in Complex with Paktide S Peptide Substrate:
2.7.11.1;

The structure of Crystal Structure of Serine/Threonine-Protein Kinase Pak 4 in Complex with Paktide S Peptide Substrate, PDB code: 4jdi was solved by B.H.Ha, T.J.Boggon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.32 / 1.85
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.912, 61.912, 181.560, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 23.3

The binding sites of Magnesium atom in the Crystal Structure of Serine/Threonine-Protein Kinase Pak 4 in Complex with Paktide S Peptide Substrate (pdb code 4jdi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Serine/Threonine-Protein Kinase Pak 4 in Complex with Paktide S Peptide Substrate, PDB code: 4jdi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Serine/Threonine-Protein Kinase Pak 4 in Complex with Paktide S Peptide Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Serine/Threonine-Protein Kinase Pak 4 in Complex with Paktide S Peptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:40.6 occ:1.00 N3B A:ANP1000 2.1 26.6 0.8 O2A A:ANP1000 2.2 29.7 0.8 O A:HOH1186 2.4 40.2 1.0 O A:HOH1123 2.4 36.7 1.0 O A:HOH1102 2.6 28.1 1.0 OD2 A:ASP458 3.0 31.7 1.0 O A:HOH1164 3.2 25.3 1.0 PB A:ANP1000 3.3 28.4 0.8 PA A:ANP1000 3.4 29.9 0.8 O A:HOH1232 3.5 34.4 1.0 O3A A:ANP1000 3.7 28.4 0.8 NH2 B:ARG-1 3.8 58.1 1.0 O1B A:ANP1000 3.9 27.3 0.8 CG A:ASP458 4.0 32.0 1.0 MG A:MG1002 4.0 28.4 0.8 O A:HOH1187 4.3 36.4 1.0 OG B:SER0 4.4 34.7 1.0 N A:SER331 4.5 35.0 1.0 O1A A:ANP1000 4.5 28.0 0.8 O5' A:ANP1000 4.5 31.6 1.0 NZ A:LYS442 4.5 28.1 1.0 C5' A:ANP1000 4.5 33.5 1.0 CE A:LYS442 4.6 27.4 1.0 CA A:GLY330 4.6 35.1 1.0 O3' A:ANP1000 4.6 36.9 1.0 O2B A:ANP1000 4.7 29.2 0.8 CB A:ASP458 4.7 28.7 1.0 OG A:SER331 4.7 39.5 1.0 OD1 A:ASP458 4.8 31.9 1.0 OD2 A:ASP440 4.9 31.2 1.0 O A:HOH1108 4.9 32.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Serine/Threonine-Protein Kinase Pak 4 in Complex with Paktide S Peptide Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Serine/Threonine-Protein Kinase Pak 4 in Complex with Paktide S Peptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:28.4 occ:0.80 O1B A:ANP1000 2.0 27.3 0.8 O A:HOH1234 2.0 33.4 1.0 OD1 A:ASP458 2.0 31.9 1.0 O A:HOH1232 2.1 34.4 1.0 O A:HOH1233 2.2 35.1 1.0 OD2 A:ASP458 2.2 31.7 1.0 CG A:ASP458 2.4 32.0 1.0 PB A:ANP1000 3.2 28.4 0.8 N3B A:ANP1000 3.4 26.6 0.8 CB A:ASP458 3.9 28.7 1.0 MG A:MG1001 4.0 40.6 1.0 NZ A:LYS350 4.2 32.1 1.0 OD2 A:ASP440 4.2 31.2 1.0 O2B A:ANP1000 4.3 29.2 0.8 O3A A:ANP1000 4.3 28.4 0.8 O A:HOH1116 4.4 35.1 1.0 O A:ASP458 4.4 25.5 1.0 N A:GLY460 4.5 26.0 1.0 O A:HOH1103 4.6 25.9 1.0 CA A:GLY460 4.6 27.3 1.0 C A:ASP458 4.6 26.4 1.0 OG B:SER0 4.6 34.7 1.0 CA A:ASP458 4.6 26.2 1.0 O2A A:ANP1000 4.7 29.7 0.8 CG2 A:THR332 4.7 33.9 1.0 O A:HOH1102 4.8 28.1 1.0 CD2 A:PHE461 4.8 35.4 1.0 OG1 A:THR332 4.8 30.9 1.0 PA A:ANP1000 4.8 29.9 0.8 O1A A:ANP1000 4.8 28.0 0.8 CG A:PHE461 4.9 32.6 1.0 N A:PHE461 4.9 26.1 1.0 CE2 A:PHE461 4.9 36.9 1.0 OE2 A:GLU366 5.0 34.5 1.0

C.Chen, B.H.Ha, A.F.Thevenin, H.J.Lou, R.Zhang, K.Y.Yip, J.R.Peterson, M.Gerstein, P.M.Kim, P.Filippakopoulos, S.Knapp, T.J.Boggon, B.E.Turk. Identification of A Major Determinant For Serine-Threonine Kinase Phosphoacceptor Specificity. Mol.Cell V. 53 140 2014.
ISSN: ISSN 1097-2765
PubMed: 24374310
DOI: 10.1016/J.MOLCEL.2013.11.013