Sodium in PDB 6eq9: Crystal Structure of JNK3 in Complex with Amp-Pcp

All present enzymatic activity of Crystal Structure of JNK3 in Complex with Amp-Pcp:
2.7.11.24;

The structure of Crystal Structure of JNK3 in Complex with Amp-Pcp, PDB code: 6eq9 was solved by J.T.Macedo, T.Stehle, B.S.Blaum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.23 / 1.83
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	156.729, 110.490, 43.951, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.2

The structure of Crystal Structure of JNK3 in Complex with Amp-Pcp also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of JNK3 in Complex with Amp-Pcp (pdb code 6eq9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of JNK3 in Complex with Amp-Pcp, PDB code: 6eq9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of JNK3 in Complex with Amp-Pcp


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 JNK3 in Complex with Amp-Pcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:36.9 occ:1.00 O A:ILE123 2.7 22.4 1.0 O A:HOH693 2.8 30.1 1.0 N A:HIS120 3.1 25.5 1.0 O A:HIS120 3.1 25.0 1.0 O A:VAL118 3.5 30.4 1.0 C A:ILE123 3.6 21.9 1.0 O A:ILE124 3.7 32.6 1.0 CA A:ASN119 3.7 29.4 1.0 O A:HOH725 3.7 31.9 1.0 CB A:ILE123 3.8 27.1 1.0 C A:ASN119 3.9 30.2 1.0 C A:VAL118 3.9 28.9 1.0 C A:HIS120 3.9 25.1 1.0 C A:ILE124 4.0 28.3 1.0 CA A:SER125 4.0 36.9 1.0 CA A:HIS120 4.1 26.1 1.0 CB A:SER125 4.1 40.8 1.0 N A:ASN119 4.1 31.2 1.0 N A:SER125 4.1 31.6 1.0 CG2 A:ILE123 4.1 24.0 1.0 CG1 A:VAL118 4.2 28.1 1.0 CA A:ILE123 4.3 23.7 1.0 O A:HOH762 4.3 51.6 1.0 O A:HOH811 4.4 51.3 1.0 N A:ILE124 4.5 23.9 1.0 OD1 A:ASN119 4.5 47.5 1.0 CB A:HIS120 4.6 25.7 1.0 N A:ILE123 4.6 24.0 1.0 OG A:SER125 4.8 46.8 1.0 CB A:VAL118 4.8 26.6 1.0 CA A:ILE124 4.8 25.6 1.0 O A:HOH669 4.9 63.3 1.0 CB A:ASN119 5.0 34.9 1.0 CA A:VAL118 5.0 28.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of JNK3 in Complex with Amp-Pcp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of JNK3 in Complex with Amp-Pcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:41.2 occ:1.00 O A:HOH717 2.6 41.9 1.0 O A:PRO302 2.7 42.9 1.0 OG1 A:THR281 2.7 27.8 1.0 O A:HOH722 2.9 32.3 1.0 CG2 A:THR281 3.6 35.3 1.0 CD1 A:ILE276 3.6 34.1 1.0 C A:PRO302 3.6 43.1 1.0 CB A:THR281 3.7 30.9 1.0 CB A:ARG301 3.7 42.5 1.0 O A:ARG301 3.8 35.5 1.0 CA A:LYS303 4.0 43.1 1.0 C A:ARG301 4.1 37.1 1.0 O A:VAL298 4.1 36.3 1.0 CD A:LYS303 4.2 51.3 1.0 N A:LYS303 4.2 42.2 1.0 CA A:THR281 4.3 29.9 1.0 CB A:ILE276 4.4 28.8 1.0 CD2 A:TYR304 4.4 33.9 1.0 CA A:ARG301 4.5 38.9 1.0 CE A:MET287 4.5 48.5 1.0 N A:PRO302 4.5 36.7 1.0 CG1 A:ILE276 4.5 32.2 1.0 N A:TYR304 4.6 38.0 1.0 CG2 A:ILE276 4.6 29.8 1.0 CA A:PRO302 4.7 40.7 1.0 C A:LYS303 4.7 39.6 1.0 CG A:ARG301 4.9 40.9 1.0 N A:THR281 5.0 30.2 1.0 CE2 A:TYR304 5.0 36.9 1.0 N A:ARG301 5.0 39.8 1.0

F.Ansideri, J.T.Macedo, M.Eitel, A.El-Gokha, D.S.Zinad, C.Scarpellini, M.Kudolo, D.Schollmeyer, F.M.Boeckler, B.S.Blaum, S.A.Laufer, P.Koch. Structural Optimization of A Pyridinylimidazole Scaffold: Shifting the Selectivity From P38 Alpha Mitogen-Activated Protein Kinase to C-Jun N-Terminal Kinase 3. Acs Omega V. 3 7809 2018.
ISSN: ESSN 2470-1343
PubMed: 30087925
DOI: 10.1021/ACSOMEGA.8B00668