Sodium in PDB 4qxk: Joint X-Ray/Neutron Structure of Pkgibeta in Complex with Cgmp

All present enzymatic activity of Joint X-Ray/Neutron Structure of Pkgibeta in Complex with Cgmp:
2.7.11.12;

The structure of Joint X-Ray/Neutron Structure of Pkgibeta in Complex with Cgmp, PDB code: 4qxk was solved by C.Kim, O.Gerlits, A.Kovalevsky, G.Y.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	48.746, 48.746, 104.861, 90.00, 90.00, 90.00
R / Rfree (%)	27.7 / 31.8

The binding sites of Sodium atom in the Joint X-Ray/Neutron Structure of Pkgibeta in Complex with Cgmp (pdb code 4qxk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Joint X-Ray/Neutron Structure of Pkgibeta in Complex with Cgmp, PDB code: 4qxk:

Sodium binding site 1 out of 1 in the Joint X-Ray/Neutron Structure of Pkgibeta in Complex with Cgmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Joint X-Ray/Neutron Structure of Pkgibeta in Complex with Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:17.1 occ:1.00 O A:GLN311 2.4 18.5 1.0 O A:DOD1011 2.4 24.7 1.0 O A:LYS308 2.5 18.1 1.0 O A:GLU313 2.5 15.5 1.0 O A:DOD1031 2.6 49.1 1.0 D1 A:DOD1031 2.6 50.5 1.0 O A:DOD1013 2.7 25.9 1.0 D A:GLU313 2.9 17.4 1.0 D2 A:DOD1011 3.0 24.5 1.0 D1 A:DOD1011 3.1 22.5 1.0 D2 A:DOD1031 3.2 50.2 1.0 D2 A:DOD1013 3.2 28.0 1.0 N A:GLU313 3.3 18.0 1.0 D1 A:DOD1013 3.4 28.2 1.0 HB3 A:GLU313 3.4 22.1 1.0 C A:GLU313 3.5 16.3 1.0 HA A:ALA309 3.5 14.1 1.0 C A:GLN311 3.5 17.1 1.0 C A:LYS308 3.5 16.8 1.0 D A:GLN311 3.6 15.6 0.9 H A:GLN311 3.6 15.6 0.1 CA A:GLU313 3.8 18.6 1.0 HB3 A:LYS308 3.9 19.6 1.0 HA3 A:GLY312 4.0 17.7 1.0 HB2 A:GLN311 4.0 20.1 1.0 C A:GLY312 4.0 18.5 1.0 CB A:GLU313 4.2 20.7 1.0 H A:VAL315 4.2 15.4 0.6 D A:VAL315 4.2 15.4 0.4 CA A:ALA309 4.2 14.2 1.0 N A:ALA309 4.3 15.4 1.0 N A:GLN311 4.3 16.9 1.0 CA A:GLY312 4.3 18.6 1.0 N A:GLY312 4.3 19.2 1.0 HA A:LYS308 4.3 17.6 1.0 CA A:GLN311 4.4 19.0 1.0 O A:DOD1041 4.4 58.7 1.0 CA A:LYS308 4.5 17.9 1.0 C A:ALA309 4.5 14.1 1.0 HA A:ASP314 4.5 15.8 1.0 O A:DOD1048 4.6 38.0 0.5 N A:ASP314 4.6 15.2 1.0 O A:VAL315 4.7 15.2 1.0 CB A:LYS308 4.7 20.4 1.0 CB A:GLN311 4.7 21.6 1.0 HG12 A:VAL315 4.8 15.7 1.0 D1 A:DOD1041 4.8 58.0 1.0 HG2 A:GLU313 4.8 23.1 1.0 O A:ALA309 4.8 14.1 1.0 HB2 A:GLU313 4.9 20.9 1.0 HA A:GLU313 4.9 18.5 1.0 N A:LEU310 4.9 12.5 1.0 O A:GLY312 4.9 19.6 1.0 N A:VAL315 4.9 14.5 1.0 HD2 A:LYS308 5.0 26.2 1.0 H A:LEU310 5.0 12.2 1.0 D2 A:DOD1003 5.0 22.9 1.0 D2 A:DOD1048 5.0 36.9 0.5 D2 A:DOD1041 5.0 57.5 1.0

G.Y.Huang, O.O.Gerlits, M.P.Blakeley, B.Sankaran, A.Y.Kovalevsky, C.Kim. Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Cgmp-Dependent Protein Kinase Agonist Design. Biochemistry V. 53 6725 2014.
ISSN: ISSN 0006-2960
PubMed: 25271401
DOI: 10.1021/BI501012V