Sodium in PDB 6c1k: Hypopp Mutant with LIGAND1

The structure of Hypopp Mutant with LIGAND1, PDB code: 6c1k was solved by W.A.Catterall, N.Zheng, D.Jiang, T.M.Gamal El-Din, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.31 / 2.70
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	126.394, 126.235, 191.525, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 24.6

The binding sites of Sodium atom in the Hypopp Mutant with LIGAND1 (pdb code 6c1k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Hypopp Mutant with LIGAND1, PDB code: 6c1k:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Hypopp Mutant with LIGAND1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hypopp Mutant with LIGAND1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1311 b:82.6 occ:1.00 O A:GLY1182 3.2 60.2 1.0 CE B:MET2181 3.7 28.4 1.0 CZ2 A:TRP1159 3.7 51.2 1.0 CH2 A:TRP1159 4.0 50.0 1.0 C A:GLY1182 4.0 52.7 1.0 CA A:GLY1182 4.0 40.7 1.0 CG A:PRO1186 4.4 37.9 1.0 O A:MET1181 4.9 64.0 1.0 CE2 A:TRP1159 4.9 49.7 1.0

Sodium binding site 2 out of 4 in the Hypopp Mutant with LIGAND1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hypopp Mutant with LIGAND1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1312 b:88.3 occ:1.00 OE2 A:GLU1158 2.6 83.6 1.0 NE1 A:TRP1159 2.7 51.8 1.0 CD A:GLU1158 3.5 76.1 1.0 CE B:MET2181 3.5 28.4 1.0 CE2 A:TRP1159 3.6 49.7 1.0 CD1 A:TRP1159 3.7 51.7 1.0 CD B:ARG2185 3.7 44.6 1.0 CZ2 A:TRP1159 3.9 51.2 1.0 OE1 A:GLU1158 4.0 75.7 1.0 SD B:MET2181 4.1 48.3 1.0 NE B:ARG2185 4.2 47.4 1.0 CG A:GLU1158 4.6 62.6 1.0 CZ B:ARG2185 4.7 46.0 1.0 CG B:ARG2185 4.8 44.8 1.0 CD2 A:TRP1159 4.8 60.7 1.0 CG A:TRP1159 4.9 48.2 1.0 NH1 B:ARG2185 4.9 45.8 1.0 CB B:ARG2185 5.0 29.9 1.0

Sodium binding site 3 out of 4 in the Hypopp Mutant with LIGAND1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hypopp Mutant with LIGAND1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2310 b:76.3 occ:1.00 O B:GLY2182 3.1 61.7 1.0 CZ2 B:TRP2159 3.6 51.1 1.0 CH2 B:TRP2159 3.9 50.9 1.0 C B:GLY2182 3.9 56.2 1.0 CA B:GLY2182 3.9 42.2 1.0 CG B:PRO2186 4.3 36.3 1.0 O B:MET2181 4.7 66.0 1.0 CE2 B:TRP2159 4.9 54.5 1.0

Sodium binding site 4 out of 4 in the Hypopp Mutant with LIGAND1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Hypopp Mutant with LIGAND1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2311 b:86.8 occ:1.00 NE1 B:TRP2159 2.6 50.0 1.0 OE2 B:GLU2158 2.7 80.0 1.0 CD B:GLU2158 3.4 81.7 1.0 CE2 B:TRP2159 3.6 54.5 1.0 CD1 B:TRP2159 3.6 48.5 1.0 OE1 B:GLU2158 3.8 92.5 1.0 CZ2 B:TRP2159 3.9 51.1 1.0 CG B:GLU2158 4.6 74.4 1.0 O B:HOH2403 4.8 47.6 1.0 CD2 B:TRP2159 4.8 54.2 1.0 CG B:TRP2159 4.8 47.2 1.0

D.Jiang, T.M.Gamal El-Din, C.Ing, P.Lu, R.Pomes, N.Zheng, W.A.Catterall. Structural Basis For Gating Pore Current in Periodic Paralysis. Nature V. 557 590 2018.
ISSN: ESSN 1476-4687
PubMed: 29769724
DOI: 10.1038/S41586-018-0120-4