Sodium in PDB 6c1m: Navab Normopp Mutant

The structure of Navab Normopp Mutant, PDB code: 6c1m 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 / 2.52
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	126.330, 126.244, 191.585, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 22.7

The binding sites of Sodium atom in the Navab Normopp Mutant (pdb code 6c1m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Navab Normopp Mutant, PDB code: 6c1m:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Navab Normopp Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Navab Normopp Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1312 b:63.9 occ:1.00 NE1 A:TRP1159 3.0 53.5 1.0 OE2 A:GLU1158 3.0 91.7 1.0 O B:HOH2410 3.3 62.2 1.0 OE1 A:GLU1158 3.3 0.5 1.0 CD A:GLU1158 3.4 99.7 1.0 CD B:ARG2185 3.6 45.5 1.0 CE B:MET2181 3.8 35.3 1.0 CD1 A:TRP1159 3.9 57.0 1.0 CE2 A:TRP1159 4.0 60.2 1.0 NE B:ARG2185 4.3 48.0 1.0 CZ2 A:TRP1159 4.3 57.1 1.0 SD B:MET2181 4.4 55.7 1.0 CG A:GLU1158 4.6 0.4 1.0 O A:HOH1404 4.8 46.3 1.0 CG B:ARG2185 4.8 54.2 1.0 CZ B:ARG2185 4.9 51.8 1.0 CB B:ARG2185 4.9 36.3 1.0 NH1 B:ARG2185 4.9 49.1 1.0

Sodium binding site 2 out of 4 in the Navab Normopp Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Navab Normopp Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1313 b:74.4 occ:1.00 O A:GLY1182 3.0 60.3 1.0 CA A:GLY1182 3.8 42.4 1.0 C A:GLY1182 3.8 51.6 1.0 CZ2 A:TRP1159 3.8 57.1 1.0 CE B:MET2181 3.9 35.3 1.0 CH2 A:TRP1159 4.1 58.2 1.0 CG A:PRO1186 4.1 41.6 1.0 O A:MET1181 4.5 63.8 1.0 N A:GLY1182 5.0 51.5 1.0

Sodium binding site 3 out of 4 in the Navab Normopp Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Navab Normopp Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2315 b:54.4 occ:1.00 NE1 B:TRP2159 2.9 51.7 1.0 OE2 B:GLU2158 3.0 0.2 1.0 O B:HOH2416 3.2 68.1 1.0 OE1 B:GLU2158 3.4 0.2 1.0 CD B:GLU2158 3.5 0.1 1.0 CD1 B:TRP2159 3.8 51.9 1.0 CE2 B:TRP2159 3.9 52.0 1.0 CZ2 B:TRP2159 4.2 53.4 1.0 CG B:GLU2158 4.7 0.0 1.0

Sodium binding site 4 out of 4 in the Navab Normopp Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Navab Normopp Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2316 b:79.0 occ:1.00 O B:GLY2182 3.0 51.6 1.0 O B:HOH2416 3.2 68.1 1.0 O B:HOH2417 3.6 74.1 1.0 CZ2 B:TRP2159 3.7 53.4 1.0 CA B:GLY2182 3.8 38.9 1.0 C B:GLY2182 3.8 53.9 1.0 CH2 B:TRP2159 3.9 53.3 1.0 CG B:PRO2186 4.2 40.1 1.0 O B:MET2181 4.6 61.0 1.0 CE2 B:TRP2159 4.9 52.0 1.0 N B:GLY2182 5.0 50.2 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