Sodium in PDB 6gcv: Ligand Binding Domain (Lbd) of the P. Aeruginosa Nitrate Receptor Mcpn

The structure of Ligand Binding Domain (Lbd) of the P. Aeruginosa Nitrate Receptor Mcpn, PDB code: 6gcv was solved by J.A.Gavira, T.Krell, D.Martin-Mora, A.Ortega, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.32 / 1.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.777, 87.949, 52.896, 90.00, 93.05, 90.00
R / Rfree (%)	12.5 / 15.3

The binding sites of Sodium atom in the Ligand Binding Domain (Lbd) of the P. Aeruginosa Nitrate Receptor Mcpn (pdb code 6gcv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Ligand Binding Domain (Lbd) of the P. Aeruginosa Nitrate Receptor Mcpn, PDB code: 6gcv:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Ligand Binding Domain (Lbd) of the P. Aeruginosa Nitrate Receptor Mcpn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ligand Binding Domain (Lbd) of the P. Aeruginosa Nitrate Receptor Mcpn within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:23.8 occ:1.00 O A:HOH345 2.8 21.2 1.0 O A:GLU37 2.9 13.6 1.0 N A:ASP47 2.9 15.7 1.0 CA A:GLY46 3.3 15.7 1.0 CA A:GLU37 3.6 13.2 1.0 C A:GLY46 3.6 15.4 1.0 C A:GLU37 3.7 13.1 1.0 CG A:LEU41 3.7 13.7 1.0 O A:ASP47 3.7 16.5 1.0 CB A:GLU37 3.8 13.8 1.0 CA A:ASP47 3.9 17.1 1.0 CD1 A:LEU41 4.0 14.6 1.0 O A:HOH340 4.0 20.7 1.0 CB A:GLN40 4.1 15.2 1.0 C A:ASP47 4.1 16.3 1.0 CG A:GLU37 4.2 14.9 1.0 N A:LEU41 4.2 13.4 1.0 CB A:ASP47 4.3 19.4 1.0 CD2 A:LEU41 4.5 14.3 1.0 O B:HOH420 4.5 28.7 1.0 CG A:GLN40 4.5 16.6 1.0 N A:GLY46 4.6 15.5 1.0 CB A:LEU41 4.7 13.9 1.0 C A:GLN40 4.8 13.1 1.0 CD A:GLN40 4.8 18.1 1.0 CA A:LEU41 4.9 13.1 1.0 O A:GLY46 4.9 17.5 1.0 O A:HOH370 4.9 24.3 1.0 N A:ALA38 4.9 13.0 1.0 CA A:GLN40 4.9 14.0 1.0 CB A:ALA50 5.0 16.8 1.0

Sodium binding site 2 out of 4 in the Ligand Binding Domain (Lbd) of the P. Aeruginosa Nitrate Receptor Mcpn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ligand Binding Domain (Lbd) of the P. Aeruginosa Nitrate Receptor Mcpn within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:38.6 occ:1.00 OD2 B:ASP66 2.6 21.3 1.0 O C:HOH377 2.8 30.1 1.0 O B:HOH362 2.9 20.8 1.0 O B:HOH305 3.0 38.9 1.0 O B:HOH411 3.2 45.6 1.0 CG B:ASP66 3.5 19.8 1.0 OD1 B:ASP66 3.5 25.1 1.0 CB B:ALA90 3.7 18.1 1.0 NH2 C:ARG97 3.8 23.4 1.0 O B:HOH435 4.0 25.5 1.0 O B:ARG86 4.3 18.9 1.0 O B:HOH410 4.4 24.4 1.0 O B:HOH337 4.4 18.3 1.0 CZ C:ARG97 4.4 21.5 1.0 O C:HOH402 4.4 28.7 1.0 O C:HOH307 4.4 17.9 1.0 O B:HOH313 4.7 28.8 1.0 O C:HOH365 4.8 50.7 1.0 CA B:ALA90 4.8 17.9 1.0 NH1 C:ARG97 4.8 24.1 1.0 CB B:ASP66 4.9 18.0 1.0 O B:ALA62 4.9 16.1 1.0 C B:ARG86 4.9 18.3 1.0

Sodium binding site 3 out of 4 in the Ligand Binding Domain (Lbd) of the P. Aeruginosa Nitrate Receptor Mcpn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ligand Binding Domain (Lbd) of the P. Aeruginosa Nitrate Receptor Mcpn within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:38.5 occ:1.00 O B:HOH397 2.6 31.1 1.0 O B:HOH415 2.8 38.2 1.0 O B:HOH363 2.8 24.4 1.0 O B:HOH432 2.9 35.8 1.0 O B:ASP66 3.6 22.3 1.0 CG B:ARG76 3.8 28.4 0.5 CB B:ARG76 4.0 26.8 0.5 O C:HOH393 4.0 36.6 1.0 NH2 B:ARG86 4.0 25.6 1.0 CA B:GLY78 4.0 29.2 1.0 CB B:ARG76 4.0 28.9 0.5 CD B:ARG76 4.1 29.3 0.5 O B:MET77 4.1 25.9 1.0 C B:MET77 4.2 24.5 1.0 CG B:ARG76 4.2 32.7 0.5 CD B:ARG76 4.2 37.7 0.5 N B:GLY78 4.2 27.0 1.0 N B:MET77 4.4 23.1 1.0 O B:HOH343 4.4 34.6 1.0 CA B:ARG76 4.7 26.6 0.5 CA B:ARG76 4.7 25.8 0.5 C B:ASP66 4.7 18.2 1.0 C B:ARG76 4.9 26.2 1.0 O B:HOH312 4.9 40.5 1.0 CZ B:ARG86 4.9 21.0 1.0

Sodium binding site 4 out of 4 in the Ligand Binding Domain (Lbd) of the P. Aeruginosa Nitrate Receptor Mcpn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ligand Binding Domain (Lbd) of the P. Aeruginosa Nitrate Receptor Mcpn within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:34.7 occ:1.00 O C:HOH335 2.9 19.6 1.0 O C:HOH346 3.1 19.3 1.0 O C:HOH314 3.5 30.0 1.0 CB C:ALA62 3.6 15.1 1.0 CD1 C:TRP93 3.7 16.2 1.0 NE1 C:TRP93 4.1 16.6 1.0 O C:HOH407 4.2 20.2 1.0 O C:HOH323 4.3 25.9 1.0 O C:HOH350 4.3 20.3 1.0 O B:HOH373 4.4 31.1 1.0 CE1 C:TYR58 4.5 15.1 1.0 O C:HOH355 4.6 24.9 1.0 CB C:ALA90 4.6 18.6 1.0 CG C:TRP93 4.7 14.8 1.0 O B:HOH371 4.9 30.1 1.0 CA C:ALA62 5.0 14.8 1.0 CA C:ALA90 5.0 17.1 1.0

D.Martin-Mora, A.Ortega, M.A.Matilla, S.Martinez-Rodriguez, J.A.Gavira, T.Krell. The Molecular Mechanism of Nitrate Chemotaxis Via Direct Ligand Binding to the Pilj Domain of Mcpn. Mbio V. 10 2019.
ISSN: ESSN 2150-7511
PubMed: 30782655
DOI: 10.1128/MBIO.02334-18