Sodium in PDB 8ad4: X-Ray Structure of Nqrf(129-408)of Vibrio Cholerae in Complex with Nadh

All present enzymatic activity of X-Ray Structure of Nqrf(129-408)of Vibrio Cholerae in Complex with Nadh:
7.2.1.1;

The structure of X-Ray Structure of Nqrf(129-408)of Vibrio Cholerae in Complex with Nadh, PDB code: 8ad4 was solved by G.Fritz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.38 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.2, 89.38, 95.21, 90, 90, 90
R / Rfree (%)	17.9 / 20.5

The binding sites of Sodium atom in the X-Ray Structure of Nqrf(129-408)of Vibrio Cholerae in Complex with Nadh (pdb code 8ad4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the X-Ray Structure of Nqrf(129-408)of Vibrio Cholerae in Complex with Nadh, PDB code: 8ad4:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the X-Ray Structure of Nqrf(129-408)of Vibrio Cholerae in Complex with Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Nqrf(129-408)of Vibrio Cholerae in Complex with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:20.3 occ:1.00 O A:HOH807 2.2 38.6 1.0 O A:LYS143 2.3 19.3 1.0 O A:MET317 2.4 17.3 1.0 O A:ARG315 2.5 19.5 1.0 OH A:TYR188 2.6 25.2 1.0 O A:HOH779 2.8 32.9 1.0 HH A:TYR188 3.1 30.3 1.0 HB3 A:PHE318 3.4 18.3 1.0 HA A:ALA144 3.4 22.7 1.0 C A:LYS143 3.4 16.8 1.0 HE1 A:TYR188 3.4 27.7 1.0 C A:ARG315 3.5 18.6 1.0 C A:MET317 3.6 17.2 1.0 O A:HOH713 3.6 40.0 1.0 CZ A:TYR188 3.7 22.6 1.0 HZ3 A:LYS187 3.9 53.6 1.0 HA A:ARG315 3.9 22.9 1.0 CE1 A:TYR188 3.9 23.1 1.0 HA A:GLU316 4.0 16.1 1.0 N A:MET317 4.1 15.2 1.0 CA A:ALA144 4.1 18.9 1.0 H A:MET317 4.1 18.2 1.0 N A:ALA144 4.2 17.9 1.0 C A:GLU316 4.2 14.9 1.0 HA A:PHE318 4.2 19.4 1.0 HB2 A:ALA144 4.2 19.7 1.0 HA A:LYS143 4.3 20.7 1.0 CB A:PHE318 4.3 15.3 1.0 CA A:ARG315 4.3 19.0 1.0 O A:HOH652 4.3 35.9 1.0 N A:GLU316 4.3 15.5 1.0 CA A:GLU316 4.4 13.6 1.0 CA A:MET317 4.4 15.0 1.0 CA A:LYS143 4.5 17.2 1.0 HD1 A:PHE318 4.5 18.3 1.0 N A:PHE318 4.5 15.8 1.0 O A:HOH631 4.5 35.4 1.0 HZ1 A:LYS187 4.6 53.6 1.0 CA A:PHE318 4.6 16.2 1.0 NZ A:LYS187 4.6 44.7 1.0 HB2 A:ARG315 4.7 27.8 1.0 O A:GLU316 4.7 16.6 1.0 CB A:ALA144 4.7 16.4 1.0 HB3 A:LYS143 4.7 26.6 1.0 O A:LYS314 4.7 20.7 1.0 HB2 A:PHE318 4.8 18.3 1.0 HB2 A:MET317 4.8 18.8 1.0 CE2 A:TYR188 4.9 23.3 1.0 H A:ALA144 5.0 21.5 1.0

Sodium binding site 2 out of 4 in the X-Ray Structure of Nqrf(129-408)of Vibrio Cholerae in Complex with Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of Nqrf(129-408)of Vibrio Cholerae in Complex with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:23.2 occ:1.00 O A:ALA327 2.3 23.3 1.0 O A:PHE333 2.3 18.7 1.0 O A:HOH735 2.4 28.0 1.0 O A:ASN330 2.5 22.3 1.0 O A:HOH818 2.6 30.4 1.0 O A:HOH680 2.6 30.6 1.0 HA A:ASP331 3.2 28.7 1.0 C A:ALA327 3.3 21.2 1.0 HA A:ALA327 3.3 24.7 1.0 H A:PHE333 3.4 21.6 1.0 HG12 A:VAL334 3.4 28.9 1.0 HB1 A:ALA327 3.5 25.9 1.0 C A:PHE333 3.5 17.3 1.0 C A:ASN330 3.6 22.1 1.0 CA A:ALA327 3.7 20.6 1.0 HG13 A:VAL334 3.9 28.9 1.0 CA A:ASP331 3.9 23.9 1.0 HA A:VAL334 4.0 18.9 1.0 N A:PHE333 4.1 18.0 1.0 H A:ASN330 4.1 31.1 1.0 CG1 A:VAL334 4.1 24.0 1.0 C A:ASP331 4.1 23.4 1.0 CB A:ALA327 4.1 21.5 1.0 N A:ASP331 4.2 23.9 1.0 O A:ASP331 4.2 26.6 1.0 HB3 A:PHE333 4.3 20.0 1.0 CA A:PHE333 4.3 15.4 1.0 N A:VAL334 4.4 16.8 1.0 N A:ALA328 4.4 21.3 1.0 HA A:ALA328 4.5 30.6 1.0 O A:HOH831 4.6 28.8 1.0 CA A:VAL334 4.6 15.7 1.0 N A:ASN330 4.7 25.9 1.0 CA A:ASN330 4.7 23.9 1.0 HB2 A:ALA327 4.7 25.9 1.0 N A:ASN332 4.7 20.1 1.0 HB3 A:ALA327 4.8 25.9 1.0 HG11 A:VAL334 4.8 28.9 1.0 HB2 A:ASN330 4.8 27.6 1.0 CB A:PHE333 4.9 16.6 1.0 CA A:ALA328 4.9 25.5 1.0 OD2 A:ASP331 4.9 33.7 0.8 O A:LEU326 5.0 21.8 1.0 H A:ASN332 5.0 24.1 1.0 H A:ASP331 5.0 28.8 1.0

Sodium binding site 3 out of 4 in the X-Ray Structure of Nqrf(129-408)of Vibrio Cholerae in Complex with Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of Nqrf(129-408)of Vibrio Cholerae in Complex with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:18.2 occ:1.00 HH B:TYR188 2.0 25.2 1.0 O B:LYS143 2.3 15.5 1.0 O B:MET317 2.3 17.2 1.0 O B:ARG315 2.4 18.0 1.0 O B:HOH807 2.4 32.9 1.0 O B:HOH792 2.6 32.6 1.0 OH B:TYR188 2.6 21.0 1.0 HE1 B:TYR188 3.4 24.0 1.0 HB3 B:PHE318 3.4 16.2 1.0 C B:LYS143 3.4 15.2 1.0 C B:ARG315 3.4 19.1 1.0 C B:MET317 3.5 14.8 1.0 HA B:ALA144 3.5 21.6 1.0 CZ B:TYR188 3.7 23.4 1.0 HZ3 B:LYS187 3.7 48.9 1.0 CE1 B:TYR188 3.9 19.9 1.0 HA B:ARG315 3.9 22.3 1.0 N B:MET317 3.9 16.2 1.0 H B:MET317 4.0 19.4 0.9 HA B:GLU316 4.0 18.5 1.0 H B:MET317 4.0 19.4 0.1 C B:GLU316 4.1 16.5 1.0 HE2 B:LYS187 4.1 39.9 1.0 N B:ALA144 4.1 16.7 1.0 HZ1 B:LYS187 4.2 48.9 1.0 CA B:ALA144 4.2 17.9 1.0 HA B:LYS143 4.2 19.8 1.0 HA B:PHE318 4.2 17.0 1.0 HB2 B:ALA144 4.2 20.6 1.0 N B:GLU316 4.3 15.4 1.0 CA B:ARG315 4.3 18.5 1.0 CB B:PHE318 4.3 13.5 1.0 CA B:MET317 4.3 15.3 0.1 NZ B:LYS187 4.3 40.8 1.0 CA B:MET317 4.3 15.2 0.9 CA B:GLU316 4.3 15.3 1.0 HD1 B:PHE318 4.4 18.4 1.0 CA B:LYS143 4.4 16.4 1.0 N B:PHE318 4.4 13.6 1.0 CA B:PHE318 4.5 14.2 1.0 O B:HOH677 4.6 33.0 1.0 HB2 B:MET317 4.6 20.3 0.1 O B:GLU316 4.6 16.4 1.0 O B:LYS314 4.6 16.2 1.0 HB2 B:ARG315 4.6 25.9 1.0 HB3 B:LYS143 4.7 24.2 1.0 CB B:ALA144 4.7 17.1 1.0 CE B:LYS187 4.8 33.2 1.0 HB2 B:MET317 4.8 20.4 0.9 HB2 B:PHE318 4.8 16.2 1.0 CE2 B:TYR188 4.9 20.8 1.0 H B:ALA144 5.0 20.1 1.0

Sodium binding site 4 out of 4 in the X-Ray Structure of Nqrf(129-408)of Vibrio Cholerae in Complex with Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Structure of Nqrf(129-408)of Vibrio Cholerae in Complex with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:21.5 occ:1.00 O B:ALA327 2.4 23.0 1.0 O B:HOH716 2.4 24.9 1.0 O B:PHE333 2.4 16.7 1.0 O B:HOH821 2.7 29.9 1.0 O B:HOH620 2.7 31.4 1.0 O B:ASN330 2.7 18.9 1.0 HA B:ASP331 3.1 26.1 1.0 HA B:ALA327 3.3 29.9 1.0 C B:ALA327 3.4 24.8 1.0 HB1 B:ALA327 3.4 24.1 1.0 HG12 B:VAL334 3.4 26.1 1.0 H B:PHE333 3.5 18.0 1.0 C B:PHE333 3.6 15.8 1.0 C B:ASN330 3.7 19.2 1.0 CA B:ALA327 3.7 24.8 1.0 CA B:ASP331 3.8 21.8 1.0 CB B:ALA327 4.0 20.1 1.0 C B:ASP331 4.0 18.4 1.0 HA B:VAL334 4.0 17.1 1.0 HG13 B:VAL334 4.1 26.1 1.0 O B:ASP331 4.1 20.7 1.0 N B:PHE333 4.2 14.9 1.0 CG1 B:VAL334 4.2 21.7 1.0 H B:ASN330 4.2 27.6 1.0 N B:ASP331 4.2 23.0 1.0 O B:HOH825 4.4 35.6 1.0 CA B:PHE333 4.4 14.7 1.0 HB3 B:PHE333 4.5 18.5 1.0 N B:VAL334 4.5 15.1 1.0 N B:ALA328 4.5 21.1 1.0 HB2 B:ALA327 4.5 24.1 1.0 HA B:ALA328 4.6 29.1 1.0 CA B:VAL334 4.7 14.2 1.0 HB3 B:ALA327 4.7 24.1 1.0 OD1 B:ASP331 4.7 30.2 0.8 N B:ASN332 4.7 16.4 1.0 N B:ASN330 4.8 23.0 1.0 CA B:ASN330 4.8 20.5 1.0 HG11 B:VAL334 4.8 26.1 1.0 HB2 B:ASN330 4.9 25.2 1.0 CB B:PHE333 5.0 15.4 1.0 HD2 B:PHE333 5.0 17.9 1.0

G.Fritz, G.Fritz. N/A N/A.
ISSN: ESSN 1545-9985