Sodium in PDB 2wyu: High Resolution Structure of Thermus Thermophilus Enoyl-Acyl Carrier Protein Reductase Apo-Form

All present enzymatic activity of High Resolution Structure of Thermus Thermophilus Enoyl-Acyl Carrier Protein Reductase Apo-Form:
1.3.1.10;

The structure of High Resolution Structure of Thermus Thermophilus Enoyl-Acyl Carrier Protein Reductase Apo-Form, PDB code: 2wyu was solved by J.M.Otero, A.J.Noel, P.Guardado-Calvo, A.L.Llamas-Saiz, M.J.Van Raaij, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.96 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.270, 107.800, 85.980, 90.00, 95.89, 90.00
R / Rfree (%)	17 / 20

The binding sites of Sodium atom in the High Resolution Structure of Thermus Thermophilus Enoyl-Acyl Carrier Protein Reductase Apo-Form (pdb code 2wyu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the High Resolution Structure of Thermus Thermophilus Enoyl-Acyl Carrier Protein Reductase Apo-Form, PDB code: 2wyu:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the High Resolution Structure of Thermus Thermophilus Enoyl-Acyl Carrier Protein Reductase Apo-Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Resolution Structure of Thermus Thermophilus Enoyl-Acyl Carrier Protein Reductase Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1258 b:38.5 occ:1.00 O A:GLU100 2.2 21.3 1.0 O A:HOH2197 2.3 23.7 1.0 O A:HOH2203 2.3 26.0 1.0 O A:HOH2191 2.4 39.1 1.0 O A:HOH2084 2.5 35.7 1.0 O A:GLU103 2.5 28.0 1.0 C A:GLU100 3.4 21.6 1.0 C A:GLU103 3.7 26.8 1.0 O A:ALA101 4.1 19.8 1.0 CA A:ALA101 4.1 19.7 1.0 CG A:GLU100 4.2 30.7 1.0 N A:ALA101 4.2 20.7 1.0 C A:ALA101 4.2 18.9 1.0 O A:HOH2200 4.2 22.6 1.0 O A:HOH2212 4.4 18.8 1.0 CA A:GLY104 4.4 26.6 1.0 CA A:GLU100 4.4 22.9 1.0 N A:GLY104 4.5 27.3 1.0 CD A:GLU100 4.5 39.3 1.0 O A:ARG105 4.5 17.9 1.0 CA A:GLU103 4.5 27.0 1.0 OE2 A:GLU100 4.6 42.7 1.0 N A:GLU103 4.6 24.8 1.0 O A:ASP108 4.6 19.9 1.0 N A:ARG105 4.6 22.0 1.0 C A:GLY104 4.6 25.1 1.0 CB A:GLU103 4.7 28.5 1.0 CB A:ASP108 4.8 18.6 1.0 CB A:GLU100 4.9 24.5 1.0 O A:HOH2036 4.9 44.3 1.0 C A:ASP108 4.9 18.9 1.0 N A:MET102 5.0 19.7 1.0

Sodium binding site 2 out of 3 in the High Resolution Structure of Thermus Thermophilus Enoyl-Acyl Carrier Protein Reductase Apo-Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High Resolution Structure of Thermus Thermophilus Enoyl-Acyl Carrier Protein Reductase Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1260 b:33.3 occ:1.00 O B:HOH2164 2.0 28.3 1.0 O B:HOH2160 2.2 26.1 1.0 O B:GLU100 2.5 29.5 1.0 O B:HOH2158 2.6 37.1 1.0 O B:GLU103 2.7 33.0 1.0 C B:GLU100 3.5 29.4 1.0 C B:GLU103 3.9 32.2 1.0 O B:HOH2155 4.0 41.0 1.0 O B:HOH2171 4.1 20.8 1.0 CG B:GLU100 4.1 35.9 1.0 CA B:ALA101 4.2 26.9 1.0 N B:ALA101 4.2 27.9 1.0 O B:ASP108 4.3 21.5 1.0 O B:ALA101 4.4 25.7 1.0 C B:ALA101 4.4 26.8 1.0 O B:HOH2166 4.5 27.9 1.0 CA B:GLU100 4.5 30.1 1.0 O B:ARG105 4.6 20.5 1.0 C B:ASP108 4.7 20.5 1.0 CB B:ASP108 4.7 20.8 1.0 N B:GLU103 4.8 31.6 1.0 CA B:GLY104 4.8 30.2 1.0 CA B:GLU103 4.8 33.0 1.0 N B:GLY104 4.8 31.4 1.0 CB B:GLU100 4.9 30.8 1.0 N B:ARG105 4.9 26.0 1.0 CB B:GLU103 5.0 34.2 1.0

Sodium binding site 3 out of 3 in the High Resolution Structure of Thermus Thermophilus Enoyl-Acyl Carrier Protein Reductase Apo-Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of High Resolution Structure of Thermus Thermophilus Enoyl-Acyl Carrier Protein Reductase Apo-Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1260 b:39.1 occ:1.00 O D:HOH2139 2.2 34.4 1.0 O D:HOH2137 2.3 25.7 1.0 O D:GLU100 2.3 27.6 1.0 O D:HOH2054 2.6 37.6 1.0 O D:GLU103 2.8 31.9 1.0 C D:GLU100 3.4 27.2 1.0 C D:GLU103 3.9 30.7 1.0 O D:HOH2147 4.0 21.2 1.0 CA D:ALA101 4.1 25.5 1.0 N D:ALA101 4.2 26.0 1.0 C D:ALA101 4.4 25.7 1.0 O D:ALA101 4.4 25.4 1.0 CA D:GLU100 4.4 27.8 1.0 O D:ASP108 4.4 19.2 1.0 O D:HOH2142 4.5 21.8 1.0 O D:ARG105 4.6 17.8 1.0 CB D:GLU100 4.7 28.6 1.0 N D:GLU103 4.8 30.3 1.0 CA D:GLY104 4.8 27.4 1.0 CA D:GLU103 4.8 31.9 1.0 N D:GLY104 4.8 29.2 1.0 C D:ASP108 4.8 18.2 1.0 CB D:GLU103 4.8 32.9 1.0 CB D:ASP108 4.9 18.1 1.0 N D:ARG105 4.9 22.3 1.0

J.M.Otero, A.J.Noel, P.Guardado-Calvo, A.L.Llamas-Saiz, W.Wende, B.Schierling, A.Pingoud, M.J.Van Raaij. High-Resolution Structures of Thermus Thermophilus Enoyl-Acyl Carrier Protein Reductase in the Apo Form, in Complex with Nad+ and in Complex with Nad+ and Triclosan. Acta Crystallogr. Sect. F V. 68 1139 2012STRUCT. Biol. Cryst. Commun..
ISSN: ESSN 1744-3091
PubMed: 23027736
DOI: 10.1107/S1744309112033982