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

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

The structure of High Resolution Structure of Thermus Thermophilus Enoyl-Acyl Carrier Protein Reductase Nad-Form, PDB code: 2wyv 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)	39.75 / 1.86
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 (%)	18.2 / 23.9

The binding sites of Sodium atom in the High Resolution Structure of Thermus Thermophilus Enoyl-Acyl Carrier Protein Reductase Nad-Form (pdb code 2wyv). 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 Nad-Form, PDB code: 2wyv:
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 Nad-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 Nad-Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1258 b:35.9 occ:1.00 O A:GLU100 2.3 26.8 1.0 O A:HOH2087 2.4 37.2 1.0 O A:HOH2088 2.4 27.6 1.0 O A:HOH2093 2.4 32.6 1.0 O A:GLU103 2.6 29.3 1.0 C A:GLU100 3.5 27.0 1.0 C A:GLU103 3.7 28.0 1.0 N A:ALA101 4.4 26.1 1.0 CA A:GLU100 4.4 27.9 1.0 CA A:ALA101 4.5 25.0 1.0 CA A:GLY104 4.5 26.4 1.0 C A:ALA101 4.6 24.7 1.0 N A:GLY104 4.6 27.2 1.0 O A:HOH2099 4.6 21.1 1.0 O A:HOH2090 4.6 39.8 1.0 O A:ALA101 4.6 23.8 1.0 CA A:GLU103 4.6 28.8 1.0 N A:ARG105 4.7 24.3 1.0 N A:GLU103 4.7 27.5 1.0 O A:ASP108 4.7 22.6 1.0 C A:GLY104 4.7 25.8 1.0 CB A:GLU103 4.8 30.1 1.0 O A:ARG105 4.8 20.5 1.0 CB A:GLU100 4.9 28.8 1.0 CB A:ASP108 4.9 21.9 1.0 O A:HOH2086 5.0 45.3 1.0

Sodium binding site 2 out of 3 in the High Resolution Structure of Thermus Thermophilus Enoyl-Acyl Carrier Protein Reductase Nad-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 Nad-Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1261 b:25.4 occ:1.00 O B:HOH2081 2.1 30.2 1.0 O B:GLU100 2.2 33.0 1.0 O B:HOH2075 2.5 30.6 1.0 O B:GLU103 2.5 34.3 1.0 O B:HOH2074 2.7 40.9 1.0 C B:GLU100 3.4 33.4 1.0 C B:GLU103 3.7 33.6 1.0 N B:ALA101 4.2 32.6 1.0 O B:HOH2082 4.2 26.1 1.0 CA B:ALA101 4.2 31.7 1.0 O B:ALA101 4.3 31.1 1.0 C B:ALA101 4.3 31.5 1.0 CA B:GLU100 4.4 34.6 1.0 N B:GLU103 4.4 33.4 1.0 CA B:GLU103 4.5 34.2 1.0 CB B:GLU103 4.5 34.7 1.0 O B:ASP108 4.5 26.5 1.0 O B:HOH2078 4.6 31.7 1.0 N B:GLY104 4.7 32.6 1.0 O B:ARG105 4.7 27.6 1.0 CA B:GLY104 4.7 32.5 1.0 CB B:GLU100 4.8 35.7 1.0 CB B:ASP108 4.9 26.5 1.0 N B:ARG105 4.9 30.6 1.0 C B:ASP108 4.9 26.4 1.0 N B:MET102 5.0 31.7 1.0 C B:GLY104 5.0 31.8 1.0

Sodium binding site 3 out of 3 in the High Resolution Structure of Thermus Thermophilus Enoyl-Acyl Carrier Protein Reductase Nad-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 Nad-Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1260 b:34.7 occ:1.00 O C:HOH2069 2.3 31.8 1.0 O C:GLU103 2.3 34.8 1.0 O C:GLU100 2.3 33.7 1.0 O C:HOH2066 2.5 29.5 1.0 O C:HOH2064 2.5 32.1 1.0 C C:GLU100 3.5 33.1 1.0 C C:GLU103 3.5 33.8 1.0 CG C:GLU100 4.2 39.0 1.0 CA C:ALA101 4.2 31.7 1.0 N C:ALA101 4.3 32.2 1.0 C C:ALA101 4.3 31.7 1.0 O C:ALA101 4.4 31.2 1.0 O C:HOH2072 4.4 29.3 1.0 CA C:GLY104 4.4 31.7 1.0 N C:GLY104 4.4 32.7 1.0 CA C:GLU103 4.4 34.5 1.0 N C:GLU103 4.4 33.4 1.0 O C:HOH2065 4.4 58.1 1.0 O C:HOH2070 4.4 32.1 1.0 CA C:GLU100 4.4 34.0 1.0 CD C:GLU100 4.5 43.9 1.0 OE1 C:GLU100 4.6 46.2 1.0 O C:ASP108 4.6 25.4 1.0 CB C:GLU103 4.7 35.3 1.0 O C:ARG105 4.7 24.5 1.0 C C:GLY104 4.8 30.0 1.0 N C:ARG105 4.8 27.8 1.0 CB C:ASP108 4.8 24.8 1.0 CB C:GLU100 4.9 34.8 1.0 N C:MET102 5.0 31.6 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