Sodium in PDB 8vb3: Dienelactone Hydrolase From Solimonas Fluminis

The structure of Dienelactone Hydrolase From Solimonas Fluminis, PDB code: 8vb3 was solved by J.D.F.Schnettler Fernandez, E.C.Campbell, F.Hollfelder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.63 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.143, 87.835, 71.415, 90, 99.17, 90
R / Rfree (%)	15.8 / 18.6

The binding sites of Sodium atom in the Dienelactone Hydrolase From Solimonas Fluminis (pdb code 8vb3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Dienelactone Hydrolase From Solimonas Fluminis, PDB code: 8vb3:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Dienelactone Hydrolase From Solimonas Fluminis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dienelactone Hydrolase From Solimonas Fluminis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:21.7 occ:1.00 N A:GLN72 3.2 25.5 1.0 N A:ASP73 3.3 33.1 1.0 CD1 A:PHE71 3.6 35.1 1.0 CB A:PHE71 3.8 27.1 1.0 CG A:GLN76 3.8 38.6 1.0 OD1 A:ASP73 3.9 41.0 1.0 CA A:PHE71 3.9 23.5 1.0 CB A:ASP73 4.0 37.2 1.0 CB A:GLN72 4.0 29.0 1.0 CA A:GLN72 4.0 27.0 1.0 CG A:ASP73 4.1 45.2 1.0 C A:PHE71 4.1 24.5 1.0 C A:GLN72 4.1 29.9 1.0 CA A:ASP73 4.2 33.9 1.0 CG A:PHE71 4.2 28.9 1.0 CB A:GLN76 4.2 41.3 1.0 O A:ASP73 4.3 34.9 1.0 CE1 A:PHE71 4.7 38.5 1.0 C A:ASP73 4.7 37.6 1.0 OD2 A:ASP73 4.8 45.1 1.0 CD A:GLN76 4.9 37.0 1.0

Sodium binding site 2 out of 5 in the Dienelactone Hydrolase From Solimonas Fluminis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dienelactone Hydrolase From Solimonas Fluminis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:22.6 occ:1.00 O A:ARG103 2.3 23.0 1.0 O A:HOH524 2.3 29.4 1.0 O A:GLN105 2.4 25.5 1.0 O A:VAL108 2.4 23.6 1.0 O A:HOH516 2.7 28.6 1.0 C A:ARG103 3.4 22.0 1.0 C A:GLN105 3.5 25.9 1.0 C A:VAL108 3.5 22.7 1.0 C A:ALA104 3.8 26.5 1.0 N A:GLN105 3.9 25.1 1.0 O A:ALA104 4.0 28.6 1.0 CB A:VAL108 4.0 21.8 1.0 CA A:VAL108 4.1 20.9 1.0 N A:ALA110 4.1 21.9 1.0 CA A:ALA104 4.2 23.0 1.0 N A:VAL108 4.2 23.4 1.0 CA A:PRO106 4.2 28.6 1.0 N A:ALA104 4.2 22.3 1.0 N A:PRO106 4.3 26.5 1.0 O A:PRO106 4.3 29.6 1.0 CA A:GLN105 4.3 24.8 1.0 C A:PRO106 4.4 25.9 1.0 CB A:ALA110 4.4 20.8 1.0 CA A:ARG103 4.5 20.5 1.0 CG1 A:VAL108 4.5 20.6 1.0 N A:ASP109 4.6 20.7 1.0 CA A:ALA110 4.6 21.4 1.0 C A:ASP109 4.8 21.6 1.0 O A:LEU102 4.8 20.8 1.0 CA A:ASP109 4.9 22.8 1.0

Sodium binding site 3 out of 5 in the Dienelactone Hydrolase From Solimonas Fluminis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dienelactone Hydrolase From Solimonas Fluminis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:27.9 occ:1.00 O A:SER131 2.2 18.8 1.0 O A:HOH503 2.2 29.6 1.0 O A:HOH424 2.4 27.1 1.0 O A:HOH409 2.9 38.6 1.0 C A:SER131 3.4 18.4 1.0 NZ A:LYS155 3.7 35.5 1.0 O A:HOH403 4.3 29.3 1.0 N A:GLY132 4.3 16.0 1.0 CA A:GLY132 4.3 15.9 1.0 O A:HOH462 4.3 24.9 1.0 CA A:SER131 4.4 17.4 1.0 CE A:LYS155 4.5 36.8 1.0 CD A:LYS155 4.6 28.0 1.0 OE1 A:GLN96 4.8 41.0 1.0 O A:HOH519 4.8 24.7 1.0 CB A:SER131 4.9 19.4 1.0 C A:GLY132 4.9 17.9 1.0 O A:HOH522 5.0 34.2 1.0

Sodium binding site 4 out of 5 in the Dienelactone Hydrolase From Solimonas Fluminis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Dienelactone Hydrolase From Solimonas Fluminis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:22.6 occ:1.00 O B:SER131 2.3 17.8 1.0 O B:HOH526 2.3 25.5 1.0 O B:HOH522 2.5 32.3 1.0 C B:SER131 3.5 17.0 1.0 NZ B:LYS155 4.2 29.2 1.0 CA B:GLY132 4.3 15.2 1.0 OE1 B:GLN96 4.3 29.4 1.0 N B:GLY132 4.3 15.1 1.0 CA B:SER131 4.5 15.7 1.0 O B:HOH458 4.5 23.6 1.0 CD B:LYS155 4.6 23.6 1.0 NE2 B:GLN96 4.7 37.7 1.0 CE B:LYS155 4.8 26.5 1.0 C B:GLY132 4.8 16.2 1.0 CD B:GLN96 5.0 31.7 1.0

Sodium binding site 5 out of 5 in the Dienelactone Hydrolase From Solimonas Fluminis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Dienelactone Hydrolase From Solimonas Fluminis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:27.1 occ:1.00 O B:HOH529 2.2 34.9 1.0 O B:ARG103 2.3 26.0 1.0 O B:VAL108 2.4 25.8 1.0 O B:GLN105 2.4 26.5 1.0 O B:HOH479 2.7 31.8 1.0 C B:VAL108 3.5 25.6 1.0 C B:ARG103 3.5 24.8 1.0 C B:GLN105 3.5 29.7 1.0 C B:ALA104 3.8 27.0 1.0 N B:GLN105 3.9 26.1 1.0 CB B:VAL108 4.0 23.0 1.0 CA B:VAL108 4.1 25.4 1.0 N B:VAL108 4.1 28.0 1.0 CA B:ALA104 4.1 26.6 1.0 O B:ALA104 4.1 29.7 1.0 N B:ALA110 4.2 22.5 1.0 N B:ALA104 4.2 20.4 1.0 O B:PRO106 4.2 34.2 0.7 CA B:PRO106 4.3 32.1 0.7 CA B:PRO106 4.3 32.1 0.3 N B:PRO106 4.3 29.6 0.7 C B:PRO106 4.3 32.5 0.7 CA B:GLN105 4.3 26.1 1.0 N B:PRO106 4.4 29.7 0.3 CB B:ALA110 4.4 22.6 1.0 C B:PRO106 4.4 32.5 0.3 O B:PRO106 4.4 34.2 0.3 CA B:ARG103 4.5 20.7 1.0 CG1 B:VAL108 4.6 21.4 1.0 N B:ASP109 4.6 23.1 1.0 CA B:ALA110 4.7 21.3 1.0 O B:LEU102 4.8 22.0 1.0 C B:ASP109 4.9 23.6 1.0 CA B:ASP109 4.9 23.3 1.0

J.D.F.Schnettler Fernandez, E.C.Campbell, R.Khashiev, J.O.Klein, F.Hollfelder. Metal-Independent Organophosphate Hydrolysis in A Protein Family Possessing A Catalytic Triad To Be Published.