Sodium in PDB 2p3z: Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium

All present enzymatic activity of Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium:
4.2.1.90;

The structure of Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium, PDB code: 2p3z was solved by V.N.Malashkevich, J.M.Sauder, M.Dickey, J.M.Adams, S.K.Burley, S.R.Wasserman, J.Gerlt, S.C.Almo, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.65 / 1.80
Space group	F 4 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	272.248, 272.248, 272.248, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 25.2

The binding sites of Sodium atom in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium (pdb code 2p3z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium, PDB code: 2p3z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:41.6 occ:1.00 O A:HOH557 2.2 25.8 1.0 OD2 A:ASP226 2.3 26.0 1.0 OE1 A:GLU280 2.3 38.8 1.0 OE2 A:GLU252 2.5 20.6 1.0 O A:HOH732 2.6 37.0 1.0 CD A:GLU280 3.0 36.2 1.0 CG A:ASP226 3.1 19.8 1.0 OE2 A:GLU280 3.3 34.9 1.0 OD1 A:ASP226 3.4 22.2 1.0 CD A:GLU252 3.5 18.3 1.0 NZ A:LYS189 3.9 18.2 1.0 O A:HOH683 4.0 27.0 1.0 CG A:GLU252 4.1 15.4 1.0 CE1 A:HIS329 4.2 35.6 1.0 OE1 A:GLU253 4.3 20.0 1.0 CG A:GLU280 4.3 22.7 1.0 ND1 A:HIS329 4.3 35.1 1.0 CB A:ASP226 4.4 16.5 1.0 CE A:LYS189 4.4 16.4 1.0 OE1 A:GLU252 4.4 15.8 1.0 O A:HOH530 4.5 16.7 1.0 CB A:GLU280 4.9 20.3 1.0 CD1 A:TRP228 5.0 17.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:45.7 occ:1.00 OE2 B:GLU252 2.1 33.3 1.0 OD2 B:ASP226 2.3 31.7 1.0 OE1 B:GLU280 2.3 36.8 1.0 O B:HOH579 2.3 35.0 1.0 O B:HOH715 2.9 43.1 1.0 CD B:GLU252 3.1 31.8 1.0 CG B:ASP226 3.2 30.5 1.0 CD B:GLU280 3.3 34.7 1.0 OD1 B:ASP226 3.6 30.7 1.0 OE2 B:GLU280 3.6 37.9 1.0 NZ B:LYS189 3.7 27.0 1.0 CG B:GLU252 3.7 26.2 1.0 O B:HOH768 4.1 35.2 1.0 OE1 B:GLU252 4.1 31.7 1.0 O B:HOH566 4.2 27.7 1.0 CE B:LYS189 4.2 25.5 1.0 ND1 B:HIS329 4.3 37.2 1.0 CB B:ASP226 4.4 30.0 1.0 OE1 B:GLU253 4.5 33.2 1.0 CE1 B:HIS329 4.6 38.0 1.0 CG B:GLU280 4.6 31.1 1.0 CB B:GLU280 4.7 26.5 1.0

V.N.Malashkevich, J.M.Sauder, M.Dickey, S.Ozyurt, S.R.Wasserman, J.Gerlt, S.K.Burley, S.C.Almo. Crystal Structure of L-Rhamnonate Dehydratase From Salmonella Typhimurium LT2 To Be Published.