Sodium in PDB 2hzg: Crystal Structure of Predicted Mandelate Racemase From Rhodobacter Sphaeroides

The structure of Crystal Structure of Predicted Mandelate Racemase From Rhodobacter Sphaeroides, PDB code: 2hzg was solved by U.A.Ramagopal, R.Toro, S.C.Almo, S.K.Burley, New York Sgx Research Centerfor Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.37 / 2.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.172, 117.727, 132.708, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 19.5

The binding sites of Sodium atom in the Crystal Structure of Predicted Mandelate Racemase From Rhodobacter Sphaeroides (pdb code 2hzg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Predicted Mandelate Racemase From Rhodobacter Sphaeroides, PDB code: 2hzg:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Predicted Mandelate Racemase From Rhodobacter Sphaeroides


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 Predicted Mandelate Racemase From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1101 b:22.8 occ:1.00 OE2 A:GLU254 2.2 22.2 1.0 OD2 A:ASP199 2.3 15.6 1.0 OE2 A:GLU227 2.3 19.3 1.0 O A:HOH1266 2.5 18.9 1.0 O A:HOH1258 2.6 19.1 1.0 O A:HOH1228 2.8 18.2 1.0 CG A:ASP199 3.2 16.0 1.0 CD A:GLU254 3.2 19.5 1.0 CD A:GLU227 3.4 16.0 1.0 OD1 A:ASP199 3.6 14.4 1.0 OE1 A:GLU254 3.6 22.6 1.0 CD2 A:HIS304 3.7 15.3 1.0 O A:HOH1329 3.8 25.6 1.0 NE2 A:HIS304 3.8 17.6 1.0 NZ A:LYS165 3.9 12.6 1.0 CG A:GLU227 4.1 14.0 1.0 O A:HOH1230 4.2 14.4 1.0 OE1 A:GLU227 4.3 15.1 1.0 NE1 A:TRP168 4.3 17.9 1.0 CB A:ASP199 4.3 15.2 1.0 O A:HOH1204 4.5 15.7 1.0 CG A:GLU254 4.5 18.1 1.0 O A:HOH1431 4.6 35.7 1.0 OE2 A:GLU228 4.6 22.2 1.0 CE A:LYS165 4.6 12.0 1.0 CG A:HIS304 4.9 14.3 1.0 CG A:GLU228 5.0 19.9 1.0 CB A:GLU254 5.0 16.7 1.0 OE2 A:GLU329 5.0 14.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Predicted Mandelate Racemase From Rhodobacter Sphaeroides


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 Predicted Mandelate Racemase From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1103 b:35.0 occ:1.00 O A:HOH1396 2.3 25.5 1.0 O A:GLY174 2.3 21.6 1.0 O A:HOH1400 2.3 30.0 1.0 O A:HOH1366 2.5 30.4 1.0 C A:GLY174 3.3 22.0 1.0 NH2 A:ARG214 3.9 16.3 1.0 CA A:GLY174 3.9 22.9 1.0 O A:HOH1415 4.0 39.5 1.0 O A:GLY172 4.2 20.5 1.0 N A:GLY174 4.2 23.2 1.0 O A:HOH1580 4.3 43.3 1.0 N A:THR175 4.4 21.6 1.0 O A:ARG173 4.4 24.6 1.0 C A:ARG173 4.4 23.6 1.0 O A:HOH1499 4.4 40.2 1.0 NH1 A:ARG214 4.6 14.2 1.0 CA A:THR175 4.7 21.4 1.0 CZ A:ARG214 4.7 16.0 1.0 C A:GLY172 5.0 20.4 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Predicted Mandelate Racemase From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Predicted Mandelate Racemase From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1102 b:26.1 occ:1.00 O B:HOH1363 2.4 33.4 1.0 OD2 B:ASP199 2.4 19.1 1.0 OE1 B:GLU254 2.4 32.7 1.0 OE2 B:GLU227 2.4 18.8 1.0 O B:HOH1359 2.5 19.3 1.0 CD B:GLU254 3.1 28.5 1.0 OE2 B:GLU254 3.2 31.7 1.0 CG B:ASP199 3.3 16.8 1.0 CD B:GLU227 3.3 17.5 1.0 OD1 B:ASP199 3.6 17.3 1.0 CG B:GLU227 4.1 15.0 1.0 NZ B:LYS165 4.1 15.6 1.0 OE1 B:GLU227 4.1 15.2 1.0 O B:HOH1282 4.3 18.1 1.0 O B:HOH1349 4.3 32.4 1.0 OE1 B:GLU228 4.4 29.5 1.0 CG B:GLU254 4.5 21.3 1.0 O B:HOH1213 4.5 13.2 1.0 CB B:ASP199 4.6 14.7 1.0 CD B:GLU228 4.6 25.9 1.0 NE1 B:TRP168 4.8 31.3 1.0 CE B:LYS165 4.8 13.5 1.0 CG B:GLU228 4.8 20.5 1.0 O B:HOH1514 4.9 41.8 1.0 O B:HOH1540 4.9 39.9 1.0

U.A.Ramagopal, R.Toro, S.C.Almo. Crystal Structure of Predicted Mandelate Racemase From Rhodobacter Sphaeroides To Be Published.