Sodium in PDB 3h12: Crystal Structure of Putative Mandelate Racemase From Bordetella Bronchiseptica RB50

The structure of Crystal Structure of Putative Mandelate Racemase From Bordetella Bronchiseptica RB50, PDB code: 3h12 was solved by V.N.Malashkevich, R.Toro, C.Morano, J.M.Sauder, S.K.Burley, S.C.Almo, Newyork Sgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.73 / 1.50
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	116.148, 116.148, 128.136, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 17.3

The binding sites of Sodium atom in the Crystal Structure of Putative Mandelate Racemase From Bordetella Bronchiseptica RB50 (pdb code 3h12). 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 Putative Mandelate Racemase From Bordetella Bronchiseptica RB50, PDB code: 3h12:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Putative Mandelate Racemase From Bordetella Bronchiseptica RB50


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 Putative Mandelate Racemase From Bordetella Bronchiseptica RB50 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na500 b:18.6 occ:1.00 OE2 A:GLU254 2.2 21.9 1.0 O A:HOH534 2.3 22.0 1.0 O A:HOH475 2.4 17.5 1.0 OE2 A:GLU227 2.4 15.4 1.0 OD2 A:ASP201 2.5 15.9 1.0 O A:HOH594 2.5 16.8 1.0 CD A:GLU254 3.1 24.2 1.0 CD A:GLU227 3.3 14.9 1.0 CG A:ASP201 3.4 17.9 1.0 OE1 A:GLU254 3.5 22.5 1.0 OD1 A:ASP201 3.7 16.0 1.0 NZ A:LYS173 3.8 20.9 1.0 NZ A:LYS171 3.9 14.4 1.0 CG A:GLU227 4.0 13.7 1.0 O A:HOH401 4.0 16.9 1.0 O A:HOH442 4.1 21.9 1.0 O A:HOH419 4.2 17.2 1.0 OE1 A:GLU227 4.2 15.3 1.0 CD2 A:HIS304 4.2 14.4 1.0 ND2 A:ASN203 4.3 18.1 1.0 CG A:GLU254 4.5 20.0 1.0 CE A:LYS171 4.7 15.0 1.0 CB A:ASP201 4.7 14.6 1.0 OE1 A:GLU228 4.8 16.5 1.0 O A:HOH665 4.9 34.0 1.0 NE2 A:HIS304 4.9 15.9 1.0 CG A:ASN203 5.0 16.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Putative Mandelate Racemase From Bordetella Bronchiseptica RB50


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 Putative Mandelate Racemase From Bordetella Bronchiseptica RB50 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na500 b:17.9 occ:1.00 OE1 B:GLU254 2.2 21.0 1.0 OE2 B:GLU227 2.3 16.2 1.0 O B:HOH432 2.3 21.2 1.0 O B:HOH579 2.4 18.6 1.0 OD2 B:ASP201 2.4 16.5 1.0 O B:HOH540 2.5 17.6 1.0 CD B:GLU254 3.1 22.8 1.0 CD B:GLU227 3.3 14.4 1.0 CG B:ASP201 3.4 18.5 1.0 OE2 B:GLU254 3.4 21.4 1.0 OD1 B:ASP201 3.6 17.6 1.0 NZ B:LYS171 3.7 16.1 1.0 NZ B:LYS173 3.8 17.9 1.0 O B:HOH411 3.9 16.4 1.0 CG B:GLU227 4.0 13.1 1.0 O B:HOH461 4.1 22.7 1.0 OE1 B:GLU227 4.1 14.7 1.0 ND1 B:HIS304 4.2 18.6 1.0 O B:HOH447 4.2 17.9 1.0 OD1 B:ASN203 4.3 20.2 1.0 CG B:GLU254 4.5 20.4 1.0 CE B:LYS171 4.6 15.9 1.0 CB B:ASP201 4.7 14.2 1.0 OE2 B:GLU228 4.8 17.6 1.0 CE1 B:HIS304 4.8 12.5 1.0 CG B:ASN203 5.0 16.1 1.0 CB B:GLU254 5.0 17.4 1.0

V.N.Malashkevich, R.Toro, C.Morano, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of Putative Mandelate Racemase From Bordetella Bronchiseptica RB50 To Be Published.