Sodium in PDB 3bga: Crystal Structure of Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482

The structure of Crystal Structure of Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482, PDB code: 3bga was solved by D.Kumaran, S.K.Burley, S.Swaminathan, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.76 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	88.335, 138.864, 102.818, 90.00, 109.73, 90.00
R / Rfree (%)	20 / 23.4

The structure of Crystal Structure of Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482 (pdb code 3bga). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482, PDB code: 3bga:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482


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 Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na4 b:15.5 occ:1.00 O A:PHE614 2.3 12.6 1.0 O A:HOH1589 2.3 34.9 1.0 ND2 A:ASN617 2.3 6.1 1.0 O A:HOH1054 2.4 11.8 1.0 OD2 A:ASP227 2.4 12.2 1.0 O A:HOH1333 3.2 39.4 1.0 CG A:ASP227 3.2 14.5 1.0 CG A:ASN617 3.4 12.3 1.0 C A:PHE614 3.5 15.1 1.0 OD1 A:ASP227 3.6 14.3 1.0 OD1 A:ASN617 3.8 9.9 1.0 OH A:TYR119 3.8 16.5 1.0 O A:HOH1593 3.9 23.1 1.0 NE1 A:TRP579 4.0 21.4 1.0 CA A:CYS615 4.2 17.1 1.0 O A:HOH1591 4.2 38.7 1.0 N A:CYS615 4.3 13.9 1.0 CB A:ASP227 4.4 13.7 1.0 CB A:PHE614 4.4 15.7 1.0 O A:HOH1592 4.4 16.4 1.0 NE2 A:HIS551 4.5 16.9 1.0 CA A:PHE614 4.5 15.2 1.0 O A:ASP227 4.6 10.6 1.0 C A:CYS615 4.7 16.4 1.0 CB A:ASN617 4.7 12.5 1.0 CE2 A:TRP579 4.8 20.8 1.0 CZ2 A:TRP579 4.8 18.7 1.0 CZ A:TYR119 4.9 17.1 1.0 CD1 A:TRP579 4.9 19.6 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482


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 Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na6 b:21.2 occ:1.00 O A:HOH1520 2.4 23.4 1.0 O A:PRO924 2.4 15.4 1.0 O A:ALA969 2.5 18.5 1.0 O A:HOH1099 2.5 12.7 1.0 O A:LEU966 2.6 18.5 1.0 O A:GLU967 2.8 21.1 1.0 C A:GLU967 3.4 21.7 1.0 C A:PRO924 3.5 16.7 1.0 C A:ALA969 3.6 20.3 1.0 CA A:GLU967 3.7 20.7 1.0 C A:LEU966 3.7 20.8 1.0 N A:ALA969 4.0 18.7 1.0 N A:GLU967 4.2 19.9 1.0 O A:HOH1286 4.2 21.0 1.0 ND1 A:HIS970 4.3 28.2 1.0 CA A:ALA969 4.3 20.3 1.0 N A:LYS968 4.3 22.1 1.0 CB A:PRO924 4.4 15.8 1.0 O A:HOH1163 4.4 18.5 1.0 C A:LYS968 4.4 20.7 1.0 CA A:PRO924 4.4 16.8 1.0 N A:GLN925 4.5 15.8 1.0 CA A:GLN925 4.6 17.0 1.0 CG2 A:THR923 4.6 19.1 1.0 N A:PRO924 4.7 15.6 1.0 N A:HIS970 4.7 19.9 1.0 O A:HOH1346 4.7 27.4 1.0 OE1 A:GLU967 4.7 25.4 1.0 CE1 A:HIS970 4.7 27.7 1.0 CB A:ALA969 4.8 18.5 1.0 O A:LYS968 4.8 18.9 1.0 CA A:LYS968 4.9 22.2 1.0 O A:ALA790 4.9 15.6 1.0 CA A:HIS970 4.9 21.5 1.0 CD A:PRO924 5.0 13.4 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482


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 Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3 b:18.8 occ:1.00 OD2 B:ASP227 2.2 14.9 1.0 O B:PHE614 2.3 17.8 1.0 ND2 B:ASN617 2.4 15.7 1.0 O B:HOH1039 2.4 12.9 1.0 O B:HOH1603 2.5 29.8 1.0 CG B:ASP227 3.1 16.6 1.0 O B:HOH1560 3.3 30.0 1.0 CG B:ASN617 3.4 18.5 1.0 C B:PHE614 3.5 18.6 1.0 O B:HOH1136 3.6 35.2 1.0 OD1 B:ASP227 3.7 17.8 1.0 OD1 B:ASN617 3.7 18.0 1.0 OH B:TYR119 4.0 12.5 1.0 NE1 B:TRP579 4.1 18.7 1.0 CB B:ASP227 4.3 14.2 1.0 CA B:CYS615 4.3 18.3 1.0 N B:CYS615 4.4 18.7 1.0 CB B:PHE614 4.4 16.7 1.0 O B:HOH1464 4.5 10.8 1.0 CA B:PHE614 4.5 17.8 1.0 NE2 B:HIS551 4.5 14.3 1.0 O B:HOH1604 4.6 23.3 1.0 O B:ASP227 4.7 16.3 1.0 CB B:ASN617 4.8 18.1 1.0 C B:CYS615 4.8 17.9 1.0 CE2 B:TRP579 4.9 19.3 1.0 CZ B:TYR119 5.0 17.1 1.0 CD1 B:TRP579 5.0 19.8 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na5 b:18.3 occ:1.00 O B:PRO924 2.4 14.8 1.0 O B:LEU966 2.4 16.1 1.0 O B:ALA969 2.4 17.2 1.0 O B:HOH1470 2.5 14.9 1.0 O B:GLU967 2.6 20.4 1.0 O B:HOH1547 2.8 20.7 1.0 C B:GLU967 3.2 20.1 1.0 C B:PRO924 3.5 16.1 1.0 C B:LEU966 3.5 19.1 1.0 CA B:GLU967 3.6 20.4 1.0 C B:ALA969 3.6 18.7 1.0 N B:GLU967 4.0 19.7 1.0 N B:ALA969 4.0 19.2 1.0 CB B:PRO924 4.2 14.1 1.0 CA B:ALA969 4.2 19.8 1.0 N B:LYS968 4.2 19.7 1.0 CA B:PRO924 4.3 15.6 1.0 C B:LYS968 4.3 20.8 1.0 O B:HOH1139 4.4 17.4 1.0 N B:GLN925 4.4 15.6 1.0 O B:HOH1054 4.5 19.8 1.0 CA B:GLN925 4.6 15.1 1.0 ND1 B:HIS970 4.6 26.4 1.0 N B:PRO924 4.6 15.5 1.0 CB B:ALA969 4.6 17.9 1.0 N B:HIS970 4.7 18.4 1.0 CG2 B:THR923 4.7 15.5 1.0 OE1 B:GLU967 4.7 27.7 1.0 O B:LYS968 4.8 19.4 1.0 CA B:LEU966 4.8 19.9 1.0 CA B:LYS968 4.8 21.6 1.0 CD B:PRO924 4.8 14.6 1.0 O B:ALA790 4.9 14.6 1.0 CB B:GLU967 5.0 22.4 1.0 CA B:HIS970 5.0 19.1 1.0

D.Kumaran, S.K.Burley, S.Swaminathan. Crystal Structure Analysis of Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482. To Be Published.