Sodium in PDB 1jg8: Crystal Structure of Threonine Aldolase (Low-Specificity)

All present enzymatic activity of Crystal Structure of Threonine Aldolase (Low-Specificity):
4.1.2.5;

The structure of Crystal Structure of Threonine Aldolase (Low-Specificity), PDB code: 1jg8 was solved by C.L.Kielkopf, J.Bonanno, S.Ray, 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)	20.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.890, 100.600, 149.820, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 22.2

The structure of Crystal Structure of Threonine Aldolase (Low-Specificity) also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of Threonine Aldolase (Low-Specificity) (pdb code 1jg8). 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 Threonine Aldolase (Low-Specificity), PDB code: 1jg8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Threonine Aldolase (Low-Specificity)


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 Threonine Aldolase (Low-Specificity) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na907 b:11.4 occ:1.00 O A:HOH1005 3.0 23.6 1.0 O B:HOH1045 3.1 22.9 1.0 N A:ARG76 3.2 13.9 1.0 N B:ARG76 3.2 13.5 1.0 CA A:GLN75 3.6 14.1 1.0 CA B:GLN75 3.6 14.8 1.0 CB A:GLN75 3.8 17.1 1.0 CB B:GLN75 3.8 18.1 1.0 C A:GLN75 3.9 14.3 1.0 C B:GLN75 3.9 14.0 1.0 NH2 B:ARG76 4.0 23.3 1.0 CB B:ARG76 4.0 15.6 1.0 NH2 A:ARG76 4.1 23.9 1.0 CG A:GLN75 4.1 21.4 1.0 CB A:ARG76 4.1 15.4 1.0 NE A:ARG76 4.1 22.5 1.0 CG B:GLN75 4.2 22.2 1.0 CZ A:ARG76 4.2 20.8 1.0 CZ B:ARG76 4.2 19.8 1.0 CA B:ARG76 4.2 13.8 1.0 CA A:ARG76 4.2 14.3 1.0 NE B:ARG76 4.3 20.2 1.0 CG A:ARG76 4.4 20.1 1.0 OE1 B:GLN75 4.5 30.3 1.0 OE1 A:GLN75 4.6 29.1 1.0 CG B:ARG76 4.6 18.8 1.0 O B:HOH1053 4.7 30.9 1.0 CD A:GLN75 4.8 26.6 1.0 CD B:GLN75 4.8 25.9 1.0 NH1 B:ARG76 4.9 18.9 1.0 NH1 A:ARG76 4.9 20.6 1.0 N A:GLN75 4.9 13.4 1.0 CD A:ARG76 4.9 19.6 1.0 O B:HOH995 4.9 16.4 1.0 N B:GLN75 5.0 12.9 1.0 O B:THR74 5.0 14.2 1.0 O A:THR74 5.0 11.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Threonine Aldolase (Low-Specificity)


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 Threonine Aldolase (Low-Specificity) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na908 b:13.4 occ:1.00 O C:HOH981 2.9 22.7 1.0 N C:ARG76 3.1 15.8 0.5 N C:ARG76 3.1 15.8 0.5 N D:ARG76 3.2 15.4 1.0 O C:HOH1058 3.2 24.8 1.0 CA D:GLN75 3.6 15.8 1.0 CA C:GLN75 3.6 16.8 1.0 CB C:GLN75 3.8 19.6 1.0 CG C:ARG76 3.8 20.1 0.5 CG C:ARG76 3.8 20.1 0.5 C C:GLN75 3.8 16.1 1.0 CB D:GLN75 3.9 18.5 1.0 CB C:ARG76 3.9 17.7 0.5 CB C:ARG76 3.9 17.7 0.5 C D:GLN75 3.9 15.3 1.0 CB D:ARG76 4.0 18.1 1.0 CA C:ARG76 4.1 16.7 0.5 CA C:ARG76 4.1 16.7 0.5 CG D:GLN75 4.1 23.2 1.0 CG C:GLN75 4.2 23.5 1.0 CA D:ARG76 4.2 15.9 1.0 CD C:ARG76 4.3 21.6 0.5 CD C:ARG76 4.3 21.6 0.5 CG D:ARG76 4.3 20.4 1.0 CZ D:ARG76 4.5 22.8 1.0 NE D:ARG76 4.5 22.4 1.0 NH2 D:ARG76 4.6 24.0 1.0 O D:HOH1096 4.6 23.8 1.0 O D:HOH1094 4.6 18.6 1.0 NE2 C:GLN75 4.6 28.2 1.0 O D:HOH1095 4.8 23.5 1.0 O D:THR74 4.9 15.2 1.0 CD C:GLN75 4.9 27.3 1.0 N D:GLN75 4.9 14.8 1.0 N C:GLN75 5.0 16.2 1.0 NH1 D:ARG76 5.0 19.8 1.0 O C:HOH1097 5.0 26.8 1.0

C.L.Kielkopf, J.Bonanno, S.Ray, S.K.Burley. Crystal Structure of Low-Specificity Threonine Aldolase, A Key Enzyme in Glycine Biosynthesis To Be Published.