Sodium in PDB 1v6s: Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8

All present enzymatic activity of Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8:
2.7.2.3;

The structure of Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8, PDB code: 1v6s was solved by H.Mizutani, N.Kunishima, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.50
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	143.175, 143.175, 75.641, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 21.5

The binding sites of Sodium atom in the Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8 (pdb code 1v6s). 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 Phosphoglycerate Kinase From Thermus Thermophilus HB8, PDB code: 1v6s:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8


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 Phosphoglycerate Kinase From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1405 b:24.8 occ:1.00 O A:HOH1755 2.3 31.4 1.0 O A:HOH1569 2.4 28.2 1.0 O A:GLU378 2.4 19.4 1.0 O A:HOH1757 2.4 36.5 1.0 O A:HOH1756 2.5 31.5 1.0 OG A:SER204 2.7 19.0 1.0 CB A:SER204 3.3 18.9 1.0 C A:GLU378 3.4 19.3 1.0 NH1 A:ARG208 3.8 27.1 1.0 CA A:SER204 4.1 16.9 1.0 O A:LEU377 4.1 17.9 1.0 N A:LYS379 4.2 19.3 1.0 CA A:LYS379 4.3 20.4 1.0 C A:LYS379 4.3 19.7 1.0 CA A:GLU378 4.3 18.4 1.0 O A:HOH1480 4.4 22.0 1.0 O A:LYS379 4.5 20.7 1.0 O A:HOH1606 4.6 32.0 1.0 O A:HOH1681 4.7 37.7 1.0 N A:GLY380 4.7 17.7 1.0 O A:SER204 4.8 17.4 1.0 CZ A:ARG208 4.8 26.5 1.0 C A:SER204 4.9 16.4 1.0 NH2 A:ARG208 4.9 28.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8


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 Phosphoglycerate Kinase From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1406 b:27.0 occ:1.00 O B:GLU378 2.2 20.4 1.0 O B:HOH1717 2.3 36.5 1.0 O B:HOH1718 2.4 32.2 1.0 O B:HOH1748 2.5 40.9 1.0 O B:HOH1595 2.6 35.8 1.0 OG B:SER204 2.7 22.6 1.0 C B:GLU378 3.3 21.2 1.0 CB B:SER204 3.4 19.4 1.0 O B:LEU377 3.9 20.0 1.0 NH1 B:ARG208 4.1 27.4 1.0 CA B:GLU378 4.1 20.7 1.0 CA B:SER204 4.2 18.1 1.0 N B:LYS379 4.2 20.9 1.0 CA B:LYS379 4.4 21.7 1.0 O B:HOH1560 4.5 27.9 1.0 C B:LYS379 4.5 21.2 1.0 O B:HOH1617 4.8 38.9 1.0 C B:LEU377 4.8 18.6 1.0 N B:GLY380 4.8 19.9 1.0 NH2 B:ARG208 4.9 27.7 1.0 O B:HOH1664 4.9 29.1 1.0 O B:LYS379 4.9 22.0 1.0 N B:GLU378 5.0 19.4 1.0 CZ B:ARG208 5.0 25.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8


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 Phosphoglycerate Kinase From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1407 b:43.3 occ:1.00 O B:HOH1545 2.5 34.0 1.0 O B:HOH1547 2.5 22.2 1.0 O B:HOH1668 2.6 37.0 1.0 O B:HOH1496 2.6 19.5 1.0 O B:HOH1746 2.6 43.1 1.0 O B:HOH1484 2.8 23.1 1.0 O B:ALA341 4.1 17.7 1.0 N B:GLY340 4.1 23.7 1.0 O B:LEU338 4.1 18.5 1.0 O B:HOH1733 4.2 40.3 1.0 O B:ARG362 4.3 17.9 1.0 O B:HOH1443 4.3 17.6 1.0 O B:HOH1428 4.3 15.5 1.0 O B:HOH1445 4.4 18.8 1.0 N B:ALA341 4.6 20.1 1.0 CA B:GLY340 4.8 23.7 1.0 CA B:GLU339 5.0 22.8 1.0 C B:GLU339 5.0 23.6 1.0

H.Mizutani, N.Kunishima. Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8 To Be Published.