Sodium in PDB 2gta: Crystal Structure of the Putative Pyrophosphatase Ypjd From Bacillus Subtilis. Northeast Structural Genomics Consortium Target SR428.

The structure of Crystal Structure of the Putative Pyrophosphatase Ypjd From Bacillus Subtilis. Northeast Structural Genomics Consortium Target SR428., PDB code: 2gta was solved by S.M.Vorobiev, W.Zhou, J.Seetharaman, D.Wang, L.C.Ma, T.Acton, R.Xio, G.T.Montelione, L.Tong, J.F.Hunt, Northeast Structural Genomicsconsortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.89 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.747, 79.694, 119.568, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 26.3

The binding sites of Sodium atom in the Crystal Structure of the Putative Pyrophosphatase Ypjd From Bacillus Subtilis. Northeast Structural Genomics Consortium Target SR428. (pdb code 2gta). 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 the Putative Pyrophosphatase Ypjd From Bacillus Subtilis. Northeast Structural Genomics Consortium Target SR428., PDB code: 2gta:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Putative Pyrophosphatase Ypjd From Bacillus Subtilis. Northeast Structural Genomics Consortium Target SR428.


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 the Putative Pyrophosphatase Ypjd From Bacillus Subtilis. Northeast Structural Genomics Consortium Target SR428. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:58.5 occ:1.00 OE1 A:GLU37 2.8 46.1 1.0 O A:HOH463 2.8 36.3 1.0 O A:GLU37 2.9 41.1 1.0 OE2 A:GLU66 3.1 49.6 1.0 O A:GLU66 3.3 44.3 1.0 CB A:GLU40 3.4 40.4 1.0 OE1 A:GLU40 3.5 43.2 1.0 CB A:ASP69 3.6 46.5 1.0 CA A:GLU66 3.7 46.9 1.0 C A:GLU37 3.7 42.6 1.0 CB A:GLU37 3.8 43.1 1.0 CA A:GLU37 3.8 42.7 1.0 C A:GLU66 3.9 44.5 1.0 CD A:GLU37 3.9 45.0 1.0 N A:LEU41 3.9 35.9 1.0 CB A:GLU66 4.0 48.4 1.0 OD2 A:ASP69 4.1 51.6 1.0 CG A:GLU40 4.1 40.7 1.0 CD A:GLU66 4.2 51.9 1.0 CG A:ASP69 4.3 50.9 1.0 CD A:GLU40 4.3 43.5 1.0 C A:GLU40 4.4 38.6 1.0 CG A:GLU37 4.4 43.9 1.0 CA A:GLU40 4.4 39.6 1.0 CA A:LEU41 4.5 33.1 1.0 CB A:LEU41 4.6 31.2 1.0 CG2 A:VAL70 4.7 38.6 1.0 CG A:GLU66 4.7 50.9 1.0 N A:GLU40 4.8 40.3 1.0 O A:GLU65 4.9 53.9 1.0 CA A:ASP69 4.9 44.4 1.0 N A:GLU66 4.9 49.3 1.0 OE2 A:GLU37 4.9 45.0 1.0 N A:VAL70 5.0 41.9 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Putative Pyrophosphatase Ypjd From Bacillus Subtilis. Northeast Structural Genomics Consortium Target SR428.


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 the Putative Pyrophosphatase Ypjd From Bacillus Subtilis. Northeast Structural Genomics Consortium Target SR428. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:42.5 occ:1.00 OE1 B:GLU37 2.7 50.3 1.0 OE1 B:GLU40 2.8 52.0 1.0 OE2 B:GLU66 3.0 58.8 1.0 OD2 B:ASP69 3.1 53.6 1.0 O B:GLU37 3.2 47.1 1.0 O B:GLU66 3.3 49.6 1.0 CB B:ASP69 3.3 49.9 1.0 CB B:GLU40 3.6 42.3 1.0 CD B:GLU40 3.7 52.0 1.0 CG B:ASP69 3.7 52.6 1.0 CA B:GLU66 3.7 50.6 1.0 CB B:GLU37 3.8 47.6 1.0 CD B:GLU37 3.8 51.6 1.0 CA B:GLU37 3.9 48.0 1.0 C B:GLU37 3.9 47.5 1.0 C B:GLU66 3.9 49.3 1.0 CG B:GLU40 3.9 47.6 1.0 CB B:GLU66 4.0 51.8 1.0 CD B:GLU66 4.1 57.6 1.0 N B:LEU41 4.2 36.0 1.0 CG B:GLU37 4.4 49.5 1.0 CG2 B:VAL70 4.4 43.3 1.0 C B:GLU40 4.5 37.7 1.0 CA B:ASP69 4.6 48.2 1.0 CA B:GLU40 4.6 39.7 1.0 CG B:GLU66 4.6 55.9 1.0 CA B:LEU41 4.7 33.0 1.0 OE2 B:GLU40 4.7 53.8 1.0 CB B:LEU41 4.8 30.5 1.0 N B:VAL70 4.8 47.0 1.0 OE2 B:GLU37 4.8 55.0 1.0 OD1 B:ASP69 4.9 54.9 1.0 C B:ASP69 4.9 48.5 1.0 N B:GLU66 4.9 51.8 1.0 N B:ASP69 5.0 46.6 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Putative Pyrophosphatase Ypjd From Bacillus Subtilis. Northeast Structural Genomics Consortium Target SR428.


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 the Putative Pyrophosphatase Ypjd From Bacillus Subtilis. Northeast Structural Genomics Consortium Target SR428. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:57.1 occ:1.00 OE1 C:GLU37 2.9 53.1 1.0 OE1 C:GLU66 3.0 44.8 1.0 OD2 C:ASP69 3.0 51.4 1.0 OE1 C:GLU40 3.1 52.3 1.0 O C:GLU37 3.3 44.7 1.0 CD C:GLU66 3.3 46.6 1.0 O C:GLU66 3.4 47.7 1.0 CB C:ASP69 3.5 46.2 1.0 CB C:GLU40 3.5 43.7 1.0 CA C:GLU66 3.5 46.2 1.0 OE2 C:GLU66 3.7 48.1 1.0 CG C:ASP69 3.7 50.0 1.0 CB C:GLU66 3.8 45.5 1.0 C C:GLU66 3.9 46.0 1.0 CB C:GLU37 3.9 44.8 1.0 CA C:GLU37 3.9 44.0 1.0 CD C:GLU37 4.0 52.8 1.0 C C:GLU37 4.1 44.0 1.0 CD C:GLU40 4.1 50.2 1.0 CG C:GLU66 4.1 46.5 1.0 CG C:GLU40 4.2 47.7 1.0 N C:LEU41 4.2 42.9 1.0 CG C:GLU37 4.5 50.0 1.0 C C:GLU40 4.5 43.2 1.0 CA C:GLU40 4.6 42.5 1.0 CG2 C:VAL70 4.7 37.0 1.0 N C:GLU66 4.8 47.6 1.0 CA C:ASP69 4.8 44.8 1.0 CA C:LEU41 4.8 42.8 1.0 O C:GLU65 4.9 47.9 1.0 CB C:LEU41 4.9 40.8 1.0 OE2 C:GLU37 4.9 55.1 1.0 OD1 C:ASP69 4.9 52.4 1.0 N C:VAL70 5.0 42.9 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Putative Pyrophosphatase Ypjd From Bacillus Subtilis. Northeast Structural Genomics Consortium Target SR428.


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 the Putative Pyrophosphatase Ypjd From Bacillus Subtilis. Northeast Structural Genomics Consortium Target SR428. within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:48.3 occ:1.00 OE1 D:GLU40 2.7 51.1 1.0 OE1 D:GLU37 2.8 48.5 1.0 OD2 D:ASP69 3.0 57.9 1.0 OE1 D:GLU66 3.2 66.4 1.0 CG D:ASP69 3.5 54.3 1.0 CD D:GLU66 3.5 64.3 1.0 OE2 D:GLU66 3.5 66.2 1.0 CD D:GLU40 3.6 51.1 1.0 CB D:ASP69 3.6 49.5 1.0 CB D:GLU40 3.7 43.8 1.0 CD D:GLU37 3.8 48.5 1.0 CA D:GLU66 4.1 56.1 1.0 CG D:GLU40 4.2 48.8 1.0 OE2 D:GLU40 4.3 53.4 1.0 OE2 D:GLU37 4.3 49.1 1.0 OD1 D:ASP69 4.4 57.5 1.0 CB D:GLU66 4.5 57.2 1.0 CG D:GLU66 4.6 61.5 1.0 O D:GLU66 4.6 54.0 1.0 O D:GLU37 4.8 41.6 1.0 C D:GLU66 4.8 54.3 1.0 CB D:GLU37 4.9 43.9 1.0 O D:GLU65 4.9 59.9 1.0 CA D:GLU37 4.9 42.2 1.0 CG D:GLU37 4.9 47.2 1.0 CA D:GLU40 5.0 43.1 1.0 N D:GLU66 5.0 57.6 1.0

S.M.Vorobiev, W.Zhou, J.Seetharaman, D.Wang, L.C.Ma, T.Acton, R.Xio, G.T.Montelione, L.Tong, J.F.Hunt. Crystal Structure of the Putative Pyrophosphatase Ypjd From Bacillus Subtilis. To Be Published.