Sodium in PDB 2p1r: Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases.

The structure of Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases., PDB code: 2p1r was solved by C.E.Nichols, H.K.Lamb, M.Lockyer, I.G.Charles, S.Pyne, A.R.Hawkins, D.K.Stammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.000, 70.990, 102.160, 90.00, 118.51, 90.00
R / Rfree (%)	20.6 / 25.5

The structure of Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases. also contains other interesting chemical elements:

Calcium	(Ca)	10 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases. (pdb code 2p1r). 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 Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases., PDB code: 2p1r:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases.


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 Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na300 b:23.6 occ:1.00 O A:HOH305 2.8 23.2 1.0 OD1 A:ASP67 2.8 25.2 1.0 N A:ALA100 3.1 22.4 1.0 CA A:ASN97 3.1 29.7 1.0 CD1 A:ILE70 3.2 12.0 1.0 C A:ASN97 3.3 28.0 1.0 CB A:ASN97 3.4 33.7 1.0 CB A:ALA100 3.4 19.8 1.0 O A:ASN97 3.5 23.0 1.0 N A:PHE99 3.7 27.3 1.0 CG A:ASP67 3.8 41.2 1.0 CA A:ALA100 3.9 29.1 1.0 CB A:PHE99 3.9 25.0 1.0 N A:ASP67 3.9 31.3 1.0 N A:ASP98 3.9 22.6 1.0 C A:PHE99 4.0 28.2 1.0 CA A:PHE99 4.0 29.1 1.0 C A:GLY66 4.2 34.2 1.0 CA A:ASP67 4.2 37.9 1.0 O A:ALA96 4.3 41.8 1.0 N A:ASN97 4.4 34.0 1.0 C A:ASP98 4.4 30.0 1.0 CG1 A:ILE70 4.5 27.8 1.0 OD2 A:ASP67 4.5 40.1 1.0 CB A:ASP67 4.6 38.7 1.0 CA A:GLY66 4.6 34.0 1.0 O A:GLY66 4.6 36.8 1.0 O A:GLY65 4.7 30.7 1.0 CA A:ASP98 4.8 27.4 1.0 C A:ALA96 4.8 41.3 1.0 N A:THR101 4.9 26.6 1.0 CG A:ASN97 4.9 39.6 1.0 C A:ALA100 4.9 29.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases.


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 Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na300 b:34.0 occ:1.00 N B:ALA100 2.9 26.7 1.0 OD1 B:ASP67 2.9 31.6 1.0 O B:HOH339 2.9 36.0 1.0 CA B:ASN97 3.3 25.7 1.0 CB B:ALA100 3.3 28.3 1.0 CD1 B:ILE70 3.3 6.8 1.0 C B:ASN97 3.4 30.3 1.0 CB B:ASN97 3.5 42.4 1.0 N B:PHE99 3.6 29.5 1.0 O B:ASN97 3.6 26.7 1.0 CA B:ALA100 3.7 29.7 1.0 CB B:PHE99 3.7 22.9 1.0 CG B:ASP67 3.8 40.1 1.0 C B:PHE99 3.8 25.0 1.0 CA B:PHE99 3.9 29.9 1.0 N B:ASP98 4.0 30.0 1.0 N B:ASP67 4.0 29.4 1.0 CA B:ASP67 4.3 28.6 1.0 C B:ASP98 4.4 31.7 1.0 C B:GLY66 4.4 32.2 1.0 OD2 B:ASP67 4.4 48.4 1.0 CG1 B:ILE70 4.5 17.0 1.0 O B:ALA96 4.5 45.7 1.0 N B:ASN97 4.6 32.9 1.0 CB B:ASP67 4.7 31.3 1.0 N B:THR101 4.7 21.0 1.0 C B:ALA100 4.8 28.3 1.0 CA B:ASP98 4.8 32.2 1.0 CA B:GLY66 4.8 33.0 1.0 O B:GLY66 4.8 32.6 1.0 O B:GLY65 4.9 21.7 1.0 CG B:PHE99 4.9 35.3 1.0 CG B:ASN97 5.0 50.0 1.0 O B:PHE99 5.0 28.0 1.0

C.E.Nichols, H.K.Lamb, M.Lockyer, I.G.Charles, S.Pyne, A.R.Hawkins, D.K.Stammers. Characterization of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases Proteins: V. 68 13 2007STRUCT.,Funct.,Genet..
ISSN: ISSN 0887-3585
PubMed: 17393457
DOI: 10.1002/PROT.21386