Sodium in PDB 3lp9: Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus

The structure of Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus, PDB code: 3lp9 was solved by V.Gaur, I.A.Qureshi, A.Singh, V.Chanana, D.M.Salunke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.63 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.170, 88.140, 154.530, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 26.6

The structure of Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Calcium	(Ca)	4 atoms

The binding sites of Sodium atom in the Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus (pdb code 3lp9). 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 LS24, A Seed Albumin From Lathyrus Sativus, PDB code: 3lp9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus


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 LS24, A Seed Albumin From Lathyrus Sativus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na318 b:17.1 occ:1.00 OD1 A:ASP69 2.8 15.4 1.0 O A:HOH242 3.0 15.8 1.0 N A:ARG125 3.0 16.1 1.0 N A:ALA179 3.0 15.1 1.0 CA A:TYR124 3.4 15.2 1.0 CA A:PHE178 3.6 15.2 1.0 CB A:ARG125 3.6 16.5 1.0 CB A:ALA179 3.7 14.1 1.0 CB A:TYR124 3.7 15.1 1.0 C A:TYR124 3.7 15.3 1.0 CG A:ASP69 3.8 15.5 1.0 C A:PHE178 3.8 14.8 1.0 CB A:PHE178 3.9 15.3 1.0 CA A:ALA179 3.9 15.2 1.0 CA A:ARG125 4.0 16.3 1.0 OD2 A:ASP69 4.1 14.1 1.0 N A:ARG11 4.4 15.8 1.0 O A:ALA179 4.4 15.6 1.0 N A:ASP69 4.5 15.9 1.0 CB A:PHE68 4.5 15.6 1.0 O A:ALA123 4.6 15.3 1.0 N A:TYR124 4.6 15.3 1.0 CA A:PHE68 4.6 15.7 1.0 CB A:ARG11 4.7 15.3 1.0 C A:ALA179 4.7 16.1 1.0 CA A:PHE10 4.7 15.6 1.0 N A:PHE178 4.8 15.3 1.0 O A:ARG125 4.8 15.8 1.0 C A:ARG125 4.9 15.9 1.0 O A:TYR124 5.0 15.4 1.0 O A:PHE178 5.0 14.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus


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 LS24, A Seed Albumin From Lathyrus Sativus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na319 b:17.6 occ:1.00 OD1 B:ASP69 2.7 16.5 1.0 N B:ALA179 3.0 16.1 1.0 N B:ARG125 3.1 15.9 1.0 O B:HOH321 3.1 16.3 1.0 CB B:ARG125 3.4 15.7 1.0 CG B:ASP69 3.6 17.1 1.0 CB B:ALA179 3.7 15.4 1.0 CA B:PHE178 3.7 16.3 1.0 C B:PHE178 3.8 15.7 1.0 CA B:ARG125 3.9 16.1 1.0 CA B:TYR124 3.9 16.2 1.0 CA B:ALA179 3.9 15.3 1.0 OD2 B:ASP69 3.9 16.7 1.0 C B:TYR124 4.0 16.2 1.0 CB B:PHE178 4.0 15.9 1.0 N B:ARG11 4.1 15.9 1.0 O B:ALA179 4.3 16.1 1.0 CB B:TYR124 4.3 15.6 1.0 CB B:ARG11 4.4 15.9 1.0 N B:ASP69 4.4 16.3 1.0 CA B:PHE10 4.5 16.0 1.0 C B:ALA179 4.6 15.9 1.0 O B:ARG125 4.7 15.8 1.0 CA B:PHE68 4.8 16.0 1.0 C B:ARG125 4.8 15.8 1.0 CG B:ARG125 4.8 17.0 1.0 C B:PHE10 4.8 15.9 1.0 CB B:PHE68 4.8 15.7 1.0 CA B:ARG11 4.9 16.1 1.0 CB B:ASP69 4.9 16.1 1.0 CB B:PHE10 5.0 15.8 1.0 NH2 B:ARG11 5.0 18.6 1.0 O B:ALA123 5.0 16.4 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus


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 LS24, A Seed Albumin From Lathyrus Sativus within 5.0Å range: probe atom residue distance (Å) B Occ C:Na320 b:17.0 occ:1.00 OD1 C:ASP69 2.7 17.5 1.0 O C:HOH326 2.9 17.7 1.0 N C:ALA179 3.0 16.5 1.0 N C:ARG125 3.0 16.4 1.0 CA C:TYR124 3.6 15.4 1.0 CB C:ARG125 3.6 15.9 1.0 CA C:PHE178 3.6 16.6 1.0 CB C:ALA179 3.7 15.4 1.0 CG C:ASP69 3.7 16.6 1.0 C C:TYR124 3.8 16.3 1.0 C C:PHE178 3.8 16.6 1.0 CA C:ARG125 3.9 15.6 1.0 CA C:ALA179 3.9 16.0 1.0 CB C:TYR124 4.0 14.7 1.0 CB C:PHE178 4.0 16.1 1.0 OD2 C:ASP69 4.1 16.4 1.0 N C:ARG11 4.2 15.8 1.0 N C:ASP69 4.3 15.7 1.0 CA C:PHE10 4.5 15.7 1.0 O C:ALA179 4.5 17.3 1.0 CA C:PHE68 4.5 16.2 1.0 CB C:PHE68 4.6 15.7 1.0 O C:ALA123 4.6 15.5 1.0 CB C:ARG11 4.7 16.2 1.0 O C:ARG125 4.7 15.9 1.0 C C:ALA179 4.8 16.3 1.0 N C:TYR124 4.8 15.2 1.0 C C:ARG125 4.9 15.9 1.0 C C:PHE10 4.9 15.3 1.0 CB C:PHE10 4.9 15.4 1.0 N C:PHE178 4.9 16.3 1.0 C C:PHE68 5.0 16.0 1.0 O C:TYR124 5.0 15.9 1.0 O C:PHE178 5.0 17.1 1.0 CG C:ARG125 5.0 14.9 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus


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 LS24, A Seed Albumin From Lathyrus Sativus within 5.0Å range: probe atom residue distance (Å) B Occ D:Na321 b:16.5 occ:1.00 OD2 D:ASP69 2.7 15.7 1.0 O D:HOH455 3.0 16.3 1.0 N D:ARG125 3.1 16.8 1.0 N D:ALA179 3.2 16.7 1.0 CA D:TYR124 3.5 16.0 1.0 CA D:PHE178 3.6 16.2 1.0 CG D:ASP69 3.7 15.9 1.0 CB D:ARG125 3.8 16.2 1.0 C D:TYR124 3.8 16.6 1.0 CB D:PHE178 3.9 15.7 1.0 CB D:ALA179 3.9 15.9 1.0 CB D:TYR124 3.9 15.9 1.0 C D:PHE178 3.9 16.1 1.0 OD1 D:ASP69 4.0 15.3 1.0 CA D:ARG125 4.1 16.6 1.0 CA D:ALA179 4.1 16.3 1.0 N D:ARG11 4.1 15.9 1.0 N D:ASP69 4.2 16.4 1.0 CA D:PHE68 4.5 16.0 1.0 CA D:PHE10 4.5 15.8 1.0 O D:ALA123 4.5 15.3 1.0 O D:ALA179 4.5 16.9 1.0 CB D:PHE68 4.5 15.6 1.0 CB D:ARG11 4.7 16.2 1.0 N D:TYR124 4.7 15.5 1.0 C D:PHE10 4.8 15.8 1.0 C D:ALA179 4.9 16.6 1.0 N D:PHE178 4.9 15.9 1.0 CB D:PHE10 4.9 15.3 1.0 O D:ARG125 4.9 17.1 1.0 C D:PHE68 4.9 16.2 1.0 CB D:ASP69 4.9 16.1 1.0 O D:ALA177 5.0 17.1 1.0 CG D:ARG125 5.0 18.0 1.0

V.Gaur, I.A.Qureshi, A.Singh, V.Chanana, D.M.Salunke. Crystal Structure and Functional Insights of Hemopexin Fold Protein From Grass Pea Plant Physiol. V. 152 1842 2010.
ISSN: ISSN 0032-0889
PubMed: 20147493
DOI: 10.1104/PP.109.150680