Sodium in PDB 2fcw: Structure of A Complex Between the Pair of the Ldl Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (Rap).

The structure of Structure of A Complex Between the Pair of the Ldl Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (Rap)., PDB code: 2fcw was solved by N.Beglova, C.Fisher, S.C.Blacklow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.26
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	118.523, 30.019, 58.143, 90.00, 96.57, 90.00
R / Rfree (%)	15.2 / 20.1

The structure of Structure of A Complex Between the Pair of the Ldl Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (Rap). also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Structure of A Complex Between the Pair of the Ldl Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (Rap). (pdb code 2fcw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of A Complex Between the Pair of the Ldl Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (Rap)., PDB code: 2fcw:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of A Complex Between the Pair of the Ldl Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (Rap).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Complex Between the Pair of the Ldl Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (Rap). within 5.0Å range: probe atom residue distance (Å) B Occ A:Na5001 b:11.9 occ:1.00 O A:HOH61 2.3 26.8 1.0 OE2 A:GLU269 2.3 19.3 1.0 O A:HOH73 2.4 24.3 1.0 O B:HOH5023 2.4 19.6 1.0 OE2 A:GLU265 2.4 22.8 1.0 CD A:GLU269 3.2 19.9 1.0 OE1 A:GLU269 3.5 24.8 1.0 CD A:GLU265 3.5 18.4 1.0 CG A:GLU265 3.9 17.7 1.0 O A:HOH55 4.3 24.5 0.5 OE1 A:GLU265 4.6 25.3 1.0 CG A:GLU269 4.6 19.1 1.0 O A:HOH14 4.6 16.9 1.0 OE1 B:GLN104 4.6 33.5 1.0

Sodium binding site 2 out of 4 in the Structure of A Complex Between the Pair of the Ldl Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (Rap).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Complex Between the Pair of the Ldl Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (Rap). within 5.0Å range: probe atom residue distance (Å) B Occ A:Na5003 b:31.7 occ:1.00 O A:HOH110 2.5 33.4 1.0 OD2 A:ASP228 2.6 11.0 1.0 O A:HOH68 3.0 25.4 1.0 O A:HOH174 3.3 41.6 1.0 CG A:ASP228 3.6 10.1 1.0 OD1 A:ASP228 3.8 14.6 1.0 CG2 A:ILE224 3.9 11.4 1.0 O A:HOH162 3.9 44.6 1.0 O A:HOH34 4.3 22.8 1.0 CB A:ASP228 4.9 9.9 1.0

Sodium binding site 3 out of 4 in the Structure of A Complex Between the Pair of the Ldl Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (Rap).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Complex Between the Pair of the Ldl Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (Rap). within 5.0Å range: probe atom residue distance (Å) B Occ A:Na5004 b:42.8 occ:1.00 O A:HOH121 3.0 37.5 1.0 O A:HOH91 3.1 34.1 1.0 O A:HOH40 3.3 29.0 1.0 CD2 A:LEU240 3.6 15.6 1.0 O A:HOH130 3.6 35.0 1.0 OD1 A:ASP237 4.9 15.5 1.0

Sodium binding site 4 out of 4 in the Structure of A Complex Between the Pair of the Ldl Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (Rap).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of A Complex Between the Pair of the Ldl Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (Rap). within 5.0Å range: probe atom residue distance (Å) B Occ B:Na5002 b:15.9 occ:1.00 O B:GLY98 2.2 14.7 1.0 O B:HOH5003 2.3 20.7 1.0 O B:LYS86 2.3 15.1 1.0 O B:HOH5004 2.5 12.4 1.0 O B:HOH5012 2.5 15.6 1.0 C B:GLY98 3.4 13.0 1.0 C B:LYS86 3.5 13.3 1.0 SG B:CYS100 3.7 16.1 1.0 N B:LYS86 3.9 13.1 1.0 O B:HOH5014 3.9 19.6 1.0 SG B:CYS88 4.0 18.2 1.0 CA B:GLY98 4.1 14.3 1.0 N B:LYS99 4.3 14.6 1.0 CA B:LYS86 4.3 13.4 1.0 CA B:LYS99 4.4 13.8 1.0 N B:THR87 4.5 15.6 1.0 O B:HOH5022 4.6 23.1 1.0 N B:CYS100 4.6 13.7 1.0 C B:LYS99 4.7 14.6 1.0 CA B:THR87 4.7 17.3 1.0 N B:CYS88 4.8 17.9 1.0 CG B:LYS86 4.9 14.0 1.0 C B:THR87 4.9 17.9 1.0

C.Fisher, N.Beglova, S.C.Blacklow. Structure of An Ldlr-Rap Complex Reveals A General Mode For Ligand Recognition By Lipoprotein Receptors Mol.Cell V. 22 277 2006.
ISSN: ISSN 1097-2765
PubMed: 16630895
DOI: 10.1016/J.MOLCEL.2006.02.021