Sodium in PDB 3pak: Crystal Structure of Rat Surfactant Protein A Neck and Carbohydrate Recognition Domain (Ncrd) Complexed with Mannose

The structure of Crystal Structure of Rat Surfactant Protein A Neck and Carbohydrate Recognition Domain (Ncrd) Complexed with Mannose, PDB code: 3pak was solved by F.Shang, M.J.Rynkiewicz, F.X.Mccormack, H.Wu, T.M.Cafarella, J.Head, B.A.Seaton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.10 / 1.90
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	97.796, 97.796, 45.088, 90.00, 90.00, 120.00
R / Rfree (%)	21.8 / 24.3

The structure of Crystal Structure of Rat Surfactant Protein A Neck and Carbohydrate Recognition Domain (Ncrd) Complexed with Mannose also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Rat Surfactant Protein A Neck and Carbohydrate Recognition Domain (Ncrd) Complexed with Mannose (pdb code 3pak). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Rat Surfactant Protein A Neck and Carbohydrate Recognition Domain (Ncrd) Complexed with Mannose, PDB code: 3pak:

Sodium binding site 1 out of 1 in the Crystal Structure of Rat Surfactant Protein A Neck and Carbohydrate Recognition Domain (Ncrd) Complexed with Mannose


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 Rat Surfactant Protein A Neck and Carbohydrate Recognition Domain (Ncrd) Complexed with Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:45.3 occ:1.00 OE1 A:GLU171 2.5 48.0 1.0 N A:GLY200 2.8 51.6 1.0 O A:GLU202 2.9 41.8 1.0 N A:GLU202 3.0 45.2 1.0 CA A:GLY200 3.1 49.2 1.0 CD A:GLU171 3.2 48.3 1.0 OE2 A:GLU171 3.2 49.0 1.0 OD2 A:ASP215 3.3 38.2 1.0 N A:LYS201 3.3 47.8 1.0 C A:GLU202 3.3 43.0 1.0 O A:HOH560 3.3 41.3 1.0 C A:GLY200 3.4 48.5 1.0 C A:GLY198 3.5 48.4 1.0 CA A:GLU202 3.5 43.6 1.0 CA A:GLY198 3.6 46.9 1.0 N A:GLN199 3.7 50.0 1.0 CB A:GLU202 3.7 42.5 1.0 O A:GLY198 3.9 48.6 1.0 C A:GLN199 4.0 52.5 1.0 C A:LYS201 4.1 46.9 1.0 N A:GLY198 4.1 44.8 1.0 O A:GLY200 4.2 48.8 1.0 N A:LYS203 4.3 41.5 1.0 CA A:LYS201 4.3 47.6 1.0 CG A:ASP215 4.4 36.5 1.0 CA A:GLN199 4.4 52.7 1.0 CG A:GLU202 4.6 42.7 1.0 CG A:GLU171 4.6 48.2 1.0 CB A:ASP215 4.8 33.5 1.0 CA A:LYS203 4.9 42.4 1.0 CZ A:PHE178 5.0 37.6 1.0 O A:GLN199 5.0 52.5 1.0

F.Shang, M.J.Rynkiewicz, F.X.Mccormack, H.Wu, T.M.Cafarella, J.F.Head, B.A.Seaton. Crystallographic Complexes of Surfactant Protein A and Carbohydrates Reveal Ligand-Induced Conformational Change. J.Biol.Chem. V. 286 757 2011.
ISSN: ISSN 0021-9258
PubMed: 21047777
DOI: 10.1074/JBC.M110.175265