Sodium in PDB 3paq: Surfactant Protein A Neck and Carbohydrate Recognition Domain (Ncrd) Complexed with Alpha-Methylmannose

The structure of Surfactant Protein A Neck and Carbohydrate Recognition Domain (Ncrd) Complexed with Alpha-Methylmannose, PDB code: 3paq 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)	30.73 / 2.10
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	97.452, 97.452, 44.848, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 24.4

The structure of Surfactant Protein A Neck and Carbohydrate Recognition Domain (Ncrd) Complexed with Alpha-Methylmannose also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Surfactant Protein A Neck and Carbohydrate Recognition Domain (Ncrd) Complexed with Alpha-Methylmannose (pdb code 3paq). 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 Surfactant Protein A Neck and Carbohydrate Recognition Domain (Ncrd) Complexed with Alpha-Methylmannose, PDB code: 3paq:

Sodium binding site 1 out of 1 in the Surfactant Protein A Neck and Carbohydrate Recognition Domain (Ncrd) Complexed with Alpha-Methylmannose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Surfactant Protein A Neck and Carbohydrate Recognition Domain (Ncrd) Complexed with Alpha-Methylmannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:55.7 occ:1.00 OE1 A:GLU171 2.6 56.6 1.0 O A:GLU202 2.7 49.7 1.0 N A:GLY200 3.0 59.5 1.0 N A:GLU202 3.1 55.1 1.0 CD A:GLU171 3.2 56.8 1.0 OE2 A:GLU171 3.2 58.4 1.0 C A:GLU202 3.2 51.4 1.0 OD2 A:ASP215 3.3 42.0 1.0 O A:HOH560 3.3 49.0 1.0 CA A:GLY200 3.4 58.9 1.0 CA A:GLU202 3.5 52.7 1.0 N A:LYS201 3.6 57.9 1.0 C A:GLY200 3.6 58.3 1.0 C A:GLY198 3.7 57.4 1.0 CB A:GLU202 3.8 52.2 1.0 N A:GLN199 3.9 58.8 1.0 CA A:GLY198 4.0 56.2 1.0 O A:GLY198 4.0 57.5 1.0 C A:GLN199 4.0 61.1 1.0 N A:LYS203 4.2 49.8 1.0 C A:LYS201 4.2 56.9 1.0 N A:GLY198 4.3 54.2 1.0 CG A:ASP215 4.4 41.9 1.0 CA A:GLN199 4.4 61.2 1.0 O A:GLY200 4.5 58.7 1.0 CA A:LYS201 4.5 57.5 1.0 CG A:GLU171 4.6 56.2 1.0 CZ A:PHE178 4.6 42.4 1.0 CG A:GLU202 4.7 52.5 1.0 CB A:ASP215 4.7 39.0 1.0 CA A:LYS203 4.8 49.8 1.0 CB A:GLU171 4.8 56.0 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