Sodium in PDB 5ffr: Crystal Structure of Surfactant Protein-A Complexed with Phosphocholine

The structure of Crystal Structure of Surfactant Protein-A Complexed with Phosphocholine, PDB code: 5ffr was solved by B.C.Goh, H.Wu, M.J.Rynkiewicz, K.Schulten, B.A.Seaton, F.X.Mccormack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.34 / 2.20
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	97.349, 97.349, 44.645, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 19.3

The structure of Crystal Structure of Surfactant Protein-A Complexed with Phosphocholine also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Surfactant Protein-A Complexed with Phosphocholine (pdb code 5ffr). 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 Surfactant Protein-A Complexed with Phosphocholine, PDB code: 5ffr:

Sodium binding site 1 out of 1 in the Crystal Structure of Surfactant Protein-A Complexed with Phosphocholine


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 Surfactant Protein-A Complexed with Phosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:40.5 occ:0.92 OE1 A:GLU171 2.5 43.1 1.0 N A:GLY200 2.8 63.8 1.0 O A:GLU202 3.0 40.3 1.0 N A:GLU202 3.0 44.5 1.0 OE2 A:GLU171 3.1 42.6 1.0 CA A:GLY200 3.1 50.6 1.0 CD A:GLU171 3.2 43.1 1.0 OD2 A:ASP215 3.2 38.5 1.0 O A:HOH423 3.2 32.6 1.0 N A:LYS201 3.3 50.8 1.0 C A:GLU202 3.3 49.3 1.0 C A:GLY200 3.4 56.0 1.0 C A:GLY198 3.5 44.2 1.0 CA A:GLU202 3.5 49.1 1.0 CA A:GLY198 3.7 40.4 1.0 N A:GLN199 3.7 44.5 1.0 CB A:GLU202 3.7 47.3 1.0 O A:GLY198 3.9 47.2 1.0 C A:GLN199 4.0 65.0 1.0 C A:LYS201 4.1 52.5 1.0 N A:GLY198 4.1 41.0 1.0 CG A:ASP215 4.1 38.7 1.0 O A:GLY200 4.2 53.7 1.0 N A:LYS203 4.2 40.7 1.0 CA A:LYS201 4.3 52.2 1.0 CA A:GLN199 4.4 57.8 1.0 CG A:GLU171 4.6 41.6 1.0 CG A:GLU202 4.7 45.9 1.0 O A:HOH467 4.7 45.1 1.0 CA A:LYS203 4.7 39.9 1.0 CZ A:PHE178 4.8 40.2 1.0 CB A:ASP215 4.8 29.5 1.0 OD1 A:ASP215 4.9 44.8 1.0 O A:GLN199 5.0 67.1 1.0

B.C.Goh, H.Wu, M.J.Rynkiewicz, K.Schulten, B.A.Seaton, F.X.Mccormack. Elucidation of Lipid Binding Sites on Lung Surfactant Protein A Using X-Ray Crystallography, Mutagenesis, and Molecular Dynamics Simulations. Biochemistry V. 55 3692 2016.
ISSN: ISSN 0006-2960
PubMed: 27324153
DOI: 10.1021/ACS.BIOCHEM.6B00048