Sodium in PDB 4q9c: Ignar Antibody Domain C3

The structure of Ignar Antibody Domain C3, PDB code: 4q9c was solved by J.M.Feige, M.A.Graewert, M.Marcinowski, J.Hennig, J.Behnke, D.Auslaender, E.M.Herold, J.Peschek, C.D.Castro, M.F.Flajnik, L.M.Hendershot, M.Sattler, M.Groll, J.Buchner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.80
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	99.148, 99.148, 52.281, 90.00, 90.00, 120.00
R / Rfree (%)	25.9 / 28.7

The structure of Ignar Antibody Domain C3 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Ignar Antibody Domain C3 (pdb code 4q9c). 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 Ignar Antibody Domain C3, PDB code: 4q9c:

Sodium binding site 1 out of 1 in the Ignar Antibody Domain C3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ignar Antibody Domain C3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na905 b:32.3 occ:1.00 OG1 A:THR371 2.5 23.4 1.0 O A:THR369 2.6 25.2 1.0 O A:PRO356 3.3 26.6 1.0 N A:THR371 3.5 21.9 1.0 C A:THR369 3.6 24.7 1.0 CB A:THR371 3.6 23.3 1.0 CA A:PRO357 3.7 26.4 1.0 C A:PRO356 3.8 26.6 1.0 O A:LEU355 3.9 26.1 1.0 N A:PRO357 4.0 26.5 1.0 C A:LEU370 4.1 21.1 1.0 CA A:LEU370 4.1 20.8 1.0 CA A:THR371 4.2 22.6 1.0 N A:LEU370 4.3 22.5 1.0 CB A:THR369 4.6 25.6 1.0 CB A:PRO357 4.6 26.5 1.0 C A:LEU355 4.6 26.0 1.0 C A:PRO357 4.6 26.9 1.0 CA A:THR369 4.7 25.9 1.0 N A:SER358 4.7 26.7 1.0 CG2 A:THR369 4.8 25.7 1.0 CA A:PRO356 4.9 26.6 1.0 CG2 A:THR371 4.9 23.3 1.0 CG A:PRO357 5.0 26.3 1.0

M.J.Feige, M.A.Grawert, M.Marcinowski, J.Hennig, J.Behnke, D.Auslander, E.M.Herold, J.Peschek, C.D.Castro, M.Flajnik, L.M.Hendershot, M.Sattler, M.Groll, J.Buchner. The Structural Analysis of Shark Ignar Antibodies Reveals Evolutionary Principles of Immunoglobulins. Proc.Natl.Acad.Sci.Usa V. 111 8155 2014.
ISSN: ISSN 0027-8424
PubMed: 24830426
DOI: 10.1073/PNAS.1321502111