Sodium in PDB 6c1r: Crystal Structure of Human C5A Receptor in Complex with An Orthosteric Antagonist PMX53 and An Allosteric Antagonist Avacopan

The structure of Crystal Structure of Human C5A Receptor in Complex with An Orthosteric Antagonist PMX53 and An Allosteric Antagonist Avacopan, PDB code: 6c1r was solved by H.Liu, L.Wang, Z.Wei, C.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.36 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.411, 52.608, 83.865, 90.00, 106.08, 90.00
R / Rfree (%)	19.2 / 22.4

The structure of Crystal Structure of Human C5A Receptor in Complex with An Orthosteric Antagonist PMX53 and An Allosteric Antagonist Avacopan also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Human C5A Receptor in Complex with An Orthosteric Antagonist PMX53 and An Allosteric Antagonist Avacopan (pdb code 6c1r). 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 Human C5A Receptor in Complex with An Orthosteric Antagonist PMX53 and An Allosteric Antagonist Avacopan, PDB code: 6c1r:

Sodium binding site 1 out of 1 in the Crystal Structure of Human C5A Receptor in Complex with An Orthosteric Antagonist PMX53 and An Allosteric Antagonist Avacopan


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 Human C5A Receptor in Complex with An Orthosteric Antagonist PMX53 and An Allosteric Antagonist Avacopan within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:43.3 occ:1.00 OD1 B:ASN382 2.3 38.9 1.0 O B:HOH635 2.3 32.4 1.0 O B:ASN378 2.4 37.9 1.0 O B:HOH626 2.6 34.9 1.0 OD2 B:ASP168 2.7 36.9 1.0 O B:HOH617 2.8 51.7 1.0 CG B:ASN382 3.2 33.1 1.0 OD1 B:ASP168 3.4 37.2 1.0 CG B:ASP168 3.4 38.7 1.0 C B:ASN378 3.5 32.4 1.0 ND2 B:ASN382 3.5 32.6 1.0 O B:HOH610 3.8 33.5 1.0 O B:HOH606 3.8 34.4 1.0 CA B:ASN378 4.2 31.6 1.0 CB B:ASN378 4.2 33.1 1.0 CG2 B:ILE381 4.3 24.5 1.0 CB B:ASN382 4.5 29.1 1.0 N B:CYS379 4.5 27.3 1.0 OD1 B:ASN378 4.6 45.3 1.0 O B:HOH621 4.7 29.7 1.0 CA B:CYS379 4.7 30.7 1.0 OG B:SER209 4.7 39.0 1.0 N B:ASN382 4.8 27.7 1.0 CG1 B:VAL333 4.9 24.3 1.0 CG B:ASN378 4.9 40.0 1.0 CB B:ASP168 4.9 33.5 1.0

H.Liu, H.R.Kim, R.N.V.K.Deepak, L.Wang, K.Y.Chung, H.Fan, Z.Wei, C.Zhang. Orthosteric and Allosteric Action of the C5A Receptor Antagonists. Nat. Struct. Mol. Biol. V. 25 472 2018.
ISSN: ESSN 1545-9985
PubMed: 29867214
DOI: 10.1038/S41594-018-0067-Z