Sodium in PDB 6f39: C1R Homodimer CUB1-Egf-CUB2

All present enzymatic activity of C1R Homodimer CUB1-Egf-CUB2:
3.4.21.41;

The structure of C1R Homodimer CUB1-Egf-CUB2, PDB code: 6f39 was solved by J.O.M.Almitairi, U.Venkatraman Girija, C.M.Furze, X.Simpson-Gray, F.Badakshi, J.E.Marshall, D.A.Mitchell, P.C.E.Moody, R.Wallis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.06 / 5.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	140.563, 54.620, 138.180, 90.00, 99.90, 90.00
R / Rfree (%)	30.8 / 33.8

The structure of C1R Homodimer CUB1-Egf-CUB2 also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Sodium atom in the C1R Homodimer CUB1-Egf-CUB2 (pdb code 6f39). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the C1R Homodimer CUB1-Egf-CUB2, PDB code: 6f39:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the C1R Homodimer CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of C1R Homodimer CUB1-Egf-CUB2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:0.9 occ:1.00 O A:ARG279 2.5 0.3 1.0 OG A:SER190 2.6 0.6 1.0 CB A:TYR197 3.0 0.2 1.0 CA A:TYR197 3.2 0.4 1.0 O A:ARG195 3.4 0.7 1.0 N A:TYR197 3.5 0.4 1.0 CA A:GLY280 3.5 0.4 1.0 C A:ARG279 3.6 0.7 1.0 O A:LEU191 3.6 0.5 1.0 CB A:SER190 3.7 0.9 1.0 O A:GLU192 3.9 1.0 1.0 N A:GLY280 4.0 0.3 1.0 C A:SER196 4.1 0.4 1.0 CG A:TYR197 4.3 0.8 1.0 CD1 A:TYR193 4.3 0.5 1.0 C A:GLU192 4.5 0.2 1.0 O A:SER196 4.5 1.0 1.0 C A:LEU191 4.6 0.6 1.0 C A:SER190 4.6 0.6 1.0 CD2 A:TYR197 4.6 0.7 1.0 C A:ARG195 4.6 1.0 1.0 CA A:TYR193 4.7 0.2 1.0 C A:TYR197 4.7 0.1 1.0 CA A:SER190 4.7 0.6 1.0 N A:TYR193 4.7 0.1 1.0 N A:LEU191 4.8 0.9 1.0 C A:GLY280 4.8 0.7 1.0 CA A:ARG279 4.8 0.8 1.0 O A:SER190 4.8 0.5 1.0 CD A:PRO198 4.9 0.6 1.0 CA A:SER196 4.9 0.7 1.0 N A:TRP281 4.9 1.0 1.0 CB A:TYR193 4.9 0.4 1.0

Sodium binding site 2 out of 2 in the C1R Homodimer CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of C1R Homodimer CUB1-Egf-CUB2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:0.2 occ:1.00 OG B:SER190 2.3 0.1 1.0 O B:ARG279 2.4 0.1 1.0 CA B:GLY280 3.0 0.8 1.0 CB B:TYR197 3.3 0.7 1.0 CB B:SER190 3.3 0.5 1.0 C B:ARG279 3.4 0.7 1.0 O B:ARG195 3.6 0.9 1.0 CA B:TYR197 3.6 0.2 1.0 N B:GLY280 3.6 0.6 1.0 N B:TYR197 3.7 0.8 1.0 O B:LEU191 3.9 0.8 1.0 O B:GLU192 4.2 0.2 1.0 C B:GLY280 4.2 0.9 1.0 C B:SER196 4.3 0.1 1.0 N B:TRP281 4.4 0.4 1.0 CG B:TYR197 4.4 0.9 1.0 CD1 B:TYR193 4.4 0.6 1.0 CA B:SER190 4.5 0.1 1.0 C B:SER190 4.6 0.5 1.0 CD1 B:TYR197 4.6 0.2 1.0 C B:GLU192 4.7 0.8 1.0 CA B:ARG279 4.7 0.5 1.0 CA B:TYR193 4.7 0.1 1.0 C B:ARG195 4.8 0.7 1.0 N B:TYR193 4.8 0.6 1.0 C B:LEU191 4.8 0.3 1.0 O B:SER190 4.8 0.3 1.0 O B:SER196 4.8 0.1 1.0 NE1 B:TRP281 4.8 0.2 1.0 CD1 B:TRP281 4.8 0.8 1.0 N B:LEU191 4.9 0.9 1.0 CB B:TYR193 4.9 0.6 1.0 CA B:SER196 4.9 0.8 1.0

J.O.M.Almitairi, U.Venkatraman Girija, C.M.Furze, X.Simpson-Gray, F.Badakshi, J.E.Marshall, W.J.Schwaeble, D.A.Mitchell, P.C.E.Moody, R.Wallis. Structure of the C1R-C1S Interaction of the C1 Complex of Complement Activation. Proc. Natl. Acad. Sci. V. 115 768 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29311313
DOI: 10.1073/PNAS.1718709115