Sodium in PDB 5ckq: CUB1-Egf-CUB2 Domains of Rat Masp-1

The structure of CUB1-Egf-CUB2 Domains of Rat Masp-1, PDB code: 5ckq was solved by R.Nan, C.M.Furze, D.W.Wright, J.Gor, R.Wallis, S.J.Perkins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.36 / 3.70
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	152.710, 152.710, 152.710, 90.00, 90.00, 90.00
R / Rfree (%)	24.8 / 29.4

The structure of CUB1-Egf-CUB2 Domains of Rat Masp-1 also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Sodium atom in the CUB1-Egf-CUB2 Domains of Rat Masp-1 (pdb code 5ckq). 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 CUB1-Egf-CUB2 Domains of Rat Masp-1, PDB code: 5ckq:

Sodium binding site 1 out of 1 in the CUB1-Egf-CUB2 Domains of Rat Masp-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of CUB1-Egf-CUB2 Domains of Rat Masp-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:0.9 occ:1.00 O A:ASN185 2.6 0.2 1.0 OG A:SER180 2.7 0.9 1.0 O A:PRO181 2.7 0.1 1.0 O A:ARG269 3.0 0.8 1.0 O A:ASP182 3.4 0.8 1.0 C A:ASP182 3.5 0.1 1.0 CA A:TYR183 3.5 0.5 1.0 N A:TYR183 3.5 0.5 1.0 N A:TYR187 3.6 0.1 1.0 CB A:SER180 3.7 0.8 1.0 C A:PRO181 3.7 0.4 1.0 CA A:TYR187 3.7 0.7 1.0 C A:ASN185 3.8 0.8 1.0 CB A:TYR187 3.8 0.1 1.0 CB A:TYR183 3.9 0.7 1.0 C A:PRO186 3.9 0.5 1.0 O A:SER180 4.0 0.5 1.0 C A:ARG269 4.0 0.8 1.0 C A:SER180 4.0 0.7 1.0 O A:PRO186 4.3 0.5 1.0 CA A:GLY270 4.3 0.3 1.0 N A:PRO181 4.3 0.4 1.0 CD1 A:TYR183 4.3 0.6 1.0 O A:PRO184 4.4 0.0 1.0 CA A:ASP182 4.4 0.1 1.0 N A:ASP182 4.4 0.2 1.0 C A:PRO184 4.4 0.8 1.0 CA A:SER180 4.4 0.6 1.0 CA A:PRO186 4.6 0.9 1.0 N A:GLY270 4.6 0.4 1.0 N A:ASN185 4.6 1.0 1.0 N A:PRO186 4.6 0.5 1.0 CG A:TYR183 4.6 0.6 1.0 CA A:PRO181 4.6 1.0 1.0 CB A:ASP182 4.8 0.9 1.0 CA A:ASN185 4.8 0.2 1.0 CD2 A:TYR187 4.8 0.2 1.0 CG A:TYR187 4.8 0.2 1.0 C A:TYR183 4.9 0.2 1.0

R.Nan, C.M.Furze, D.W.Wright, J.Gor, R.Wallis, S.J.Perkins. Flexibility in Mannan-Binding Lectin-Associated Serine Proteases-1 and -2 Provides Insight on Lectin Pathway Activation. Structure V. 25 364 2017.
ISSN: ISSN 1878-4186
PubMed: 28111019
DOI: 10.1016/J.STR.2016.12.014