Sodium in PDB 4lor: C1S CUB1-Egf-CUB2 in Complex with A Collagen-Like Peptide From C1Q

All present enzymatic activity of C1S CUB1-Egf-CUB2 in Complex with A Collagen-Like Peptide From C1Q:
3.4.21.42;

The structure of C1S CUB1-Egf-CUB2 in Complex with A Collagen-Like Peptide From C1Q, PDB code: 4lor was solved by R.Wallis, U.Venkatraman Girija, P.C.E.Moody, J.E.Marshall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.57 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.353, 71.173, 98.393, 90.00, 111.12, 90.00
R / Rfree (%)	19.6 / 25.2

The structure of C1S CUB1-Egf-CUB2 in Complex with A Collagen-Like Peptide From C1Q also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Sodium atom in the C1S CUB1-Egf-CUB2 in Complex with A Collagen-Like Peptide From C1Q (pdb code 4lor). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the C1S CUB1-Egf-CUB2 in Complex with A Collagen-Like Peptide From C1Q, PDB code: 4lor:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the C1S CUB1-Egf-CUB2 in Complex with A Collagen-Like Peptide From C1Q


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of C1S CUB1-Egf-CUB2 in Complex with A Collagen-Like Peptide From C1Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:48.2 occ:1.00 OG A:SER10 2.6 29.9 1.0 O A:PRO11 2.7 31.7 1.0 O A:GLN15 3.0 26.2 1.0 O A:THR106 3.2 42.2 1.0 CB A:SER10 3.4 26.9 1.0 CB A:TYR17 3.6 24.4 1.0 N A:TYR13 3.6 39.0 1.0 C A:THR106 3.6 42.5 1.0 N A:TYR17 3.7 25.1 1.0 C A:PRO11 3.7 40.1 1.0 CA A:TYR13 3.8 34.6 1.0 CA A:TYR17 3.9 40.9 1.0 C A:SER10 3.9 34.9 1.0 CA A:GLY107 4.0 28.0 1.0 O A:SER10 4.0 30.0 1.0 C A:ASN12 4.0 24.8 1.0 N A:GLY107 4.0 27.9 1.0 CB A:TYR13 4.1 33.4 1.0 CD2 A:TYR17 4.1 23.0 1.0 C A:ALA16 4.1 25.6 1.0 N A:PRO11 4.2 27.1 1.0 C A:GLN15 4.2 34.2 1.0 CA A:SER10 4.3 25.1 1.0 CG A:TYR17 4.3 24.9 1.0 O A:ASN12 4.4 43.8 1.0 CA A:THR106 4.5 34.9 1.0 N A:ASN12 4.5 34.0 1.0 O A:ALA16 4.5 38.0 1.0 CA A:PRO11 4.6 40.4 1.0 CA A:ASN12 4.6 31.3 1.0 CA A:ALA16 4.6 25.4 1.0 O A:PHE105 4.8 28.3 1.0 CB A:ASN12 4.9 34.4 1.0 CD1 A:TYR13 4.9 28.1 1.0 N A:PHE108 4.9 27.4 1.0 N A:ALA16 4.9 25.6 1.0 C A:GLY107 5.0 39.1 1.0

Sodium binding site 2 out of 2 in the C1S CUB1-Egf-CUB2 in Complex with A Collagen-Like Peptide From C1Q


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of C1S CUB1-Egf-CUB2 in Complex with A Collagen-Like Peptide From C1Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:41.8 occ:1.00 OG A:SER174 2.7 26.3 1.0 O A:PRO175 2.8 40.7 1.0 O A:LYS266 2.9 32.2 1.0 O A:LYS179 3.0 37.3 1.0 N A:TYR177 3.3 40.1 1.0 CA A:TYR177 3.4 39.4 1.0 CB A:TYR177 3.6 41.8 1.0 CB A:SER174 3.6 25.5 1.0 CA A:GLY267 3.7 22.6 1.0 C A:PRO175 3.7 40.0 1.0 O A:SER174 3.8 38.5 1.0 CB A:TYR181 3.8 28.3 1.0 N A:TYR181 3.8 41.6 1.0 C A:LYS266 3.8 31.9 1.0 C A:SER174 3.9 34.7 1.0 C A:ASN176 3.9 47.4 1.0 CA A:TYR181 4.0 45.3 1.0 CD1 A:TYR177 4.2 34.0 1.0 N A:GLY267 4.2 24.9 1.0 C A:PRO180 4.2 50.7 1.0 C A:LYS179 4.2 33.6 1.0 N A:PRO175 4.3 27.0 1.0 CA A:SER174 4.3 25.5 1.0 CG A:TYR177 4.4 29.6 1.0 CD2 A:TYR181 4.5 28.3 1.0 N A:ASN176 4.5 30.6 1.0 O A:ASN176 4.5 60.1 1.0 CA A:ASN176 4.6 35.4 1.0 CA A:PRO175 4.6 28.3 1.0 N A:TRP268 4.6 23.6 1.0 CG A:TYR181 4.7 44.4 1.0 O A:PRO180 4.7 62.3 1.0 C A:GLY267 4.7 25.0 1.0 CA A:PRO180 4.8 43.0 1.0 C A:TYR177 4.8 36.4 1.0 O A:LYS265 4.9 39.4 1.0 CB A:ASN176 4.9 32.7 1.0 N A:LYS179 4.9 51.1 1.0 C A:PRO178 4.9 45.5 1.0 N A:SER174 5.0 25.4 1.0 N A:PRO180 5.0 35.8 1.0 CA A:PRO178 5.0 40.6 1.0

U.Venkatraman Girija, A.R.Gingras, J.E.Marshall, R.Panchal, M.A.Sheikh, P.Gal, W.J.Schwaeble, D.A.Mitchell, P.C.Moody, R.Wallis. Structural Basis of the C1Q/C1S Interaction and Its Central Role in Assembly of the C1 Complex of Complement Activation. Proc.Natl.Acad.Sci.Usa V. 110 13916 2013.
ISSN: ISSN 0027-8424
PubMed: 23922389
DOI: 10.1073/PNAS.1311113110