Sodium in PDB 4lmf: C1S CUB1-Egf-CUB2

All present enzymatic activity of C1S CUB1-Egf-CUB2:
3.4.21.42;

The structure of C1S CUB1-Egf-CUB2, PDB code: 4lmf 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)	67.51 / 2.92
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.876, 71.668, 157.723, 90.00, 95.93, 90.00
R / Rfree (%)	20.8 / 25.2

The structure of C1S CUB1-Egf-CUB2 also contains other interesting chemical elements:

Calcium

(Ca)

12 atoms

The binding sites of Sodium atom in the C1S CUB1-Egf-CUB2 (pdb code 4lmf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the C1S CUB1-Egf-CUB2, PDB code: 4lmf:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the C1S 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 C1S CUB1-Egf-CUB2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:50.6 occ:1.00 OG A:SER10 2.4 38.3 1.0 O A:THR106 2.5 40.1 1.0 O A:PRO11 3.0 37.8 1.0 C A:THR106 3.2 35.1 1.0 O A:GLN15 3.2 49.2 1.0 CB A:SER10 3.4 36.2 1.0 CB A:TYR17 3.5 32.3 1.0 CA A:GLY107 3.6 29.4 1.0 N A:TYR13 3.6 41.3 1.0 N A:GLY107 3.7 30.5 1.0 N A:TYR17 3.8 36.9 1.0 CA A:TYR13 3.8 35.6 1.0 CA A:TYR17 3.9 37.0 1.0 C A:PRO11 3.9 39.1 1.0 C A:SER10 4.0 38.3 1.0 C A:ASN12 4.0 44.5 1.0 O A:SER10 4.0 40.1 1.0 CB A:TYR13 4.1 29.7 1.0 CD2 A:TYR17 4.1 33.0 1.0 CA A:THR106 4.2 33.7 1.0 C A:ALA16 4.3 45.5 1.0 CA A:SER10 4.3 35.6 1.0 CG A:TYR17 4.3 30.4 1.0 O A:ASN12 4.3 41.2 1.0 N A:PRO11 4.4 39.1 1.0 C A:GLN15 4.4 48.2 1.0 N A:PHE108 4.5 28.0 1.0 C A:GLY107 4.6 31.7 1.0 N A:ASN12 4.6 43.8 1.0 CA A:ASN12 4.7 46.6 1.0 O A:ALA16 4.8 49.0 1.0 CA A:PRO11 4.8 38.5 1.0 CA A:ALA16 4.9 49.6 1.0 CB A:ASN12 4.9 45.2 1.0 CD1 A:TYR13 4.9 24.0 1.0

Sodium binding site 2 out of 4 in the C1S 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 C1S CUB1-Egf-CUB2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:51.0 occ:1.00 O B:LYS266 2.5 30.2 1.0 OG B:SER174 2.6 23.2 1.0 O B:LYS179 3.1 44.6 1.0 O B:PRO175 3.2 36.9 1.0 CA B:GLY267 3.3 23.7 1.0 C B:LYS266 3.4 29.4 1.0 CB B:TYR181 3.7 24.3 1.0 CB B:SER174 3.7 25.1 1.0 N B:GLY267 3.7 29.1 1.0 N B:TYR181 3.7 18.9 1.0 CA B:TYR177 3.7 43.4 1.0 N B:TYR177 3.8 41.7 1.0 CD1 B:TYR177 3.9 33.8 1.0 CA B:TYR181 3.9 17.4 1.0 CB B:TYR177 4.0 38.8 1.0 CD2 B:TYR181 4.0 21.9 1.0 O B:SER174 4.1 37.4 1.0 C B:PRO180 4.2 23.4 1.0 C B:ASN176 4.2 40.7 1.0 C B:SER174 4.2 31.8 1.0 C B:LYS179 4.2 43.2 1.0 C B:PRO175 4.3 32.5 1.0 C B:GLY267 4.3 28.2 1.0 CG B:TYR181 4.4 26.6 1.0 O B:LYS265 4.4 27.3 1.0 CG B:TYR177 4.4 34.9 1.0 N B:TRP268 4.4 30.0 1.0 O B:ASN176 4.4 43.0 1.0 CA B:SER174 4.5 26.7 1.0 CA B:PRO180 4.6 27.8 1.0 CA B:LYS266 4.7 30.4 1.0 C B:PRO178 4.7 43.4 1.0 N B:PRO175 4.8 28.6 1.0 O B:PRO180 4.8 18.8 1.0 O B:PRO178 4.9 39.8 1.0 CA B:PRO178 4.9 47.7 1.0 CE1 B:TYR177 4.9 36.0 1.0 N B:PRO180 4.9 35.7 1.0 N B:LYS179 5.0 42.2 1.0 CA B:ASN176 5.0 37.2 1.0

Sodium binding site 3 out of 4 in the C1S CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of C1S CUB1-Egf-CUB2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:56.1 occ:1.00 O C:PRO175 2.5 33.6 1.0 OG C:SER174 2.5 28.6 1.0 CB C:SER174 3.3 24.5 1.0 O C:LYS266 3.4 27.4 1.0 CB C:TYR181 3.4 25.7 1.0 C C:PRO175 3.5 32.5 1.0 O C:SER174 3.5 39.2 1.0 N C:TYR177 3.6 42.5 1.0 C C:SER174 3.6 31.1 1.0 O C:LYS179 3.6 42.7 1.0 CA C:TYR177 3.7 42.9 1.0 CA C:GLY267 3.8 29.0 1.0 CA C:TYR181 3.8 23.9 1.0 N C:TYR181 3.9 24.7 1.0 CB C:TYR177 3.9 34.5 1.0 C C:ASN176 3.9 44.3 1.0 N C:PRO175 4.0 29.5 1.0 CA C:SER174 4.0 25.2 1.0 CD2 C:TYR181 4.1 21.4 1.0 C C:LYS266 4.2 29.2 1.0 CD1 C:TYR177 4.2 29.6 1.0 CG C:TYR181 4.3 25.6 1.0 CA C:PRO175 4.3 27.5 1.0 N C:ASN176 4.3 40.5 1.0 O C:ASN176 4.4 47.9 1.0 N C:GLY267 4.4 27.1 1.0 C C:PRO180 4.4 29.3 1.0 CA C:ASN176 4.5 45.8 1.0 CG C:TYR177 4.6 29.8 1.0 N C:TRP268 4.7 27.1 1.0 CB C:ASN176 4.7 51.0 1.0 N C:SER174 4.8 26.8 1.0 C C:GLY267 4.8 31.0 1.0 C C:LYS179 4.8 43.4 1.0 CD C:PRO175 4.8 28.2 1.0 O C:PRO180 4.9 29.0 1.0 O C:LYS265 5.0 25.2 1.0

Sodium binding site 4 out of 4 in the C1S CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of C1S CUB1-Egf-CUB2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:43.6 occ:1.00 OG D:SER10 2.5 33.4 1.0 O D:THR106 2.6 46.2 1.0 O D:GLN15 2.9 50.1 1.0 O D:PRO11 2.9 48.7 1.0 N D:TYR13 3.3 48.0 1.0 C D:THR106 3.3 42.7 1.0 CA D:TYR13 3.4 39.8 1.0 CB D:SER10 3.6 29.5 1.0 CB D:TYR17 3.6 41.8 1.0 C D:ASN12 3.6 51.4 1.0 N D:TYR17 3.7 42.9 1.0 CB D:TYR13 3.8 37.1 1.0 CA D:TYR17 3.8 44.7 1.0 C D:PRO11 3.8 42.8 1.0 O D:ASN12 3.9 50.9 1.0 N D:GLY107 4.0 38.4 1.0 CA D:GLY107 4.0 35.9 1.0 O D:SER10 4.0 34.5 1.0 C D:SER10 4.1 32.2 1.0 C D:GLN15 4.1 47.8 1.0 C D:ALA16 4.1 43.1 1.0 CA D:THR106 4.1 39.5 1.0 CA D:ASN12 4.4 51.2 1.0 CA D:SER10 4.4 31.2 1.0 N D:ASN12 4.4 46.0 1.0 O D:ALA16 4.5 41.4 1.0 N D:PRO11 4.5 31.0 1.0 CD2 D:TYR17 4.5 33.5 1.0 CG D:TYR17 4.6 36.3 1.0 CB D:ASN12 4.7 50.4 1.0 N D:GLN15 4.7 50.4 1.0 CA D:ALA16 4.7 44.4 1.0 CD1 D:TYR13 4.8 27.0 1.0 CA D:PRO11 4.8 32.9 1.0 CG D:TYR13 4.8 32.1 1.0 N D:PHE108 4.9 31.7 1.0 N D:ALA16 4.9 46.9 1.0 C D:TYR13 4.9 33.1 1.0 CB D:THR106 4.9 36.0 1.0 C D:PRO14 4.9 42.9 1.0 C D:GLY107 4.9 36.6 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