Calcium 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:

Sodium

(Na)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where determined in the C1S CUB1-Egf-CUB2 in Complex with A Collagen-Like Peptide From C1Q, PDB code: 4lor:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 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 Calcium with other atoms in the Ca 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:Ca301 b:34.6 occ:1.00 OD1 A:ASP98 2.3 45.2 1.0 OD1 A:ASN101 2.3 42.5 1.0 OE1 A:GLU45 2.4 36.6 1.0 O A:HOH408 2.5 47.7 1.0 O A:SER100 2.5 44.9 1.0 OD2 A:ASP53 2.6 47.8 1.0 OD1 A:ASP53 2.7 29.9 1.0 CG A:ASP53 2.9 47.8 1.0 C A:SER100 3.3 42.2 1.0 CG A:ASN101 3.3 31.8 1.0 CG A:ASP98 3.5 36.4 1.0 CD A:GLU45 3.5 43.6 1.0 N A:ASN101 3.9 40.5 1.0 N A:ASP98 4.0 35.0 1.0 CA A:ASN101 4.1 36.3 1.0 ND2 A:ASN101 4.1 44.4 1.0 OD2 A:ASP98 4.1 46.0 1.0 NZ D:LYS15 4.2 39.5 1.0 N A:SER100 4.2 35.2 1.0 OE2 A:GLU45 4.2 48.6 1.0 CB A:ASN101 4.3 31.8 1.0 CA A:SER100 4.3 43.3 1.0 CB A:GLU45 4.4 34.9 1.0 CB A:ASP53 4.4 29.4 1.0 O A:ASP98 4.5 47.7 1.0 C A:ASP98 4.5 49.9 1.0 CG A:GLU45 4.6 33.5 1.0 CA A:ASP98 4.6 35.9 1.0 CB A:ASP98 4.6 36.8 1.0 OH A:TYR17 4.7 31.6 1.0 CE1 A:TYR17 4.7 26.1 1.0 CB A:SER97 4.8 32.6 1.0 C A:SER97 4.9 34.5 1.0

Calcium binding site 2 out of 3 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 Calcium with other atoms in the Ca 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:Ca302 b:36.6 occ:1.00 O A:ILE117 2.4 50.5 1.0 O A:GLY138 2.4 42.3 1.0 OD1 A:ASN134 2.4 25.3 1.0 O A:PHE135 2.5 31.6 1.0 O A:HOH401 2.6 33.9 1.0 OD1 A:ASP116 2.6 24.7 1.0 OE1 A:GLU119 2.9 38.7 1.0 N A:GLY138 3.2 30.6 1.0 OD2 A:ASP116 3.3 28.4 1.0 CG A:ASP116 3.3 31.6 1.0 C A:GLY138 3.3 48.5 1.0 OE2 A:GLU119 3.5 38.4 1.0 C A:ILE117 3.5 33.4 1.0 CD A:GLU119 3.6 38.9 1.0 CG A:ASN134 3.6 41.8 1.0 CA A:GLY138 3.6 39.9 1.0 C A:PHE135 3.7 29.9 1.0 N A:GLY137 3.9 24.1 1.0 ND2 A:ASN134 4.1 32.6 1.0 N A:PHE135 4.1 24.1 1.0 N A:ILE117 4.2 34.9 1.0 C A:GLY137 4.2 34.4 1.0 CA A:ILE117 4.4 32.2 1.0 N A:ASN118 4.5 31.5 1.0 CA A:GLY137 4.5 24.5 1.0 N A:TYR139 4.5 25.7 1.0 CA A:PHE135 4.6 34.2 1.0 CA A:ASN118 4.6 43.6 1.0 N A:ILE136 4.6 27.8 1.0 CA A:ILE136 4.6 31.8 1.0 C A:ILE136 4.6 27.7 1.0 O A:GLY32 4.7 40.0 1.0 CB A:ASP116 4.8 32.1 1.0 CB A:ILE117 4.8 39.1 1.0 N A:GLU119 4.8 35.1 1.0 CB A:ASN134 4.8 25.2 1.0 C A:ASP116 4.9 32.2 1.0 CB A:TYR139 5.0 26.2 1.0 C A:ASN134 5.0 24.2 1.0

Calcium binding site 3 out of 3 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 Calcium with other atoms in the Ca binding site number 3 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:Ca303 b:31.7 occ:1.00 OD1 A:ASP260 2.3 39.7 1.0 O A:GLY263 2.3 28.9 1.0 OD2 A:ASP221 2.4 38.6 1.0 OE1 A:GLU211 2.4 60.5 1.0 O A:THR262 2.5 46.7 1.0 O A:HOH405 2.5 45.8 1.0 OD1 A:ASP221 2.6 30.4 1.0 CG A:ASP221 2.8 39.3 1.0 C A:GLY263 3.4 45.8 1.0 C A:THR262 3.5 43.4 1.0 CG A:ASP260 3.5 43.3 1.0 CD A:GLU211 3.6 66.4 1.0 CA A:GLY263 3.9 34.7 1.0 N A:GLY263 4.1 44.9 1.0 NE2 A:GLN264 4.1 44.6 1.0 OD2 A:ASP260 4.1 38.2 1.0 N A:ASP260 4.1 34.8 1.0 CB A:ASP221 4.3 28.7 1.0 CB A:GLU211 4.3 32.9 1.0 O A:ASP260 4.4 47.2 1.0 OE2 A:GLU211 4.5 72.0 1.0 N A:GLN264 4.5 43.7 1.0 CG A:GLU211 4.5 34.9 1.0 OH A:TYR181 4.6 36.5 1.0 N A:THR262 4.6 44.5 1.0 C A:ASP260 4.6 29.6 1.0 CA A:THR262 4.6 42.1 1.0 CB A:ASP260 4.7 30.3 1.0 CA A:ASP260 4.7 42.3 1.0 CE1 A:TYR181 4.8 29.2 1.0 CA A:GLN264 4.9 43.8 1.0 CD A:GLN264 4.9 40.4 1.0 CG A:GLN264 4.9 38.4 1.0 N A:ASP221 4.9 30.2 1.0 CB A:THR259 4.9 31.5 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