Calcium in PDB 6cxo: Complement Component-9

The structure of Complement Component-9, PDB code: 6cxo was solved by R.H.P.Law, B.A.Spicer, T.T.Caradoc-Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.74 / 2.20
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	52.588, 149.213, 165.827, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.1

The structure of Complement Component-9 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	5 atoms

The binding sites of Calcium atom in the Complement Component-9 (pdb code 6cxo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Complement Component-9, PDB code: 6cxo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Complement Component-9


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complement Component-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:65.7 occ:1.00 OD2 A:ASP108 2.1 73.3 1.0 OD1 A:ASN98 2.2 69.9 1.0 O A:ASP100 2.3 70.8 1.0 OE2 A:GLU109 2.4 63.0 1.0 O A:LEU95 2.5 76.4 1.0 OD2 A:ASP102 2.6 75.4 1.0 CG A:ASN98 3.3 78.6 1.0 CG A:ASP108 3.3 72.2 1.0 C A:ASP100 3.4 69.2 1.0 CD A:GLU109 3.4 76.1 1.0 CG A:ASP102 3.5 73.0 1.0 C A:LEU95 3.7 76.7 1.0 CB A:ASP102 3.8 63.7 1.0 N A:ASP100 3.8 65.6 1.0 N A:ASP102 3.9 62.7 1.0 CA A:ASP100 4.0 63.2 1.0 CG A:GLU109 4.0 76.2 1.0 N A:ASN98 4.1 73.9 1.0 ND2 A:ASN98 4.1 61.8 1.0 CB A:ASP100 4.1 62.7 1.0 CB A:ASP108 4.2 70.5 1.0 OD1 A:ASP108 4.3 69.4 1.0 N A:ASN101 4.4 66.0 1.0 CB A:ASN98 4.4 70.7 1.0 OE1 A:GLU109 4.4 73.0 1.0 CA A:ASP102 4.5 61.2 1.0 OD1 A:ASP102 4.6 75.2 1.0 N A:CYS97 4.6 76.0 1.0 N A:GLY99 4.6 69.3 1.0 CA A:ASN98 4.6 73.1 1.0 CA A:LEU95 4.6 70.5 1.0 N A:LEU96 4.6 74.8 1.0 O A:ASP108 4.6 72.3 1.0 CB A:LEU95 4.7 68.1 1.0 CA A:LEU96 4.7 75.5 1.0 CA A:ASN101 4.7 65.5 1.0 C A:ASN98 4.7 74.1 1.0 C A:ASN101 4.7 66.7 1.0 C A:LEU96 4.7 79.3 1.0 C A:ASP108 4.8 73.8 1.0 C A:GLY99 4.9 71.1 1.0 O A:HOH702 5.0 57.8 1.0

Calcium binding site 2 out of 2 in the Complement Component-9


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complement Component-9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:49.5 occ:1.00 O B:ASP100 2.3 53.1 1.0 O B:LEU95 2.3 53.2 1.0 OD2 B:ASP108 2.3 59.2 1.0 OD1 B:ASN98 2.3 51.0 1.0 OE2 B:GLU109 2.4 55.5 1.0 OD2 B:ASP102 2.5 45.6 1.0 CG B:ASN98 3.4 60.0 1.0 CG B:ASP108 3.4 55.7 1.0 C B:ASP100 3.4 52.9 1.0 CD B:GLU109 3.5 70.9 1.0 C B:LEU95 3.5 53.5 1.0 CG B:ASP102 3.5 46.5 1.0 CG B:GLU109 3.9 60.6 1.0 CB B:ASP102 3.9 44.5 1.0 N B:ASP100 4.0 52.1 1.0 ND2 B:ASN98 4.0 45.0 1.0 N B:ASP102 4.0 45.7 1.0 N B:ASN98 4.1 57.5 1.0 CA B:ASP100 4.1 49.0 1.0 CB B:ASP108 4.2 55.4 1.0 OD1 B:ASP108 4.3 53.1 1.0 CA B:LEU95 4.4 48.0 1.0 CB B:ASP100 4.4 48.4 1.0 N B:CYS97 4.4 60.4 1.0 N B:ASN101 4.5 50.1 1.0 N B:LEU96 4.5 52.7 1.0 CB B:ASN98 4.5 52.6 1.0 CB B:LEU95 4.5 46.5 1.0 O B:ASP108 4.5 56.6 1.0 OE1 B:GLU109 4.6 70.1 1.0 OD1 B:ASP102 4.6 49.1 1.0 CA B:LEU96 4.6 53.7 1.0 CA B:ASP102 4.6 44.1 1.0 C B:LEU96 4.6 61.8 1.0 N B:GLY99 4.7 54.0 1.0 CA B:ASN98 4.7 55.5 1.0 CA B:ASN101 4.7 49.2 1.0 C B:ASN101 4.8 50.6 1.0 C B:ASP108 4.8 58.8 1.0 C B:ASN98 4.8 58.6 1.0 C B:GLY99 5.0 56.8 1.0

B.A.Spicer, R.H.P.Law, T.T.Caradoc-Davies, S.M.Ekkel, C.Bayly-Jones, S.S.Pang, P.J.Conroy, G.Ramm, M.Radjainia, H.Venugopal, J.C.Whisstock, M.A.Dunstone. The First Transmembrane Region of Complement Component-9 Acts As A Brake on Its Self-Assembly. Nat Commun V. 9 3266 2018.
ISSN: ESSN 2041-1723
PubMed: 30111885
DOI: 10.1038/S41467-018-05717-0