Sodium in PDB 5fob: Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice)

The structure of Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice), PDB code: 5fob was solved by F.Forneris, J.Wu, X.Xue, P.Gros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.356 / 2.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	68.891, 83.311, 127.377, 75.03, 76.20, 68.50
R / Rfree (%)	19.8 / 22.95

The structure of Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice) also contains other interesting chemical elements:

Iodine	(I)	7 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice) (pdb code 5fob). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice), PDB code: 5fob:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1676 b:55.4 occ:1.00 O A:VAL555 2.2 60.6 1.0 OD1 A:ASP557 2.4 78.1 1.0 O A:PRO527 2.4 55.3 1.0 OD1 A:ASP554 2.4 92.0 1.0 C A:PRO527 3.3 62.4 1.0 C A:VAL555 3.4 65.8 1.0 CB A:PRO527 3.5 54.7 1.0 CG A:ASP554 3.5 88.2 1.0 CG A:ASP557 3.5 71.4 1.0 N A:VAL555 3.6 63.0 1.0 CA A:PRO527 3.7 64.1 1.0 OD2 A:ASP554 4.0 94.5 1.0 OD2 A:ASP557 4.0 69.5 1.0 CA A:VAL555 4.1 65.2 1.0 N A:ASP557 4.2 72.9 1.0 N A:SER528 4.4 66.6 1.0 N A:LYS556 4.4 71.3 1.0 C A:LYS556 4.5 72.0 1.0 C A:ASP554 4.6 74.3 1.0 CG A:PRO527 4.6 54.5 1.0 CA A:LYS556 4.6 58.3 1.0 CB A:ASP557 4.7 65.7 1.0 CB A:ASP554 4.7 72.9 1.0 CB A:SER528 4.7 55.0 1.0 CA A:ASP554 4.8 76.7 1.0 CB A:VAL555 4.8 70.7 1.0 CA A:ASP557 4.8 63.7 1.0 CA A:SER528 4.9 72.2 1.0 OE2 A:GLU621 5.0 61.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2677 b:85.7 occ:1.00 N B:LEU833 2.1 44.1 1.0 OD1 B:ASP832 2.4 66.5 1.0 O B:HOH2023 2.4 54.0 1.0 O B:LEU833 2.6 53.8 1.0 C B:ASP832 2.8 46.5 1.0 C B:LEU833 2.9 45.8 1.0 CA B:LEU833 2.9 40.0 1.0 CA B:ASP832 3.1 50.9 1.0 NZ B:LYS927 3.1 56.9 1.0 CG B:ASP832 3.4 60.1 1.0 CB B:LEU833 3.6 33.2 1.0 CE B:LYS927 3.7 52.9 1.0 O B:ASP832 3.8 48.0 1.0 CB B:ASP832 3.8 45.4 1.0 N B:ARG834 3.9 53.9 1.0 N B:ASP832 4.3 44.8 1.0 O B:ILE831 4.3 43.8 1.0 OD2 B:ASP832 4.5 70.4 1.0 CD B:LYS927 4.5 47.2 1.0 CD B:ARG834 4.7 64.5 1.0 CG1 B:VAL925 4.7 35.4 1.0 CA B:ARG834 4.7 46.5 1.0 C B:ILE831 4.7 37.0 1.0 CG B:LEU833 4.9 38.7 1.0

F.Forneris, J.Wu, X.Xue, D.Ricklin, Z.Lin, G.Sfyroera, A.Tzekou, E.Volokhina, J.C.Granneman, R.Hauhart, P.Bertram, M.K.Liszewski, J.P.Atkinson, J.D.Lambris, P.Gros. Regulators of Complement Activity Mediate Inhibitory Mechanisms Through A Common C3B-Binding Mode. Embo J. V. 35 1133 2016.
ISSN: ISSN 0261-4189
PubMed: 27013439
DOI: 10.15252/EMBJ.201593673