Magnesium in PDB 6rur: Structure of the Scin Stabilized C3BBB Convertase Bound to Properdin

All present enzymatic activity of Structure of the Scin Stabilized C3BBB Convertase Bound to Properdin:
3.4.21.47;

The structure of Structure of the Scin Stabilized C3BBB Convertase Bound to Properdin, PDB code: 6rur was solved by D.V.Pedersen, T.A.F.Gadeberg, G.R.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.76 / 6.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	634.870, 121.980, 264.420, 90.00, 112.91, 90.00
R / Rfree (%)	23.4 / 27.2

The binding sites of Magnesium atom in the Structure of the Scin Stabilized C3BBB Convertase Bound to Properdin (pdb code 6rur). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the Scin Stabilized C3BBB Convertase Bound to Properdin, PDB code: 6rur:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the Scin Stabilized C3BBB Convertase Bound to Properdin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Scin Stabilized C3BBB Convertase Bound to Properdin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2003 b:0.1 occ:1.00 OG L:SER253 2.1 1.0 1.0 OXT B:ASN1641 2.1 0.0 1.0 OG L:SER255 2.2 1.0 1.0 OG1 L:THR328 2.2 0.1 1.0 CB L:SER253 2.6 0.3 1.0 C B:ASN1641 2.9 0.8 1.0 O B:ASN1641 2.9 0.3 1.0 CB L:SER255 3.4 0.8 1.0 CB L:THR328 3.5 0.4 1.0 OD2 L:ASP364 3.8 0.9 1.0 CG2 L:THR328 3.8 0.4 1.0 OD2 L:ASP251 3.9 0.6 1.0 CA L:SER253 4.1 0.8 1.0 OD1 L:ASP364 4.1 0.1 1.0 N L:SER255 4.1 0.8 1.0 CG L:ASP364 4.2 0.1 1.0 ND2 L:ASN368 4.2 0.4 1.0 CA B:ASN1641 4.3 0.7 1.0 O L:LEU366 4.3 0.6 1.0 CA L:SER255 4.4 0.4 1.0 O L:GLY327 4.4 0.9 1.0 C L:SER253 4.5 0.1 1.0 CG B:ASN1641 4.5 1.0 1.0 CA L:THR328 4.6 0.3 1.0 CB B:ASN1641 4.6 0.1 1.0 OD1 B:ASN1641 4.6 0.8 1.0 N L:GLY254 4.6 0.8 1.0 OD1 L:ASP251 4.7 1.0 1.0 CG L:ASP251 4.7 0.9 1.0 C L:GLY327 4.8 0.4 1.0 N L:SER253 4.8 0.0 1.0 N L:THR328 4.8 0.8 1.0 ND2 B:ASN1641 5.0 0.2 1.0

Magnesium binding site 2 out of 2 in the Structure of the Scin Stabilized C3BBB Convertase Bound to Properdin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Scin Stabilized C3BBB Convertase Bound to Properdin within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg2003 b:0.8 occ:1.00 OXT H:ASN1641 2.1 0.8 1.0 OG J:SER253 2.1 0.9 1.0 OG1 J:THR328 2.2 0.7 1.0 OG J:SER255 2.2 0.9 1.0 CB J:SER253 2.7 0.8 1.0 C H:ASN1641 2.9 0.9 1.0 O H:ASN1641 3.0 0.1 1.0 OD2 J:ASP364 3.2 0.1 1.0 CB J:THR328 3.5 0.3 1.0 CB J:SER255 3.5 0.8 1.0 OD1 J:ASP364 3.6 0.3 1.0 CG J:ASP364 3.6 0.2 1.0 CG2 J:THR328 3.9 0.4 1.0 OD2 J:ASP251 4.0 0.9 1.0 CA J:SER253 4.1 0.2 1.0 OD1 H:ASN1641 4.3 0.7 1.0 CA H:ASN1641 4.3 0.9 1.0 N J:SER255 4.3 0.4 1.0 O J:GLY327 4.5 1.0 1.0 O J:LEU366 4.5 0.4 1.0 CA J:SER255 4.6 0.4 1.0 CA J:THR328 4.6 0.5 1.0 ND2 J:ASN368 4.6 0.9 1.0 C J:SER253 4.6 0.6 1.0 CG H:ASN1641 4.7 0.6 1.0 OD1 J:ASP251 4.7 0.2 1.0 CG J:ASP251 4.7 0.6 1.0 N J:SER253 4.8 0.2 1.0 C J:GLY327 4.8 0.4 1.0 N J:THR328 4.9 0.9 1.0 N J:GLY254 4.9 0.2 1.0 CB J:ASP364 4.9 0.2 1.0 CB H:ASN1641 4.9 0.5 1.0

D.V.Pedersen, T.A.F.Gadeberg, C.Thomas, Y.Wang, N.Joram, R.K.Jensen, S.M.M.Mazarakis, M.Revel, C.El Sissy, S.V.Petersen, K.Lindorff-Larsen, S.Thiel, N.S.Laursen, V.Fremeaux-Bacchi, G.R.Andersen. Structural Basis For Properdin Oligomerization and Convertase Stimulation in the Human Complement System. Front Immunol V. 10 2007 2019.
ISSN: ESSN 1664-3224
PubMed: 31507604
DOI: 10.3389/FIMMU.2019.02007