Magnesium in PDB 6ruv: Structure of the Scin Stabilized C3BBB Convertase Bound to Properdin and A the Non-Inhibitory Nanobody HFPNB1

All present enzymatic activity of Structure of the Scin Stabilized C3BBB Convertase Bound to Properdin and A the Non-Inhibitory Nanobody HFPNB1:
3.4.21.47;

The structure of Structure of the Scin Stabilized C3BBB Convertase Bound to Properdin and A the Non-Inhibitory Nanobody HFPNB1, PDB code: 6ruv was solved by D.V.Pedersen, G.R.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.82 / 6.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	123.990, 354.030, 367.840, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 27.1

The binding sites of Magnesium atom in the Structure of the Scin Stabilized C3BBB Convertase Bound to Properdin and A the Non-Inhibitory Nanobody HFPNB1 (pdb code 6ruv). 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 and A the Non-Inhibitory Nanobody HFPNB1, PDB code: 6ruv:
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 and A the Non-Inhibitory Nanobody HFPNB1


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 and A the Non-Inhibitory Nanobody HFPNB1 within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg801 b:0.5 occ:1.00 OG J:SER253 2.1 0.6 1.0 OXT H:ASN1641 2.1 0.5 1.0 OG1 J:THR328 2.2 0.5 1.0 OG J:SER255 2.2 0.9 1.0 CB J:SER253 2.5 0.8 1.0 C H:ASN1641 2.9 0.5 1.0 O H:ASN1641 2.9 1.0 1.0 CB J:THR328 3.4 0.8 1.0 CB J:SER255 3.5 0.8 1.0 OD2 J:ASP364 3.5 0.6 1.0 CG2 J:THR328 3.6 0.2 1.0 OD2 J:ASP251 3.7 0.9 1.0 OD1 J:ASP364 4.0 1.0 1.0 CA J:SER253 4.0 0.5 1.0 CG J:ASP364 4.0 0.1 1.0 O J:LEU366 4.1 0.5 1.0 N J:SER255 4.2 0.6 1.0 CA H:ASN1641 4.3 0.7 1.0 ND2 J:ASN368 4.3 0.6 1.0 C J:SER253 4.4 0.8 1.0 CA J:SER255 4.5 1.0 1.0 O J:GLY327 4.5 0.3 1.0 CA J:THR328 4.5 0.6 1.0 OD1 J:ASP251 4.5 0.4 1.0 CG J:ASP251 4.5 0.2 1.0 CB H:ASN1641 4.6 0.8 1.0 N J:GLY254 4.6 0.5 1.0 CG H:ASN1641 4.6 0.2 1.0 N J:SER253 4.8 0.3 1.0 OD1 H:ASN1641 4.8 0.5 1.0 N J:THR328 4.8 0.2 1.0 C J:GLY327 4.9 0.8 1.0 ND2 H:ASN1641 5.0 0.7 1.0

Magnesium binding site 2 out of 2 in the Structure of the Scin Stabilized C3BBB Convertase Bound to Properdin and A the Non-Inhibitory Nanobody HFPNB1


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 and A the Non-Inhibitory Nanobody HFPNB1 within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg801 b:0.8 occ:1.00 OG L:SER253 2.1 0.4 1.0 OXT B:ASN1641 2.1 0.6 1.0 OG1 L:THR328 2.2 0.3 1.0 OG L:SER255 2.2 0.9 1.0 CB L:SER253 2.5 0.7 1.0 C B:ASN1641 2.9 0.8 1.0 O B:ASN1641 2.9 0.1 1.0 CB L:THR328 3.5 0.9 1.0 CB L:SER255 3.5 0.2 1.0 CG2 L:THR328 3.7 0.6 1.0 OD2 L:ASP251 3.7 0.5 1.0 OD2 L:ASP364 3.7 0.4 1.0 CA L:SER253 3.9 0.2 1.0 OD1 L:ASP364 4.0 0.5 1.0 CG L:ASP364 4.1 0.7 1.0 N L:SER255 4.2 0.4 1.0 O L:LEU366 4.3 0.3 1.0 O L:GLY327 4.3 0.9 1.0 CA B:ASN1641 4.4 0.8 1.0 C L:SER253 4.4 0.1 1.0 OD1 L:ASP251 4.4 0.6 1.0 CG L:ASP251 4.5 0.5 1.0 CA L:SER255 4.5 0.5 1.0 ND2 L:ASN368 4.5 0.6 1.0 CA L:THR328 4.5 0.8 1.0 N L:GLY254 4.6 0.8 1.0 N L:SER253 4.7 0.2 1.0 CB B:ASN1641 4.8 0.4 1.0 C L:GLY327 4.8 0.6 1.0 N L:THR328 4.8 0.2 1.0 CG B:ASN1641 4.9 0.6 1.0 O L:SER326 4.9 0.2 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