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

Enzymatic activity of 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;

Protein crystallography data

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

Magnesium Binding Sites:

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 6ruv

Go back to Magnesium Binding Sites List in 6ruv
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 6ruv

Go back to Magnesium Binding Sites List in 6ruv
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

Reference:

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
Page generated: Tue Dec 15 00:01:56 2020

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