Magnesium in PDB 8aom: Complex of Pd-L1 with VHH1

The structure of Complex of Pd-L1 with VHH1, PDB code: 8aom was solved by T.Kang-Pettinger, G.Hall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.32 / 2.20
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	149.512, 149.512, 149.512, 90, 90, 90
R / Rfree (%)	20.8 / 24.5

The binding sites of Magnesium atom in the Complex of Pd-L1 with VHH1 (pdb code 8aom). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Complex of Pd-L1 with VHH1, PDB code: 8aom:

Magnesium binding site 1 out of 1 in the Complex of Pd-L1 with VHH1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complex of Pd-L1 with VHH1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:88.1 occ:1.00 OD2 A:ASP49 3.3 103.7 1.0 OD1 A:ASP49 3.6 133.3 1.0 CG A:ASP49 3.8 117.0 1.0 HA3 A:GLY119 4.2 75.7 1.0 CZ A:TYR118 4.3 100.9 1.0 CE2 A:TYR118 4.3 103.5 1.0 HA2 A:GLY119 4.5 75.7 1.0 HE2 A:TYR118 4.5 103.5 1.0 N A:GLY119 4.5 73.4 1.0 H A:GLY119 4.6 73.4 1.0 OH A:TYR118 4.6 105.2 1.0 CA A:GLY119 4.6 75.7 1.0 CE1 A:TYR118 4.6 94.2 1.0 CD2 A:TYR118 4.7 98.0 1.0 HB1 A:ALA52 4.8 72.0 1.0 HH A:TYR118 4.8 105.2 0.0 HB3 A:ALA52 4.9 72.0 1.0 C A:TYR118 4.9 81.3 1.0 CD1 A:TYR118 4.9 92.5 1.0 CG A:TYR118 5.0 89.1 1.0 HE1 A:TYR118 5.0 94.2 1.0

T.Kang-Pettinger, K.Walker, R.Brown, R.Cowan, H.Wright, R.Baravalle, L.C.Waters, F.W.Muskett, M.W.Bowler, K.Sawmynaden, P.J.Coombs, M.D.Carr, G.Hall. Identification, Binding, and Structural Characterization of Single Domain Anti-Pd-L1 Antibodies Inhibitory of Immune Regulatory Proteins Pd-1 and CD80. J.Biol.Chem. V. 299 02769 2023.
ISSN: ESSN 1083-351X
PubMed: 36470427
DOI: 10.1016/J.JBC.2022.102769