Magnesium in PDB 7vux: Complex Structure of PD1 and 609A-Fab

The structure of Complex Structure of PD1 and 609A-Fab, PDB code: 7vux was solved by H.Huang, Z.Zhu, J.Zhao, L.Jiang, H.Yang, L.Deng, X.Meng, J.Ding, S.Yang, L.Zhao, W.Xu, X.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.91 / 1.64
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.29, 68.41, 77.31, 90, 99.44, 90
R / Rfree (%)	16 / 20.2

The structure of Complex Structure of PD1 and 609A-Fab also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Complex Structure of PD1 and 609A-Fab (pdb code 7vux). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Complex Structure of PD1 and 609A-Fab, PDB code: 7vux:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Complex Structure of PD1 and 609A-Fab


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complex Structure of PD1 and 609A-Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg301 b:42.3 occ:1.00 O A:HOH464 2.5 44.4 1.0 O L:HOH587 2.5 22.6 1.0 O H:ASP105 2.8 18.9 1.0 O L:HOH455 3.2 29.1 1.0 C H:ASP105 3.6 14.8 1.0 OG A:SER87 3.6 24.4 1.0 CA H:ASP105 3.7 13.9 1.0 CB H:ASP105 3.7 13.6 1.0 CB L:LEU46 4.0 13.7 1.0 O H:HOH587 4.0 54.7 1.0 CD2 L:LEU46 4.5 15.9 1.0 N L:LEU46 4.6 11.6 1.0 CB A:SER87 4.6 21.8 1.0 O L:LEU46 4.8 13.1 1.0 N H:VAL106 4.8 13.3 1.0 CG L:LEU46 4.8 13.9 1.0 CA L:LEU46 4.9 12.0 1.0 CG H:ASP105 4.9 14.5 1.0 O L:HOH615 4.9 30.2 1.0 O L:HOH618 5.0 25.2 1.0

Magnesium binding site 2 out of 2 in the Complex Structure of PD1 and 609A-Fab


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complex Structure of PD1 and 609A-Fab within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg307 b:35.4 occ:1.00 O L:HOH405 1.6 31.2 1.0 O L:SER176 2.6 13.3 0.4 O1 H:EDO307 2.6 42.4 1.0 OG L:SER176 2.8 13.4 0.6 O L:GLN160 2.9 15.6 1.0 OG1 L:THR178 3.0 15.5 1.0 C1 H:EDO307 3.2 36.8 1.0 C L:SER176 3.3 14.2 0.4 O2 H:EDO306 3.4 25.8 1.0 O L:SER176 3.4 13.1 0.6 N L:THR178 3.4 13.6 1.0 C L:SER176 3.6 14.0 0.6 C L:GLN160 3.7 15.5 1.0 CB L:SER176 3.7 15.1 0.6 CB L:THR178 3.8 15.2 1.0 OG L:SER176 3.8 11.2 0.4 O H:HOH491 3.8 26.1 1.0 C L:SER177 3.8 16.3 1.0 CA L:SER177 3.8 15.5 1.0 N L:SER162 3.8 14.7 0.6 N L:SER177 3.8 14.7 1.0 CA L:GLU161 3.9 18.6 1.0 N L:SER162 4.0 15.1 0.4 C L:GLU161 4.0 16.5 1.0 N L:GLU161 4.1 15.6 1.0 CA L:THR178 4.2 13.7 1.0 CB L:SER176 4.2 13.0 0.4 C2 H:EDO307 4.3 39.0 1.0 CA L:SER176 4.3 13.5 0.6 O2 H:EDO307 4.3 35.0 1.0 CA L:SER176 4.3 12.9 0.4 CB L:SER162 4.4 16.1 0.6 C2 H:EDO306 4.4 28.1 1.0 OG L:SER162 4.4 18.6 0.4 O1 H:EDO306 4.5 28.9 1.0 O L:SER177 4.6 16.0 1.0 CA L:SER162 4.7 14.9 0.6 O L:GLU161 4.8 17.0 1.0 CA L:GLN160 4.8 17.4 1.0 C1 H:EDO306 4.8 29.4 1.0 CB L:GLN160 4.9 18.8 1.0

H.Huang, Z.Zhu, J.Zhao, L.Jiang, H.Yang, L.Deng, X.Meng, J.Ding, S.Yang, L.Zhao, W.Xu, X.Wang. A Strategy For the Efficient Construction of Anti-PD1-Based Bispecific Antibodies with Desired Igg-Like Properties To Be Published.