Copper in PDB 8qya: J22.9-Fny, Fully Humanized, Cdr Optimized Fab Fragment Based on Chimeric J22.9-XI Igg Against Bcma; with Vh CDR2 Glycosylation

The structure of J22.9-Fny, Fully Humanized, Cdr Optimized Fab Fragment Based on Chimeric J22.9-XI Igg Against Bcma; with Vh CDR2 Glycosylation, PDB code: 8qya was solved by S.F.Marino, O.Daumke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.76 / 2.72
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.266, 55.371, 69.486, 90, 108.01, 90
R / Rfree (%)	24.4 / 29.7

The binding sites of Copper atom in the J22.9-Fny, Fully Humanized, Cdr Optimized Fab Fragment Based on Chimeric J22.9-XI Igg Against Bcma; with Vh CDR2 Glycosylation (pdb code 8qya). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the J22.9-Fny, Fully Humanized, Cdr Optimized Fab Fragment Based on Chimeric J22.9-XI Igg Against Bcma; with Vh CDR2 Glycosylation, PDB code: 8qya:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the J22.9-Fny, Fully Humanized, Cdr Optimized Fab Fragment Based on Chimeric J22.9-XI Igg Against Bcma; with Vh CDR2 Glycosylation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of J22.9-Fny, Fully Humanized, Cdr Optimized Fab Fragment Based on Chimeric J22.9-XI Igg Against Bcma; with Vh CDR2 Glycosylation within 5.0Å range: probe atom residue distance (Å) B Occ L:Cu301 b:38.4 occ:1.00 HE2 L:HIS189 1.6 110.9 1.0 NE2 L:HIS189 2.1 79.2 1.0 CE1 L:HIS189 2.7 79.4 1.0 HE1 L:HIS189 2.8 109.8 1.0 CD2 L:HIS189 3.2 78.5 1.0 HD2 L:HIS189 3.5 107.8 1.0 ND1 L:HIS189 3.8 80.0 1.0 OD1 L:ASP185 3.9 90.3 1.0 HB3 L:LYS188 3.9 111.8 1.0 CG L:HIS189 4.0 79.1 1.0 HB2 L:LYS188 4.7 111.8 1.0 HG2 L:LYS188 4.7 118.4 1.0 CB L:LYS188 4.7 85.2 1.0 O L:ASP185 5.0 87.5 1.0

Copper binding site 2 out of 2 in the J22.9-Fny, Fully Humanized, Cdr Optimized Fab Fragment Based on Chimeric J22.9-XI Igg Against Bcma; with Vh CDR2 Glycosylation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of J22.9-Fny, Fully Humanized, Cdr Optimized Fab Fragment Based on Chimeric J22.9-XI Igg Against Bcma; with Vh CDR2 Glycosylation within 5.0Å range: probe atom residue distance (Å) B Occ H:Cu301 b:45.6 occ:1.00 NE2 H:HIS171 2.0 29.5 1.0 HD21 L:ASN137 2.0 65.8 1.0 OD1 L:ASN137 2.2 58.8 1.0 ND2 L:ASN137 2.6 58.0 1.0 CG L:ASN137 2.7 57.2 1.0 CD2 H:HIS171 2.8 29.9 1.0 CE1 H:HIS171 2.9 29.1 1.0 HD2 H:HIS171 3.0 41.3 1.0 HD22 L:ASN138 3.1 91.1 1.0 HE1 H:HIS171 3.2 40.8 1.0 HD22 L:ASN137 3.4 65.8 1.0 HA2 H:GLY169 3.5 69.3 1.0 HG1 H:THR190 3.8 51.9 1.0 CG H:HIS171 4.0 29.6 1.0 ND1 H:HIS171 4.0 29.1 1.0 ND2 L:ASN138 4.0 74.7 1.0 HB3 L:ASN138 4.0 80.2 1.0 O H:GLY169 4.1 54.1 1.0 H L:ASN138 4.2 75.7 1.0 CB L:ASN137 4.2 54.4 1.0 OG1 H:THR190 4.2 42.5 1.0 CA H:GLY169 4.3 55.3 1.0 HG21 H:THR190 4.4 54.7 1.0 HD21 L:ASN138 4.4 91.1 1.0 C H:GLY169 4.5 55.1 1.0 OG L:SER174 4.5 32.4 1.0 HG23 H:THR190 4.5 54.7 1.0 HB3 L:ASN137 4.6 58.7 1.0 N L:ASN138 4.6 73.1 1.0 HG L:SER174 4.7 50.6 1.0 HB2 L:ASN137 4.7 58.7 1.0 HA3 H:GLY169 4.7 69.3 1.0 HD1 H:HIS171 4.8 41.0 1.0 CB L:ASN138 4.8 72.4 1.0 HA L:ASN137 4.8 58.1 1.0 CG2 H:THR190 4.9 43.3 1.0 CG L:ASN138 4.9 74.3 1.0 CA L:ASN137 5.0 54.6 1.0

S.F.Marino, O.Daumke. Structure-Based Humanization of A Therapeutic Antibody For Multiple Myeloma To Be Published.