Calcium in PDB 6vrt: LT1009 Humanized Antibody Fab Fragment in Complex with Calcium

The structure of LT1009 Humanized Antibody Fab Fragment in Complex with Calcium, PDB code: 6vrt was solved by J.K.Fleming, T.Huxford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.23 / 2.56
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.802, 114.408, 133.702, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 26

The binding sites of Calcium atom in the LT1009 Humanized Antibody Fab Fragment in Complex with Calcium (pdb code 6vrt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the LT1009 Humanized Antibody Fab Fragment in Complex with Calcium, PDB code: 6vrt:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the LT1009 Humanized Antibody Fab Fragment in Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of LT1009 Humanized Antibody Fab Fragment in Complex with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca301 b:89.8 occ:1.00 O L:HOH410 2.3 64.9 1.0 OD1 L:ASP32 2.6 69.6 1.0 OD1 L:ASP30 2.6 83.8 1.0 OD1 L:ASP31 2.6 76.3 1.0 O L:HOH405 2.9 63.7 1.0 CG L:ASP32 3.5 70.4 1.0 CA L:CA302 3.6 97.4 1.0 CG L:ASP30 3.8 83.5 1.0 CG L:ASP31 3.8 79.2 1.0 OD2 L:ASP32 3.8 66.7 1.0 OE1 L:GLU50 4.2 73.7 1.0 OD2 L:ASP31 4.3 74.6 1.0 OD2 L:ASP30 4.4 77.1 1.0 N L:ASP31 4.6 72.8 1.0 N L:ASP32 4.7 66.5 1.0 CD L:GLU50 4.7 75.0 1.0 C L:ASP31 4.7 75.2 1.0 CB L:ASP32 4.8 71.2 1.0 CB L:ASP30 4.9 77.7 1.0 CB L:ASP31 5.0 71.1 1.0 CA L:ASP31 5.0 73.7 1.0

Calcium binding site 2 out of 2 in the LT1009 Humanized Antibody Fab Fragment in Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of LT1009 Humanized Antibody Fab Fragment in Complex with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca302 b:97.4 occ:1.00 OD2 L:ASP32 2.1 66.7 1.0 OD2 L:ASP30 2.5 77.1 1.0 OD2 L:ASP92 2.6 72.1 1.0 CG L:ASP32 3.1 70.4 1.0 OD1 L:ASP30 3.1 83.8 1.0 CG L:ASP30 3.2 83.5 1.0 OD1 L:ASP32 3.4 69.6 1.0 CA L:CA301 3.6 89.8 1.0 CG L:ASP92 3.8 75.2 1.0 CB L:ASP32 4.4 71.2 1.0 CB L:ASP92 4.5 73.5 1.0 CA L:ASP92 4.6 66.5 1.0 CB L:ASP30 4.7 77.7 1.0 OD1 L:ASP92 4.8 64.7 1.0 O L:ASP92 4.8 71.4 1.0 O L:ILE29 4.9 74.7 1.0

E.Farokhi, J.K.Fleming, M.F.Erasmus, A.D.Ward, Y.Wu, M.G.Gutierrez, J.M.Wojciak, T.Huxford. Ion Binding Properties of A Naturally Occurring Metalloantibody Antibodies V. 9 10 2020.
ISSN: ISSN 2073-4468
DOI: 10.3390/ANTIB9020010