Calcium in PDB 5vco: The Crystal Structure of Der P 1 Allergen Complexed with Fab Fragment of Mab 10B9

The structure of The Crystal Structure of Der P 1 Allergen Complexed with Fab Fragment of Mab 10B9, PDB code: 5vco was solved by T.Osinski, K.A.Majorek, A.Pomes, L.R.Offermann, S.Osinski, J.Glesner, L.D.Vailes, M.D.Chapman, W.Minor, M.Chruszcz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.26 / 2.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.685, 74.852, 184.103, 90.00, 97.42, 90.00
R / Rfree (%)	20 / 26.1

The binding sites of Calcium atom in the The Crystal Structure of Der P 1 Allergen Complexed with Fab Fragment of Mab 10B9 (pdb code 5vco). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The Crystal Structure of Der P 1 Allergen Complexed with Fab Fragment of Mab 10B9, PDB code: 5vco:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The Crystal Structure of Der P 1 Allergen Complexed with Fab Fragment of Mab 10B9


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of Der P 1 Allergen Complexed with Fab Fragment of Mab 10B9 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca302 b:44.6 occ:1.00 OD1 E:ASP56 2.4 29.3 1.0 OE2 E:GLU59 2.4 34.5 1.0 OE1 E:GLU91 2.4 37.6 1.0 O E:LEU57 2.4 30.9 1.0 CD E:GLU91 3.3 35.9 1.0 CD E:GLU59 3.4 34.4 1.0 CG E:ASP56 3.5 30.4 1.0 C E:LEU57 3.6 31.1 1.0 OE1 E:GLU59 3.7 35.1 1.0 OD2 E:ASP56 4.0 32.0 1.0 OE2 E:GLU91 4.0 37.1 1.0 CG E:GLU91 4.0 34.7 1.0 N E:LEU57 4.1 31.0 1.0 CB E:GLU91 4.2 33.7 1.0 NE E:ARG26 4.3 31.1 1.0 N E:GLU59 4.4 31.9 1.0 C E:ASP56 4.5 31.1 1.0 CA E:LEU57 4.5 31.2 1.0 N E:ALA58 4.6 31.1 1.0 OE2 E:GLU44 4.6 34.0 1.0 CA E:ALA58 4.6 31.8 1.0 CZ E:ARG26 4.7 30.9 1.0 CD E:ARG26 4.7 31.7 1.0 CB E:ASP56 4.7 30.5 1.0 CG E:GLU59 4.8 33.6 1.0 O E:HOH402 4.8 33.1 1.0 NH2 E:ARG26 4.8 30.4 1.0 CA E:ASP56 4.9 31.0 1.0 O E:ASP56 5.0 31.6 1.0 CA E:GLU91 5.0 32.9 1.0

Calcium binding site 2 out of 2 in the The Crystal Structure of Der P 1 Allergen Complexed with Fab Fragment of Mab 10B9


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of Der P 1 Allergen Complexed with Fab Fragment of Mab 10B9 within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca302 b:61.1 occ:1.00 OE1 F:GLU91 2.4 48.2 1.0 OD1 F:ASP56 2.5 56.6 1.0 O F:LEU57 2.5 59.1 1.0 OE2 F:GLU59 2.5 62.9 1.0 OE1 F:GLU59 3.1 59.3 1.0 CD F:GLU59 3.2 61.2 1.0 OE2 F:GLU44 3.5 48.1 1.0 CG F:ASP56 3.5 54.2 1.0 NE F:ARG26 3.5 51.6 1.0 CD F:GLU91 3.6 53.1 1.0 C F:LEU57 3.6 56.6 1.0 N F:LEU57 3.7 53.5 1.0 CZ F:ARG26 4.0 51.4 1.0 NH2 F:ARG26 4.0 51.4 1.0 OD2 F:ASP56 4.1 54.6 1.0 C F:ASP56 4.2 54.1 1.0 CD F:ARG26 4.2 51.5 1.0 CA F:LEU57 4.3 54.4 1.0 CG1 F:VAL40 4.3 47.5 1.0 CD F:GLU44 4.4 48.3 1.0 OE2 F:GLU91 4.4 56.0 1.0 CA F:ASP56 4.4 54.6 1.0 CG F:ARG26 4.5 51.2 1.0 OE1 F:GLU44 4.5 48.5 1.0 CG F:GLU91 4.6 51.1 1.0 CB F:ASP56 4.6 54.1 1.0 CG F:GLU59 4.7 61.4 1.0 N F:ALA58 4.7 57.5 1.0 N F:GLU59 4.7 61.5 1.0 CB F:GLU91 4.8 50.1 1.0 NH1 F:ARG26 5.0 52.0 1.0

T.Osinski, A.Pomes, K.A.Majorek, J.Glesner, L.R.Offermann, L.D.Vailes, M.D.Chapman, W.Minor, M.Chruszcz. Structural Analysis of Der P 1-Antibody Complexes and Comparison with Complexes of Proteins or Peptides with Monoclonal Antibodies. J. Immunol. V. 195 307 2015.
ISSN: ESSN 1550-6606
PubMed: 26026055
DOI: 10.4049/JIMMUNOL.1402199