Calcium in PDB 5vcn: The Crystal Structure of Der P 1 Allergen Complexed with Fab Fragment of Mab 5H8

The structure of The Crystal Structure of Der P 1 Allergen Complexed with Fab Fragment of Mab 5H8, PDB code: 5vcn 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)	50.00 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.743, 73.263, 200.340, 90.00, 91.09, 90.00
R / Rfree (%)	21.9 / 26.5

The binding sites of Calcium atom in the The Crystal Structure of Der P 1 Allergen Complexed with Fab Fragment of Mab 5H8 (pdb code 5vcn). 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 5H8, PDB code: 5vcn:
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 5H8


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 5H8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:50.4 occ:1.00 OE1 A:GLU91 2.2 36.0 1.0 OD1 A:ASP56 2.5 45.8 1.0 O A:LEU57 2.7 34.6 1.0 OE2 A:GLU59 2.7 39.6 1.0 OE1 A:GLU59 3.1 37.4 1.0 CD A:GLU91 3.2 38.0 1.0 CD A:GLU59 3.2 37.5 1.0 CG A:GLU91 3.5 37.7 1.0 OE2 A:GLU44 3.5 34.7 1.0 CG A:ASP56 3.7 42.9 1.0 NE A:ARG26 3.7 50.4 1.0 C A:LEU57 3.8 34.5 1.0 N A:LEU57 3.9 34.7 1.0 CD A:ARG26 3.9 49.5 1.0 C A:ASP56 4.2 35.7 1.0 CZ A:ARG26 4.4 51.1 1.0 OE2 A:GLU91 4.4 38.5 1.0 CA A:LEU57 4.4 34.5 1.0 OD2 A:ASP56 4.4 45.9 1.0 CA A:ASP56 4.4 37.5 1.0 CD A:GLU44 4.6 34.7 1.0 CG1 A:VAL40 4.6 34.1 1.0 CG A:GLU59 4.7 37.4 1.0 CB A:ASP56 4.7 40.4 1.0 CG A:ARG26 4.7 48.0 1.0 O A:ASP56 4.8 35.3 1.0 N A:GLU59 4.8 36.0 1.0 NH2 A:ARG26 4.8 50.9 1.0 OE1 A:GLU44 4.8 35.0 1.0 N A:ALA58 4.9 34.4 1.0 CB A:GLU91 4.9 37.1 1.0 NH1 A:ARG26 5.0 53.1 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 5H8


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 5H8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:45.0 occ:1.00 OE1 B:GLU91 2.3 40.6 1.0 OD1 B:ASP56 2.4 42.9 1.0 O B:LEU57 2.6 33.7 1.0 OE2 B:GLU59 2.8 34.5 1.0 OE1 B:GLU59 3.1 34.3 1.0 CD B:GLU91 3.2 42.0 1.0 CD B:GLU59 3.3 34.2 1.0 CG B:GLU91 3.4 40.3 1.0 OE2 B:GLU44 3.5 33.9 1.0 CG B:ASP56 3.6 42.8 1.0 C B:LEU57 3.7 33.4 1.0 N B:LEU57 3.8 33.8 1.0 NE B:ARG26 3.9 47.4 1.0 CD B:ARG26 3.9 46.5 1.0 C B:ASP56 4.1 34.3 1.0 CA B:LEU57 4.3 33.4 1.0 OE2 B:GLU91 4.3 43.6 1.0 CA B:ASP56 4.3 36.7 1.0 OD2 B:ASP56 4.4 46.7 1.0 CZ B:ARG26 4.5 48.6 1.0 CD B:GLU44 4.6 34.0 1.0 CB B:ASP56 4.6 39.9 1.0 CG1 B:VAL40 4.6 35.4 1.0 O B:ASP56 4.6 34.5 1.0 CG B:GLU59 4.7 33.9 1.0 CG B:ARG26 4.7 45.9 1.0 N B:ALA58 4.8 33.3 1.0 N B:GLU59 4.8 33.5 1.0 CB B:GLU91 4.8 39.6 1.0 OE1 B:GLU44 4.9 34.6 1.0 NH2 B:ARG26 5.0 47.8 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