Calcium in PDB 5otj: Monomeric Polcalcin (Phl P 7) in Complex with Two Identical Allergen- Specific Antibodies

The structure of Monomeric Polcalcin (Phl P 7) in Complex with Two Identical Allergen- Specific Antibodies, PDB code: 5otj was solved by A.N.Mitropoulou, A.M.Davies, A.J.Beavil, J.M.Mcdonnell, B.J.Sutton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.00 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.760, 178.671, 66.070, 90.00, 94.82, 90.00
R / Rfree (%)	19.9 / 23.5

The binding sites of Calcium atom in the Monomeric Polcalcin (Phl P 7) in Complex with Two Identical Allergen- Specific Antibodies (pdb code 5otj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Monomeric Polcalcin (Phl P 7) in Complex with Two Identical Allergen- Specific Antibodies, PDB code: 5otj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Monomeric Polcalcin (Phl P 7) in Complex with Two Identical Allergen- Specific Antibodies


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Monomeric Polcalcin (Phl P 7) in Complex with Two Identical Allergen- Specific Antibodies within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:21.8 occ:1.00 OD1 D:ASN15 2.2 24.3 1.0 O D:LYS19 2.3 23.3 1.0 OD1 D:ASP17 2.4 29.4 1.0 OE2 D:GLU24 2.5 37.7 1.0 OD1 D:ASP13 2.5 28.7 1.0 O D:HOH309 2.5 48.1 1.0 OE1 D:GLU24 2.6 24.5 1.0 CD D:GLU24 2.8 29.5 1.0 CG D:ASN15 3.1 22.9 1.0 CG D:ASP17 3.2 29.0 1.0 OD2 D:ASP17 3.4 36.2 1.0 ND2 D:ASN15 3.4 21.4 1.0 C D:LYS19 3.5 26.9 1.0 O D:HOH312 3.6 51.9 1.0 CG D:ASP13 3.7 28.2 1.0 CG D:GLU24 4.3 27.2 1.0 N D:LYS19 4.3 28.5 1.0 N D:ILE20 4.4 27.3 1.0 CA D:LYS19 4.4 28.3 1.0 CA D:ILE20 4.4 28.0 1.0 CB D:ASN15 4.4 24.0 1.0 N D:SER21 4.5 24.2 1.0 CB D:ASP17 4.5 22.2 1.0 CA D:ASP13 4.5 26.7 1.0 N D:ASN15 4.5 24.1 1.0 OD2 D:ASP13 4.5 29.7 1.0 N D:ASP17 4.5 21.3 1.0 CB D:ASP13 4.6 26.7 1.0 C D:ASP13 4.8 24.7 1.0 CB D:LYS19 4.8 34.5 1.0 N D:THR14 4.8 23.6 1.0 N D:GLY16 4.9 25.1 1.0 CA D:ASN15 4.9 23.9 1.0 C D:ILE20 4.9 28.7 1.0 CA D:ASP17 5.0 27.3 1.0 OG D:SER21 5.0 34.9 1.0

Calcium binding site 2 out of 4 in the Monomeric Polcalcin (Phl P 7) in Complex with Two Identical Allergen- Specific Antibodies


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Monomeric Polcalcin (Phl P 7) in Complex with Two Identical Allergen- Specific Antibodies within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:25.5 occ:1.00 OD2 D:ASP50 2.3 42.0 1.0 OD1 D:ASP48 2.4 30.2 1.0 OD2 D:ASP52 2.4 29.1 1.0 O D:PHE54 2.4 22.3 1.0 OE2 D:GLU59 2.4 28.7 1.0 O D:HOH307 2.5 30.3 1.0 OE1 D:GLU59 2.7 31.8 1.0 CD D:GLU59 2.9 30.8 1.0 CG D:ASP52 3.3 30.3 1.0 CG D:ASP50 3.3 37.2 1.0 C D:PHE54 3.5 25.0 1.0 CG D:ASP48 3.5 32.6 1.0 OD1 D:ASP52 3.7 35.0 1.0 OD1 D:ASP50 3.7 35.1 1.0 OD1 D:ASP56 3.8 52.8 1.0 N D:PHE54 4.2 25.7 1.0 OD2 D:ASP48 4.3 33.7 1.0 CA D:ASP48 4.3 31.9 1.0 N D:ASP56 4.4 31.1 1.0 N D:ASP52 4.4 26.1 1.0 N D:ILE55 4.4 22.4 1.0 CG D:GLU59 4.4 28.4 1.0 CA D:PHE54 4.4 22.9 1.0 N D:ASP50 4.4 28.6 1.0 CB D:ASP48 4.4 29.3 1.0 CA D:ILE55 4.4 23.6 1.0 CB D:ASP52 4.5 31.6 1.0 CB D:ASP50 4.6 31.3 1.0 CG D:ASP56 4.6 47.2 1.0 N D:GLY51 4.6 31.6 1.0 N D:THR49 4.6 34.3 1.0 C D:ASP48 4.7 34.7 1.0 CB D:PHE54 4.8 22.1 1.0 CA D:ASP50 4.9 29.2 1.0 C D:ILE55 4.9 28.1 1.0 CA D:ASP52 4.9 27.9 1.0 N D:GLY53 5.0 24.4 1.0

Calcium binding site 3 out of 4 in the Monomeric Polcalcin (Phl P 7) in Complex with Two Identical Allergen- Specific Antibodies


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Monomeric Polcalcin (Phl P 7) in Complex with Two Identical Allergen- Specific Antibodies within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:29.2 occ:1.00 OD1 C:ASN15 2.3 36.3 1.0 OE2 C:GLU24 2.3 27.3 1.0 O C:LYS19 2.3 23.8 1.0 OD1 C:ASP17 2.4 24.1 1.0 O C:HOH301 2.5 23.5 1.0 OD1 C:ASP13 2.6 29.6 1.0 OE1 C:GLU24 2.8 26.7 1.0 CD C:GLU24 2.8 26.1 1.0 CG C:ASN15 3.1 31.0 1.0 CG C:ASP17 3.2 26.4 1.0 ND2 C:ASN15 3.3 24.4 1.0 OD2 C:ASP17 3.4 28.8 1.0 C C:LYS19 3.5 25.9 1.0 CG C:ASP13 3.8 29.8 1.0 CG C:GLU24 4.3 25.1 1.0 N C:LYS19 4.3 22.8 1.0 N C:ILE20 4.3 27.4 1.0 O C:HOH302 4.4 30.3 1.0 CA C:LYS19 4.4 27.6 1.0 CA C:ILE20 4.4 27.4 1.0 N C:SER21 4.4 21.8 1.0 CB C:ASN15 4.5 29.3 1.0 CA C:ASP13 4.5 23.1 1.0 CB C:ASP17 4.6 20.1 1.0 N C:ASN15 4.6 28.9 1.0 OD2 C:ASP13 4.6 31.4 1.0 CB C:ASP13 4.6 25.6 1.0 N C:ASP17 4.7 19.1 1.0 CB C:LYS19 4.8 32.4 1.0 OG C:SER21 4.8 21.9 1.0 C C:ILE20 4.8 27.0 1.0 C C:ASP13 4.9 24.7 1.0 N C:THR14 5.0 26.0 1.0 CA C:ASN15 5.0 27.1 1.0

Calcium binding site 4 out of 4 in the Monomeric Polcalcin (Phl P 7) in Complex with Two Identical Allergen- Specific Antibodies


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Monomeric Polcalcin (Phl P 7) in Complex with Two Identical Allergen- Specific Antibodies within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:22.6 occ:1.00 OD1 C:ASP48 2.4 29.0 1.0 O C:PHE54 2.4 32.8 1.0 OD2 C:ASP52 2.4 35.9 1.0 OD2 C:ASP50 2.4 30.6 1.0 OE2 C:GLU59 2.5 23.8 1.0 O C:HOH317 2.5 47.6 1.0 OE1 C:GLU59 2.7 31.1 1.0 CD C:GLU59 2.9 26.6 1.0 CG C:ASP50 3.3 33.5 1.0 CG C:ASP52 3.3 31.1 1.0 OD1 C:ASP50 3.4 37.0 1.0 CG C:ASP48 3.5 31.7 1.0 C C:PHE54 3.5 30.6 1.0 OD1 C:ASP52 3.7 33.9 1.0 OD2 C:ASP48 4.2 35.4 1.0 N C:PHE54 4.3 26.1 1.0 N C:ASP56 4.3 26.2 1.0 N C:ILE55 4.3 28.7 1.0 CA C:ASP48 4.4 30.2 1.0 N C:ASP52 4.4 19.9 1.0 CA C:ILE55 4.4 24.6 1.0 CA C:PHE54 4.4 25.2 1.0 CB C:ASP48 4.4 31.1 1.0 CG C:GLU59 4.4 22.7 1.0 CB C:ASP52 4.4 26.8 1.0 N C:ASP50 4.5 26.0 1.0 CB C:ASP50 4.6 28.5 1.0 N C:GLY51 4.7 27.1 1.0 N C:THR49 4.7 34.4 1.0 C C:ASP48 4.7 31.6 1.0 CB C:PHE54 4.8 25.0 1.0 C C:ILE55 4.8 25.9 1.0 CG C:ASP56 4.9 49.2 1.0 OD2 C:ASP56 4.9 51.9 1.0 CA C:ASP52 4.9 24.0 1.0 O C:HOH320 4.9 31.5 1.0 CA C:ASP50 5.0 27.2 1.0

A.N.Mitropoulou, H.Bowen, T.S.Dodev, A.M.Davies, H.J.Bax, R.L.Beavil, A.J.Beavil, H.J.Gould, L.K.James, B.J.Sutton. Structure of A Patient-Derived Antibody in Complex with Allergen Reveals Simultaneous Conventional and Superantigen-Like Recognition. Proc. Natl. Acad. Sci. V. 115 E8707 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30150373
DOI: 10.1073/PNAS.1806840115