Calcium in PDB 1k9u: Crystal Structure of the Calcium-Binding Pollen Allergen Phl P 7 (Polcalcin) at 1.75 Angstroem

The structure of Crystal Structure of the Calcium-Binding Pollen Allergen Phl P 7 (Polcalcin) at 1.75 Angstroem, PDB code: 1k9u was solved by P.Verdino, K.Westritschnig, R.Valenta, W.Keller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	13.92 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	31.084, 56.205, 37.238, 90.00, 90.23, 90.00
R / Rfree (%)	19.2 / 22.3

The binding sites of Calcium atom in the Crystal Structure of the Calcium-Binding Pollen Allergen Phl P 7 (Polcalcin) at 1.75 Angstroem (pdb code 1k9u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Calcium-Binding Pollen Allergen Phl P 7 (Polcalcin) at 1.75 Angstroem, PDB code: 1k9u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Calcium-Binding Pollen Allergen Phl P 7 (Polcalcin) at 1.75 Angstroem


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Calcium-Binding Pollen Allergen Phl P 7 (Polcalcin) at 1.75 Angstroem within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:10.2 occ:1.00 OD1 A:ASP13 2.3 11.4 1.0 O A:LYS19 2.3 11.4 1.0 OD1 A:ASN15 2.3 13.7 1.0 OD1 A:ASP17 2.4 11.6 1.0 OE1 A:GLU24 2.4 10.5 1.0 O A:HOH2002 2.5 13.3 1.0 OE2 A:GLU24 2.6 11.4 1.0 CD A:GLU24 2.8 11.8 1.0 CG A:ASP17 3.3 14.0 1.0 CG A:ASN15 3.4 14.8 1.0 CG A:ASP13 3.5 14.5 1.0 C A:LYS19 3.5 10.3 1.0 OD2 A:ASP17 3.7 13.5 1.0 ND2 A:ASN15 4.0 19.4 1.0 CA A:ASP13 4.2 15.0 1.0 N A:ASP17 4.2 14.4 1.0 N A:LYS19 4.2 11.4 1.0 OD2 A:ASP13 4.3 13.0 1.0 N A:ASN15 4.3 16.6 1.0 CB A:ASP13 4.3 14.7 1.0 CG A:GLU24 4.3 9.3 1.0 C A:ASP13 4.4 15.0 1.0 N A:ILE20 4.4 8.4 0.5 N A:ILE20 4.4 8.2 0.5 CA A:ILE20 4.4 8.8 0.5 CA A:ILE20 4.4 8.4 0.5 N A:SER21 4.4 8.7 1.0 CA A:LYS19 4.4 11.3 1.0 CB A:ASP17 4.5 12.9 1.0 N A:THR14 4.6 15.1 1.0 N A:GLY16 4.6 13.6 1.0 CG A:LYS19 4.6 20.8 1.0 CB A:ASN15 4.6 16.9 1.0 CA A:ASN15 4.8 14.8 1.0 CA A:ASP17 4.8 12.5 1.0 C A:ASN15 4.8 15.5 1.0 O A:ASP13 4.9 17.0 1.0 C A:ILE20 4.9 8.8 0.5 C A:ILE20 4.9 9.0 0.5 N A:GLY18 4.9 11.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Calcium-Binding Pollen Allergen Phl P 7 (Polcalcin) at 1.75 Angstroem


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Calcium-Binding Pollen Allergen Phl P 7 (Polcalcin) at 1.75 Angstroem within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:23.4 occ:1.00 OD1 A:ASP52 2.2 34.9 1.0 O A:PHE54 2.3 19.4 1.0 OD1 A:ASP48 2.3 19.5 1.0 O A:HOH2003 2.4 27.7 1.0 OD1 A:ASP50 2.4 31.6 1.0 OE1 A:GLU59 2.4 16.3 1.0 OE2 A:GLU59 2.6 21.1 1.0 CD A:GLU59 2.8 16.5 1.0 CG A:ASP50 3.2 33.9 1.0 CG A:ASP52 3.3 36.2 1.0 CG A:ASP48 3.4 21.6 1.0 OD2 A:ASP50 3.4 35.6 1.0 C A:PHE54 3.5 18.1 1.0 OD2 A:ASP52 4.0 37.7 1.0 OD2 A:ASP48 4.1 20.0 1.0 N A:ASP52 4.2 33.4 1.0 N A:ASP56 4.3 14.6 1.0 CA A:ILE55 4.3 15.8 1.0 CB A:ASP48 4.3 19.8 1.0 CA A:ASP48 4.3 20.6 1.0 N A:ILE55 4.3 16.1 1.0 N A:PHE54 4.3 21.7 1.0 CG A:GLU59 4.3 17.8 1.0 N A:ASP50 4.3 32.4 1.0 CB A:ASP52 4.4 34.6 1.0 CA A:PHE54 4.4 20.4 1.0 CB A:ASP50 4.5 33.7 1.0 N A:GLY51 4.5 34.5 1.0 C A:ASP48 4.6 23.2 1.0 OD2 A:ASP56 4.7 23.3 1.0 N A:THR49 4.7 25.6 1.0 C A:ILE55 4.7 15.0 1.0 CG A:ASP56 4.7 17.5 1.0 CA A:ASP50 4.8 33.5 1.0 CA A:ASP52 4.8 32.0 1.0 C A:ASP50 4.9 34.3 1.0 CB A:PHE54 4.9 22.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Calcium-Binding Pollen Allergen Phl P 7 (Polcalcin) at 1.75 Angstroem


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Calcium-Binding Pollen Allergen Phl P 7 (Polcalcin) at 1.75 Angstroem within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:15.4 occ:1.00 O B:LYS19 2.2 16.6 0.5 O B:LYS19 2.2 16.6 0.5 OD1 B:ASP13 2.3 14.4 1.0 O B:HOH2004 2.3 18.4 1.0 OD1 B:ASN15 2.4 21.4 1.0 OE1 B:GLU24 2.4 13.3 1.0 OD1 B:ASP17 2.5 21.4 1.0 OE2 B:GLU24 2.5 16.1 1.0 CD B:GLU24 2.8 13.8 1.0 CG B:ASP17 3.4 22.9 1.0 CG B:ASP13 3.4 16.0 1.0 CG B:ASN15 3.4 23.7 1.0 C B:LYS19 3.5 18.1 0.5 C B:LYS19 3.5 18.0 0.5 OD2 B:ASP17 3.8 22.0 1.0 ND2 B:ASN15 4.0 23.9 1.0 N B:LYS19 4.2 18.7 0.5 N B:ASP17 4.2 21.1 1.0 N B:LYS19 4.2 18.5 0.5 OD2 B:ASP13 4.2 16.4 1.0 CA B:ASP13 4.3 14.8 1.0 CG B:GLU24 4.3 13.2 1.0 CB B:ASP13 4.3 14.1 1.0 N B:ASN15 4.4 23.8 1.0 CA B:LYS19 4.4 19.5 0.5 N B:ILE20 4.4 16.2 1.0 CA B:LYS19 4.4 19.2 0.5 O B:HOH2085 4.4 36.0 1.0 CA B:ILE20 4.4 14.5 1.0 C B:ASP13 4.5 17.1 1.0 CG B:LYS19 4.5 23.7 0.5 O B:HOH2026 4.5 29.2 1.0 CB B:ASP17 4.5 20.4 1.0 N B:SER21 4.5 12.9 1.0 N B:GLY16 4.6 23.5 1.0 CB B:ASN15 4.6 22.1 1.0 N B:THR14 4.7 17.0 1.0 CA B:ASP17 4.8 20.6 1.0 CA B:ASN15 4.9 24.1 1.0 C B:ASN15 4.9 24.6 1.0 N B:GLY18 4.9 20.2 1.0 CB B:LYS19 4.9 22.6 0.5 C B:ILE20 5.0 15.0 1.0 O B:ASP13 5.0 17.4 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Calcium-Binding Pollen Allergen Phl P 7 (Polcalcin) at 1.75 Angstroem


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Calcium-Binding Pollen Allergen Phl P 7 (Polcalcin) at 1.75 Angstroem within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1004 b:12.2 occ:1.00 OD1 B:ASP48 2.3 10.7 1.0 O B:PHE54 2.3 9.6 1.0 O B:HOH2005 2.3 12.3 1.0 OE1 B:GLU59 2.4 12.6 1.0 OD1 B:ASP50 2.4 12.8 1.0 OD1 B:ASP52 2.4 13.7 1.0 OE2 B:GLU59 2.5 12.4 1.0 CD B:GLU59 2.8 12.7 1.0 CG B:ASP50 3.2 18.1 1.0 CG B:ASP52 3.3 17.5 1.0 CG B:ASP48 3.4 12.5 1.0 OD2 B:ASP50 3.4 17.2 1.0 C B:PHE54 3.5 10.9 1.0 OD2 B:ASP52 3.7 17.3 1.0 N B:ASP52 4.1 14.3 1.0 N B:PHE54 4.1 11.1 1.0 CB B:ASP48 4.2 9.6 1.0 CA B:ASP48 4.2 12.2 1.0 CG B:GLU59 4.2 11.3 1.0 OD2 B:ASP48 4.3 13.4 1.0 N B:ASP56 4.3 10.0 1.0 CA B:PHE54 4.4 11.2 1.0 N B:ILE55 4.4 8.6 1.0 N B:ASP50 4.4 14.3 1.0 CA B:ILE55 4.4 10.6 1.0 CB B:ASP52 4.5 17.3 1.0 CB B:ASP50 4.5 16.1 1.0 N B:GLY51 4.5 15.4 1.0 C B:ASP48 4.5 12.7 1.0 OD2 B:ASP56 4.6 18.5 1.0 CA B:ASP52 4.7 15.3 1.0 N B:GLY53 4.7 13.0 1.0 CA B:ASP50 4.7 15.2 1.0 C B:ASP50 4.8 16.1 1.0 CG B:ASP56 4.8 13.9 1.0 N B:THR49 4.8 11.8 1.0 C B:ILE55 4.8 11.9 1.0 CB B:PHE54 4.9 12.1 1.0 C B:ASP52 5.0 15.1 1.0

P.Verdino, K.Westritschnig, R.Valenta, W.Keller. The Cross-Reactive Calcium-Binding Pollen Allergen, Phl P 7, Reveals A Novel Dimer Assembly Embo J. V. 21 5007 2002.
ISSN: ISSN 0261-4189
PubMed: 12356717
DOI: 10.1093/EMBOJ/CDF526