Calcium in PDB 3flr: Crystal Structure of Native Octameric Sap-Like Pentraxin From Limulus Polyphemus

The structure of Crystal Structure of Native Octameric Sap-Like Pentraxin From Limulus Polyphemus, PDB code: 3flr was solved by A.K.Shrive, T.J.Greenhough, P.B.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.90 / 3.00
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	173.330, 173.330, 98.810, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 23.2

The binding sites of Calcium atom in the Crystal Structure of Native Octameric Sap-Like Pentraxin From Limulus Polyphemus (pdb code 3flr). 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 Native Octameric Sap-Like Pentraxin From Limulus Polyphemus, PDB code: 3flr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Native Octameric Sap-Like Pentraxin From Limulus Polyphemus


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 Native Octameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:24.0 occ:1.00 OE2 A:GLU145 2.3 37.5 1.0 OD2 A:ASP59 2.4 34.0 1.0 OD1 A:ASN60 2.4 29.2 1.0 O A:GLN146 2.4 33.4 1.0 OD1 A:ASP147 2.5 30.2 1.0 OE1 A:GLU145 2.7 36.8 1.0 CD A:GLU145 2.8 35.4 1.0 CG A:ASP59 3.4 35.6 1.0 CG A:ASN60 3.5 29.9 1.0 C A:GLN146 3.5 33.8 1.0 CG A:ASP147 3.6 30.5 1.0 CA A:ASP147 3.8 33.1 1.0 CA A:CA302 3.9 31.6 1.0 ND2 A:ASN60 3.9 30.7 1.0 O A:ASP59 3.9 31.7 1.0 N A:ASP147 4.0 33.6 1.0 CB A:ASP59 4.1 34.6 1.0 OD1 A:ASP59 4.2 37.1 1.0 CG A:GLU145 4.3 34.5 1.0 CB A:ASP147 4.3 31.5 1.0 C A:ASP59 4.3 31.7 1.0 OD2 A:ASP147 4.6 31.9 1.0 CA A:GLN146 4.7 34.0 1.0 N A:GLN146 4.7 34.2 1.0 CB A:ASN60 4.7 29.4 1.0 N A:ASN60 4.8 29.7 1.0 CD1 A:ILE63 4.9 28.2 1.0 C A:GLU145 4.9 34.4 1.0 CA A:ASP59 4.9 33.3 1.0 CA A:ASN60 5.0 28.8 1.0 O A:GLU145 5.0 37.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Native Octameric Sap-Like Pentraxin From Limulus Polyphemus


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 Native Octameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:31.6 occ:1.00 OE2 A:GLU157 2.0 29.6 1.0 OE1 A:GLU145 2.3 36.8 1.0 OD2 A:ASP147 2.5 31.9 1.0 OD1 A:ASP147 2.6 30.2 1.0 CG A:ASP147 2.8 30.5 1.0 OE1 A:GLU154 3.1 41.2 1.0 CD A:GLU157 3.2 28.6 1.0 CD A:GLU145 3.5 35.4 1.0 CG A:GLU154 3.7 38.2 1.0 CD A:GLU154 3.7 39.2 1.0 CA A:CA301 3.9 24.0 1.0 OE1 A:GLU157 3.9 29.3 1.0 O A:GLU145 4.1 37.1 1.0 CG A:GLU157 4.3 27.6 1.0 CB A:ASP147 4.3 31.5 1.0 CB A:GLU154 4.3 38.1 1.0 CG A:GLU145 4.4 34.5 1.0 OE2 A:GLU145 4.4 37.5 1.0 O A:GLY152 4.5 33.6 1.0 CB A:GLU145 4.6 33.0 1.0 O A:GLN146 4.8 33.4 1.0 OE2 A:GLU154 4.8 39.5 1.0 C A:GLU145 4.8 34.4 1.0 CB A:GLU157 5.0 27.8 1.0 C A:GLN146 5.0 33.8 1.0 CA A:ASP147 5.0 33.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Native Octameric Sap-Like Pentraxin From Limulus Polyphemus


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 Native Octameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:35.5 occ:1.00 OD1 B:ASN60 2.3 34.6 1.0 OD1 B:ASP147 2.4 42.6 1.0 O B:GLN146 2.4 34.9 1.0 OD2 B:ASP59 2.5 37.4 1.0 OE1 B:GLU145 2.6 42.6 1.0 OE2 B:GLU145 2.7 45.0 1.0 CD B:GLU145 3.0 42.1 1.0 CG B:ASP59 3.5 37.5 1.0 CG B:ASN60 3.5 34.9 1.0 C B:GLN146 3.5 35.5 1.0 CG B:ASP147 3.6 40.3 1.0 CA B:ASP147 3.7 36.6 1.0 O B:ASP59 3.9 34.3 1.0 CA B:CA302 4.0 47.5 1.0 ND2 B:ASN60 4.0 35.4 1.0 N B:ASP147 4.0 36.0 1.0 CB B:ASP59 4.1 36.2 1.0 CB B:ASP147 4.2 37.6 1.0 C B:ASP59 4.3 34.2 1.0 OD1 B:ASP59 4.3 40.0 1.0 CG B:GLU145 4.5 39.4 1.0 OD2 B:ASP147 4.6 40.9 1.0 CB B:ASN60 4.7 33.5 1.0 CA B:GLN146 4.7 35.8 1.0 N B:ASN60 4.8 32.5 1.0 N B:GLN146 4.8 36.1 1.0 CA B:ASP59 4.9 35.4 1.0 CA B:ASN60 4.9 31.9 1.0 CD1 B:ILE63 5.0 23.4 1.0 C B:GLU145 5.0 36.7 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Native Octameric Sap-Like Pentraxin From Limulus Polyphemus


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 Native Octameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:47.5 occ:1.00 OE1 B:GLU157 2.1 41.9 1.0 OD2 B:ASP147 2.3 40.9 1.0 OD1 B:ASP147 2.4 42.6 1.0 CG B:ASP147 2.6 40.3 1.0 OE1 B:GLU145 2.7 42.6 1.0 OE1 B:GLU154 2.9 49.1 1.0 CD B:GLU157 3.0 39.0 1.0 OE2 B:GLU157 3.1 38.7 1.0 CD B:GLU154 3.3 47.4 1.0 CG B:GLU154 3.5 45.0 1.0 CD B:GLU145 3.9 42.1 1.0 CA B:CA301 4.0 35.5 1.0 CB B:ASP147 4.2 37.6 1.0 OE2 B:GLU154 4.2 48.4 1.0 O B:GLU145 4.2 38.9 1.0 CB B:GLU154 4.3 40.9 1.0 CG B:GLU157 4.4 38.4 1.0 O B:GLY152 4.5 35.9 1.0 CG B:GLU145 4.7 39.4 1.0 CB B:GLU145 4.7 36.7 1.0 OE2 B:GLU145 4.8 45.0 1.0 O B:GLN146 4.8 34.9 1.0 C B:GLU145 5.0 36.7 1.0 CA B:ASP147 5.0 36.6 1.0

A.K.Shrive, I.Burns, H.T.Chou, H.Stahlberg, P.B.Armstrong, T.J.Greenhough. Crystal Structures of Limulus Sap-Like Pentraxin Reveal Two Molecular Aggregations. J.Mol.Biol. V. 386 1240 2009.
ISSN: ISSN 0022-2836
PubMed: 19452596