Calcium in PDB 3flt: Crystal Structure of Pe-Bound Octameric Sap-Like Pentraxin From Limulus Polyphemus

The structure of Crystal Structure of Pe-Bound Octameric Sap-Like Pentraxin From Limulus Polyphemus, PDB code: 3flt 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)	60.68 / 2.70
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	172.390, 172.390, 98.370, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 24.3

The binding sites of Calcium atom in the Crystal Structure of Pe-Bound Octameric Sap-Like Pentraxin From Limulus Polyphemus (pdb code 3flt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Pe-Bound Octameric Sap-Like Pentraxin From Limulus Polyphemus, PDB code: 3flt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Pe-Bound 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 Pe-Bound Octameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:28.9 occ:1.00 O A:GLN146 2.1 30.7 1.0 OD1 A:ASN60 2.4 22.2 1.0 OE1 A:GLU145 2.4 33.0 1.0 O2 A:OPE400 2.5 39.5 1.0 OE2 A:GLU145 2.5 35.5 1.0 OD2 A:ASP59 2.6 32.1 1.0 OD1 A:ASP147 2.7 27.0 1.0 CD A:GLU145 2.8 33.4 1.0 C A:GLN146 3.2 29.6 1.0 CG A:ASN60 3.5 23.1 1.0 CA A:ASP147 3.6 30.0 1.0 CG A:ASP59 3.6 32.8 1.0 CG A:ASP147 3.7 28.2 1.0 N A:ASP147 3.8 29.4 1.0 P A:OPE400 3.8 37.5 1.0 CA A:CA302 3.8 27.4 1.0 ND2 A:ASN60 3.9 21.0 1.0 O A:ASP59 4.0 26.8 1.0 O1 A:OPE400 4.1 37.2 1.0 CB A:ASP59 4.1 29.6 1.0 CB A:ASP147 4.2 28.3 1.0 C A:ASP59 4.3 26.7 1.0 CG A:GLU145 4.3 31.2 1.0 CA A:GLN146 4.4 29.4 1.0 N A:GLN146 4.5 28.9 1.0 CA A:OPE400 4.6 45.8 1.0 OD2 A:ASP147 4.6 32.3 1.0 OD1 A:ASP59 4.6 34.4 1.0 C A:GLU145 4.7 28.8 1.0 O3 A:OPE400 4.7 39.0 1.0 N A:ASN60 4.8 24.2 1.0 O A:GLU145 4.8 30.4 1.0 CB A:ASN60 4.8 23.8 1.0 O4 A:OPE400 4.8 42.2 1.0 C A:ASP147 4.8 30.1 1.0 CA A:ASP59 4.9 28.6 1.0 CA A:ASN60 4.9 24.8 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Pe-Bound 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 Pe-Bound Octameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:27.4 occ:1.00 OE1 A:GLU157 2.3 31.8 1.0 O1 A:OPE400 2.3 37.2 1.0 OE1 A:GLU145 2.4 33.0 1.0 OD1 A:ASP147 2.5 27.0 1.0 OD2 A:ASP147 2.5 32.3 1.0 OE2 A:GLU154 2.7 35.2 1.0 CG A:ASP147 2.8 28.2 1.0 CD A:GLU157 3.4 32.2 1.0 CD A:GLU154 3.5 34.5 1.0 CG A:GLU154 3.5 34.0 1.0 CD A:GLU145 3.6 33.4 1.0 P A:OPE400 3.6 37.5 1.0 O2 A:OPE400 3.7 39.5 1.0 O A:GLU145 3.7 30.4 1.0 CA A:CA301 3.8 28.9 1.0 CA A:CA303 3.9 47.0 1.0 OE2 A:GLU157 4.0 36.6 1.0 CB A:ASP147 4.2 28.3 1.0 CB A:GLU145 4.2 27.6 1.0 CG A:GLU145 4.3 31.2 1.0 O A:GLY152 4.3 28.0 1.0 CA A:OPE400 4.4 45.8 1.0 C A:GLU145 4.5 28.8 1.0 CB A:GLU154 4.5 30.6 1.0 OE2 A:GLU145 4.5 35.5 1.0 O A:GLN146 4.5 30.7 1.0 O3 A:OPE400 4.6 39.0 1.0 O4 A:OPE400 4.6 42.2 1.0 CG A:GLU157 4.7 31.7 1.0 C A:GLN146 4.7 29.6 1.0 OE1 A:GLU154 4.7 37.1 1.0 CA A:ASP147 4.8 30.0 1.0 N A:ASP147 4.8 29.4 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Pe-Bound 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 Pe-Bound Octameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:47.0 occ:1.00 OE2 A:GLU154 2.3 35.2 1.0 O1 A:OPE400 2.6 37.2 1.0 OE2 A:GLU157 3.1 36.6 1.0 CD A:GLU154 3.2 34.5 1.0 OE1 A:GLU154 3.5 37.1 1.0 CD A:GLU157 3.5 32.2 1.0 OE1 A:GLU157 3.5 31.8 1.0 P A:OPE400 3.6 37.5 1.0 O4 A:OPE400 3.9 42.2 1.0 O3 A:OPE400 3.9 39.0 1.0 CA A:CA302 3.9 27.4 1.0 NE2 A:GLN156 4.3 38.1 1.0 CA A:OPE400 4.4 45.8 1.0 CG A:GLU154 4.5 34.0 1.0 CG A:GLU157 4.7 31.7 1.0 O2 A:OPE400 4.9 39.5 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Pe-Bound 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 Pe-Bound Octameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:31.6 occ:1.00 O B:GLN146 2.3 33.2 1.0 OD1 B:ASN60 2.3 30.4 1.0 O2 B:OPE400 2.4 42.3 1.0 OD2 B:ASP59 2.5 32.9 1.0 OD1 B:ASP147 2.6 35.5 1.0 OE2 B:GLU145 2.6 40.5 1.0 OE1 B:GLU145 2.7 39.6 1.0 CD B:GLU145 3.0 38.1 1.0 C B:GLN146 3.3 32.5 1.0 CG B:ASN60 3.4 29.4 1.0 CG B:ASP59 3.4 35.2 1.0 CA B:ASP147 3.5 34.2 1.0 CG B:ASP147 3.6 36.7 1.0 P B:OPE400 3.8 40.3 1.0 N B:ASP147 3.8 32.5 1.0 ND2 B:ASN60 3.8 26.5 1.0 CA B:CA302 4.0 35.0 1.0 CB B:ASP59 4.0 33.1 1.0 O B:ASP59 4.0 30.1 1.0 CB B:ASP147 4.1 34.5 1.0 O1 B:OPE400 4.2 41.3 1.0 C B:ASP59 4.3 30.7 1.0 OD1 B:ASP59 4.3 35.0 1.0 O3 B:OPE400 4.4 39.8 1.0 OD2 B:ASP147 4.5 40.8 1.0 CG B:GLU145 4.5 35.7 1.0 CA B:GLN146 4.6 31.4 1.0 CB B:ASN60 4.7 29.5 1.0 N B:ASN60 4.7 29.1 1.0 N B:GLN146 4.7 31.3 1.0 C B:ASP147 4.7 34.5 1.0 CA B:ASP59 4.8 31.7 1.0 CA B:ASN60 4.9 28.9 1.0 C B:GLU145 4.9 31.8 1.0 O4 B:OPE400 4.9 43.9 1.0 O B:GLU145 4.9 32.7 1.0 CA B:OPE400 5.0 48.2 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Pe-Bound 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 5 of Crystal Structure of Pe-Bound Octameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:35.0 occ:1.00 OE1 B:GLU157 2.2 41.4 1.0 O1 B:OPE400 2.3 41.3 1.0 OD2 B:ASP147 2.4 40.8 1.0 OD1 B:ASP147 2.4 35.5 1.0 OE1 B:GLU145 2.4 39.6 1.0 CG B:ASP147 2.7 36.7 1.0 OE1 B:GLU154 3.1 38.6 1.0 CD B:GLU154 3.2 38.2 1.0 CD B:GLU157 3.3 40.5 1.0 P B:OPE400 3.6 40.3 1.0 CD B:GLU145 3.6 38.1 1.0 CG B:GLU154 3.7 37.8 1.0 OE2 B:GLU154 3.7 40.1 1.0 O2 B:OPE400 3.7 42.3 1.0 CA B:CA303 3.8 43.4 1.0 OE2 B:GLU157 3.8 42.0 1.0 O B:GLU145 4.0 32.7 1.0 CA B:CA301 4.0 31.6 1.0 CB B:ASP147 4.2 34.5 1.0 CG B:GLU145 4.4 35.7 1.0 CB B:GLU145 4.4 32.2 1.0 CB B:GLU154 4.4 34.6 1.0 O B:GLY152 4.5 29.4 1.0 O3 B:OPE400 4.5 39.8 1.0 OE2 B:GLU145 4.6 40.5 1.0 CG B:GLU157 4.6 38.5 1.0 C B:GLU145 4.7 31.8 1.0 CA B:OPE400 4.7 48.2 1.0 O B:GLN146 4.8 33.2 1.0 O4 B:OPE400 4.8 43.9 1.0 CA B:ASP147 4.9 34.2 1.0 C B:GLN146 4.9 32.5 1.0 N B:ASP147 5.0 32.5 1.0 CB B:GLU157 5.0 35.2 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Pe-Bound 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 6 of Crystal Structure of Pe-Bound Octameric Sap-Like Pentraxin From Limulus Polyphemus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:43.4 occ:1.00 O1 B:OPE400 2.5 41.3 1.0 OE2 B:GLU154 2.7 40.1 1.0 OE1 B:GLU154 2.8 38.6 1.0 OE2 B:GLU157 3.0 42.0 1.0 CD B:GLU154 3.1 38.2 1.0 CD B:GLU157 3.5 40.5 1.0 OE1 B:GLU157 3.6 41.4 1.0 P B:OPE400 3.7 40.3 1.0 CA B:CA302 3.8 35.0 1.0 O4 B:OPE400 4.0 43.9 1.0 O3 B:OPE400 4.1 39.8 1.0 CA B:OPE400 4.3 48.2 1.0 NE2 B:GLN156 4.5 48.8 1.0 CG B:GLU154 4.6 37.8 1.0 CG B:GLU157 4.7 38.5 1.0 O2 B:OPE400 4.9 42.3 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