Calcium in PDB 3l2y: The Structure of C-Reactive Protein Bound to Phosphoethanolamine

The structure of The Structure of C-Reactive Protein Bound to Phosphoethanolamine, PDB code: 3l2y was solved by H.Mikolajek, S.E.Kolstoe, S.P.Wood, M.B.Pepys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	124.53 / 2.70
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	278.448, 278.448, 92.111, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 24.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Calcium atom in the The Structure of C-Reactive Protein Bound to Phosphoethanolamine (pdb code 3l2y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 40 binding sites of Calcium where determined in the The Structure of C-Reactive Protein Bound to Phosphoethanolamine, PDB code: 3l2y:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 40 in the The Structure of C-Reactive Protein Bound to Phosphoethanolamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of C-Reactive Protein Bound to Phosphoethanolamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:47.9 occ:1.00 O1 A:OPE550 2.4 51.1 1.0 O A:GLN139 2.4 45.2 1.0 OD1 A:ASN61 2.5 53.9 1.0 OE1 A:GLU138 2.6 49.4 1.0 OD1 A:ASP140 2.6 52.2 1.0 OE2 A:GLU138 2.7 56.8 1.0 OD2 A:ASP60 2.7 59.8 1.0 CD A:GLU138 2.9 55.5 1.0 CG A:ASN61 3.3 50.5 1.0 ND2 A:ASN61 3.4 41.9 1.0 C A:GLN139 3.5 55.1 1.0 O2 A:OPE550 3.5 28.2 1.0 CG A:ASP60 3.6 61.9 1.0 P A:OPE550 3.6 54.1 1.0 CG A:ASP140 3.8 57.4 1.0 CA A:ASP140 3.8 55.4 1.0 CA A:CA302 3.9 53.3 1.0 N A:ASP140 4.0 52.4 1.0 CB A:ASP60 4.1 46.5 1.0 CB A:ASP140 4.4 54.4 1.0 CG A:GLU138 4.4 53.9 1.0 OD1 A:ASP60 4.5 71.1 1.0 O4 A:OPE550 4.5 41.2 1.0 O A:ASP60 4.5 51.8 1.0 O3 A:OPE550 4.5 47.0 1.0 C A:ASP60 4.6 51.2 1.0 CA A:GLN139 4.7 48.7 1.0 N A:GLN139 4.7 50.4 1.0 CB A:ASN61 4.7 37.8 1.0 CA A:OPE550 4.8 42.3 1.0 OD2 A:ASP140 4.8 64.6 1.0 N A:ASN61 4.9 47.2 1.0 C A:ASP140 4.9 58.3 1.0

Calcium binding site 2 out of 40 in the The Structure of C-Reactive Protein Bound to Phosphoethanolamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of C-Reactive Protein Bound to Phosphoethanolamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:53.3 occ:1.00 O2 A:OPE550 2.3 28.2 1.0 OD1 A:ASP140 2.5 52.2 1.0 OE1 A:GLU138 2.6 49.4 1.0 OE2 A:GLU147 2.6 66.9 1.0 OE1 A:GLN150 2.6 43.3 1.0 OD2 A:ASP140 2.6 64.6 1.0 CG A:ASP140 2.8 57.4 1.0 CD A:GLU147 3.5 77.1 1.0 CG A:GLU147 3.6 59.8 1.0 CD A:GLN150 3.6 49.7 1.0 P A:OPE550 3.7 54.1 1.0 CD A:GLU138 3.8 55.5 1.0 CA A:CA301 3.9 47.9 1.0 NE2 A:GLN150 4.1 53.7 1.0 O1 A:OPE550 4.1 51.1 1.0 CB A:ASP140 4.2 54.4 1.0 O4 A:OPE550 4.3 41.2 1.0 O A:GLU138 4.3 53.5 1.0 CB A:GLU147 4.3 57.1 1.0 CB A:GLU138 4.4 46.9 1.0 CG A:GLU138 4.4 53.9 1.0 OE1 A:GLU147 4.6 81.2 1.0 O3 A:OPE550 4.7 47.0 1.0 OE2 A:GLU138 4.7 56.8 1.0 O A:GLN139 4.8 45.2 1.0 C A:GLU138 4.8 54.2 1.0 N A:ASP140 4.8 52.4 1.0 CA A:ASP140 4.8 55.4 1.0 C A:GLN139 4.9 55.1 1.0 O A:ASN145 4.9 54.0 1.0 CG A:GLN150 4.9 53.6 1.0 N A:GLU147 5.0 58.4 1.0

Calcium binding site 3 out of 40 in the The Structure of C-Reactive Protein Bound to Phosphoethanolamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of C-Reactive Protein Bound to Phosphoethanolamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:42.0 occ:1.00 OE1 B:GLU138 2.5 46.2 1.0 O3 B:OPE950 2.5 37.0 1.0 OD1 B:ASN61 2.5 57.7 1.0 O B:GLN139 2.6 45.3 1.0 OE2 B:GLU138 2.6 55.8 1.0 OD1 B:ASP140 2.7 53.9 1.0 OD2 B:ASP60 2.8 43.5 1.0 CD B:GLU138 2.9 53.2 1.0 CG B:ASN61 3.3 48.8 1.0 ND2 B:ASN61 3.3 42.5 1.0 P B:OPE950 3.5 44.4 1.0 O1 B:OPE950 3.6 50.2 1.0 C B:GLN139 3.6 50.9 1.0 CG B:ASP60 3.7 59.3 1.0 CG B:ASP140 3.9 61.3 1.0 CA B:CA302 3.9 39.4 1.0 CA B:ASP140 4.0 51.1 1.0 O4 B:OPE950 4.1 30.7 1.0 N B:ASP140 4.2 50.8 1.0 CB B:ASP60 4.3 45.3 1.0 CG B:GLU138 4.3 47.5 1.0 CB B:ASP140 4.6 60.3 1.0 CA B:OPE950 4.6 35.6 1.0 OD1 B:ASP60 4.6 60.2 1.0 O B:ASP60 4.7 48.8 1.0 CB B:ASN61 4.7 38.7 1.0 C B:ASP60 4.8 53.0 1.0 N B:GLN139 4.8 44.6 1.0 OD2 B:ASP140 4.8 69.5 1.0 CA B:GLN139 4.8 49.4 1.0 O2 B:OPE950 4.8 35.4 1.0

Calcium binding site 4 out of 40 in the The Structure of C-Reactive Protein Bound to Phosphoethanolamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structure of C-Reactive Protein Bound to Phosphoethanolamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:39.4 occ:1.00 OE1 B:GLU138 2.5 46.2 1.0 OE1 B:GLN150 2.5 47.0 1.0 O1 B:OPE950 2.5 50.2 1.0 OD1 B:ASP140 2.6 53.9 1.0 OD2 B:ASP140 2.7 69.5 1.0 OE2 B:GLU147 2.7 68.7 1.0 CG B:ASP140 2.9 61.3 1.0 CD B:GLU147 3.5 75.4 1.0 CD B:GLN150 3.6 50.1 1.0 CG B:GLU147 3.6 64.1 1.0 CD B:GLU138 3.6 53.2 1.0 P B:OPE950 3.8 44.4 1.0 CA B:CA301 3.9 42.0 1.0 O B:GLU138 4.0 56.5 1.0 NE2 B:GLN150 4.1 54.4 1.0 CB B:GLU138 4.2 43.8 1.0 CG B:GLU138 4.2 47.5 1.0 CB B:GLU147 4.2 52.1 1.0 O3 B:OPE950 4.3 37.0 1.0 CB B:ASP140 4.3 60.3 1.0 O4 B:OPE950 4.3 30.7 1.0 C B:GLU138 4.6 48.8 1.0 O B:GLN139 4.6 45.3 1.0 OE2 B:GLU138 4.7 55.8 1.0 OE1 B:GLU147 4.7 79.9 1.0 C B:GLN139 4.8 50.9 1.0 N B:ASP140 4.8 50.8 1.0 N B:GLU147 4.8 57.1 1.0 CG B:GLN150 4.8 46.8 1.0 O B:ASN145 4.8 56.6 1.0 CA B:ASP140 4.9 51.1 1.0 O2 B:OPE950 5.0 35.4 1.0

Calcium binding site 5 out of 40 in the The Structure of C-Reactive Protein Bound to Phosphoethanolamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Structure of C-Reactive Protein Bound to Phosphoethanolamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:42.0 occ:1.00 O2 C:OPE650 2.3 42.3 1.0 O C:GLN139 2.4 40.7 1.0 OD1 C:ASN61 2.4 47.4 1.0 OE1 C:GLU138 2.6 45.4 1.0 OD2 C:ASP60 2.6 50.2 1.0 OE2 C:GLU138 2.6 58.2 1.0 OD1 C:ASP140 2.7 52.3 1.0 CD C:GLU138 3.0 47.5 1.0 CG C:ASN61 3.3 48.6 1.0 ND2 C:ASN61 3.4 36.1 1.0 C C:GLN139 3.5 52.6 1.0 CG C:ASP60 3.5 57.5 1.0 P C:OPE650 3.6 36.2 1.0 O3 C:OPE650 3.7 43.9 1.0 CA C:ASP140 3.8 46.8 1.0 CG C:ASP140 3.8 53.1 1.0 CB C:ASP60 4.0 46.0 1.0 N C:ASP140 4.0 46.0 1.0 CA C:CA302 4.1 43.6 1.0 O1 C:OPE650 4.4 37.1 1.0 CB C:ASP140 4.4 48.5 1.0 O C:ASP60 4.4 49.2 1.0 CG C:GLU138 4.5 40.4 1.0 OD1 C:ASP60 4.5 58.4 1.0 C C:ASP60 4.5 51.5 1.0 CA C:GLN139 4.6 44.8 1.0 N C:GLN139 4.7 38.8 1.0 CB C:ASN61 4.7 42.3 1.0 O4 C:OPE650 4.7 65.0 1.0 OD2 C:ASP140 4.8 68.5 1.0 NH1 I:ARG58 4.8 62.5 1.0 NH2 I:ARG58 4.8 0.7 1.0 N C:ASN61 4.8 46.1 1.0 CA C:OPE650 4.9 40.5 1.0 C C:ASP140 4.9 48.8 1.0 CA C:ASP60 5.0 50.3 1.0

Calcium binding site 6 out of 40 in the The Structure of C-Reactive Protein Bound to Phosphoethanolamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Structure of C-Reactive Protein Bound to Phosphoethanolamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:43.6 occ:1.00 O3 C:OPE650 2.4 43.9 1.0 O C:HOH212 2.4 51.7 1.0 OE1 C:GLN150 2.5 42.0 1.0 OE1 C:GLU138 2.6 45.4 1.0 OE2 C:GLU147 2.6 64.4 1.0 OD1 C:ASP140 2.6 52.3 1.0 OD2 C:ASP140 2.8 68.5 1.0 CG C:ASP140 3.0 53.1 1.0 CD C:GLU147 3.4 72.5 1.0 CG C:GLU147 3.5 63.4 1.0 CD C:GLN150 3.5 45.6 1.0 P C:OPE650 3.7 36.2 1.0 CD C:GLU138 3.7 47.5 1.0 NE2 C:GLN150 4.0 55.6 1.0 O2 C:OPE650 4.0 42.3 1.0 CA C:CA301 4.1 42.0 1.0 CB C:GLU147 4.2 47.0 1.0 O C:GLU138 4.3 54.6 1.0 CB C:GLU138 4.3 43.9 1.0 CG C:GLU138 4.3 40.4 1.0 CB C:ASP140 4.4 48.5 1.0 OE1 C:GLU147 4.6 75.6 1.0 O4 C:OPE650 4.6 65.0 1.0 O C:HOH218 4.7 48.1 1.0 O1 C:OPE650 4.7 37.1 1.0 OE2 C:GLU138 4.7 58.2 1.0 CG C:GLN150 4.8 38.0 1.0 C C:GLU138 4.8 48.7 1.0 O C:GLN139 4.9 40.7 1.0 N C:GLU147 4.9 48.7 1.0 O C:ASN145 4.9 40.0 1.0 N C:ASP140 4.9 46.0 1.0 C C:GLN139 5.0 52.6 1.0 CA C:ASP140 5.0 46.8 1.0

Calcium binding site 7 out of 40 in the The Structure of C-Reactive Protein Bound to Phosphoethanolamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Structure of C-Reactive Protein Bound to Phosphoethanolamine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:48.3 occ:1.00 OE1 D:GLU138 2.5 45.9 1.0 OD1 D:ASP140 2.5 48.5 1.0 O D:GLN139 2.5 53.3 1.0 OD1 D:ASN61 2.6 56.5 1.0 OE2 D:GLU138 2.7 54.3 1.0 OD2 D:ASP60 2.8 47.8 1.0 O1 D:OPE450 2.8 33.9 1.0 CD D:GLU138 2.9 56.9 1.0 O3 D:OPE450 3.2 48.9 1.0 CG D:ASN61 3.4 50.4 1.0 ND2 D:ASN61 3.5 39.0 1.0 C D:GLN139 3.5 58.5 1.0 P D:OPE450 3.6 47.6 1.0 CG D:ASP140 3.7 58.0 1.0 CG D:ASP60 3.7 56.5 1.0 CA D:ASP140 3.8 52.3 1.0 CA D:CA302 4.0 46.9 1.0 N D:ASP140 4.1 52.1 1.0 CB D:ASP60 4.2 42.5 1.0 O4 D:OPE450 4.3 55.9 1.0 CB D:ASP140 4.4 50.6 1.0 CG D:GLU138 4.4 60.4 1.0 OD1 D:ASP60 4.6 68.4 1.0 CA D:OPE450 4.6 38.6 1.0 OD2 D:ASP140 4.6 65.1 1.0 O D:ASP60 4.7 60.9 1.0 CA D:GLN139 4.7 53.4 1.0 C D:ASP60 4.8 55.4 1.0 N D:GLN139 4.8 45.2 1.0 CB D:ASN61 4.9 30.0 1.0 O2 D:OPE450 4.9 60.6 1.0 C D:ASP140 5.0 53.7 1.0

Calcium binding site 8 out of 40 in the The Structure of C-Reactive Protein Bound to Phosphoethanolamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Structure of C-Reactive Protein Bound to Phosphoethanolamine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:46.9 occ:1.00 OE1 D:GLN150 2.5 50.4 1.0 OE1 D:GLU138 2.6 45.9 1.0 O1 D:OPE450 2.6 33.9 1.0 OE2 D:GLU147 2.6 73.2 1.0 OD1 D:ASP140 2.7 48.5 1.0 OD2 D:ASP140 2.7 65.1 1.0 CG D:ASP140 2.9 58.0 1.0 CD D:GLU147 3.4 81.6 1.0 CG D:GLU147 3.4 64.8 1.0 CD D:GLN150 3.6 50.2 1.0 CD D:GLU138 3.8 56.9 1.0 CA D:CA301 4.0 48.3 1.0 P D:OPE450 4.0 47.6 1.0 O D:GLU138 4.0 53.0 1.0 CB D:GLU147 4.1 65.1 1.0 NE2 D:GLN150 4.2 61.6 1.0 CB D:GLU138 4.2 48.4 1.0 CB D:ASP140 4.2 50.6 1.0 CG D:GLU138 4.3 60.4 1.0 O4 D:OPE450 4.4 55.9 1.0 O2 D:OPE450 4.5 60.6 1.0 C D:GLU138 4.6 48.9 1.0 OE1 D:GLU147 4.6 83.0 1.0 N D:GLU147 4.6 62.5 1.0 O D:ASN145 4.7 59.2 1.0 N D:ASP140 4.8 52.1 1.0 OE2 D:GLU138 4.8 54.3 1.0 CG D:GLN150 4.8 52.9 1.0 O D:GLN139 4.8 53.3 1.0 C D:GLN139 4.8 58.5 1.0 CA D:ASP140 4.8 52.3 1.0 O3 D:OPE450 5.0 48.9 1.0

Calcium binding site 9 out of 40 in the The Structure of C-Reactive Protein Bound to Phosphoethanolamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The Structure of C-Reactive Protein Bound to Phosphoethanolamine within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca301 b:47.5 occ:1.00 OE1 E:GLU138 2.5 49.5 1.0 OD1 E:ASN61 2.5 47.6 1.0 O E:GLN139 2.5 49.5 1.0 OD1 E:ASP140 2.6 49.0 1.0 OD2 E:ASP60 2.7 53.2 1.0 OE2 E:GLU138 2.8 55.5 1.0 O2 E:OPE350 2.8 37.5 1.0 CD E:GLU138 2.9 56.2 1.0 O3 E:OPE350 3.1 38.5 1.0 CG E:ASN61 3.3 47.8 1.0 ND2 E:ASN61 3.4 41.4 1.0 P E:OPE350 3.6 56.1 1.0 C E:GLN139 3.6 57.2 1.0 CG E:ASP60 3.7 59.1 1.0 CG E:ASP140 3.8 62.2 1.0 CA E:ASP140 3.9 54.7 1.0 CA E:CA302 4.1 46.7 1.0 N E:ASP140 4.1 57.7 1.0 CB E:ASP60 4.2 42.9 1.0 CG E:GLU138 4.4 49.8 1.0 CB E:ASP140 4.4 56.2 1.0 O4 E:OPE350 4.5 56.6 1.0 OD1 E:ASP60 4.6 63.6 1.0 O E:ASP60 4.6 52.9 1.0 CA E:OPE350 4.7 48.1 1.0 O1 E:OPE350 4.7 76.9 1.0 C E:ASP60 4.7 54.8 1.0 OD2 E:ASP140 4.7 72.2 1.0 CA E:GLN139 4.8 49.9 1.0 CB E:ASN61 4.8 39.0 1.0 N E:GLN139 4.8 43.4 1.0

Calcium binding site 10 out of 40 in the The Structure of C-Reactive Protein Bound to Phosphoethanolamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of The Structure of C-Reactive Protein Bound to Phosphoethanolamine within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca302 b:46.7 occ:1.00 O3 E:OPE350 2.4 38.5 1.0 OE2 E:GLU147 2.5 67.7 1.0 OE1 E:GLN150 2.6 50.9 1.0 OD2 E:ASP140 2.6 72.2 1.0 OD1 E:ASP140 2.6 49.0 1.0 OE1 E:GLU138 2.7 49.5 1.0 CG E:ASP140 2.9 62.2 1.0 CD E:GLU147 3.3 73.8 1.0 CG E:GLU147 3.4 65.3 1.0 CD E:GLN150 3.6 45.3 1.0 CD E:GLU138 3.9 56.2 1.0 P E:OPE350 3.9 56.1 1.0 CB E:GLU147 4.1 54.5 1.0 CA E:CA301 4.1 47.5 1.0 NE2 E:GLN150 4.1 59.3 1.0 O E:GLU138 4.1 49.4 1.0 CB E:ASP140 4.2 56.2 1.0 CB E:GLU138 4.3 41.1 1.0 CG E:GLU138 4.4 49.8 1.0 OE1 E:GLU147 4.5 76.9 1.0 O1 E:OPE350 4.5 76.9 1.0 N E:GLU147 4.7 53.2 1.0 O4 E:OPE350 4.7 56.6 1.0 O2 E:OPE350 4.7 37.5 1.0 C E:GLU138 4.7 47.8 1.0 O E:ASN145 4.7 51.2 1.0 CG E:GLN150 4.8 40.7 1.0 N E:ASP140 4.8 57.7 1.0 O E:GLN139 4.8 49.5 1.0 C E:GLN139 4.9 57.2 1.0 CA E:ASP140 4.9 54.7 1.0 OE2 E:GLU138 4.9 55.5 1.0

H.Mikolajek, S.E.Kolstoe, V.E.Pye, P.Mangione, M.B.Pepys, S.P.Wood. Structural Basis of Ligand Specificity in the Human Pentraxins, C-Reactive Protein and Serum Amyloid P Component. J.Mol.Recognit. V. 24 371 2011.
ISSN: ISSN 0952-3499
PubMed: 21360619
DOI: 10.1002/JMR.1090