Calcium in PDB 4avt: Structure of Cphpc Bound to Serum Amyloid P Component

The structure of Structure of Cphpc Bound to Serum Amyloid P Component, PDB code: 4avt was solved by S.E.Kolstoe, A.Purvis, S.P.Wood, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.942 / 3.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	230.864, 230.864, 281.393, 90.00, 90.00, 90.00
R / Rfree (%)	18.89 / 19.74

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Calcium atom in the Structure of Cphpc Bound to Serum Amyloid P Component (pdb code 4avt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 20 binding sites of Calcium where determined in the Structure of Cphpc Bound to Serum Amyloid P Component, PDB code: 4avt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 20 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1205 b:0.5 occ:1.00 OE2 A:GLU136 2.2 88.1 1.0 O2 B:GHE1207 2.3 0.2 1.0 OD1 A:ASP58 2.3 89.1 1.0 OD1 A:ASP138 2.4 98.8 1.0 O A:GLN137 2.4 0.4 1.0 OD1 A:ASN59 2.4 85.0 1.0 OD2 A:ASP58 2.5 91.8 1.0 CG A:ASP58 2.7 91.8 1.0 CD A:GLU136 3.0 88.5 1.0 OE1 A:GLU136 3.0 89.9 1.0 CG A:ASP138 3.2 99.6 1.0 CG A:ASN59 3.3 87.2 1.0 C1 B:GHE1207 3.3 0.2 1.0 C A:GLN137 3.4 0.9 1.0 CA A:ASP138 3.5 0.3 1.0 ND2 A:ASN59 3.5 86.7 1.0 O1 B:GHE1207 3.7 0.2 1.0 CB A:ASP138 3.8 0.8 1.0 N A:ASP138 3.9 99.1 1.0 OD2 A:ASP138 4.0 0.3 1.0 CB A:ASP58 4.3 94.1 1.0 CA A:CA1206 4.3 0.6 1.0 CG A:GLU136 4.4 87.5 1.0 N A:ASN59 4.5 89.8 1.0 C2 B:GHE1207 4.6 0.2 1.0 CB A:ASN59 4.7 89.2 1.0 C A:ASP138 4.8 0.1 1.0 CA A:GLN137 4.8 0.3 1.0 N A:GLN137 4.9 0.9 1.0 C3 B:GHE1207 4.9 0.2 1.0

Calcium binding site 2 out of 20 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1206 b:0.6 occ:1.00 OD2 A:ASP138 2.0 0.3 1.0 OE1 A:GLN148 2.3 87.0 1.0 OD1 A:ASP138 2.5 98.8 1.0 O1 B:GHE1207 2.6 0.2 1.0 OE1 A:GLU136 2.6 89.9 1.0 CG A:ASP138 2.6 99.6 1.0 CD A:GLN148 3.4 85.8 1.0 C1 B:GHE1207 3.6 0.2 1.0 CB A:ASP145 3.8 0.4 1.0 CD A:GLU136 3.8 88.5 1.0 O2 B:GHE1207 3.9 0.2 1.0 NE2 A:GLN148 3.9 85.3 1.0 CB A:ASP138 4.1 0.8 1.0 OD2 A:ASP145 4.1 0.2 1.0 CA A:CA1205 4.3 0.5 1.0 C9 B:GHE1207 4.4 0.2 1.0 CG A:ASP145 4.5 0.1 1.0 O A:GLU136 4.6 90.9 1.0 OE2 A:GLU136 4.6 88.1 1.0 CG A:GLN148 4.6 85.5 1.0 CG A:GLU136 4.8 87.5 1.0 C10 B:GHE1207 4.8 0.2 1.0 CB A:GLU136 4.9 88.5 1.0 C2 B:GHE1207 4.9 0.2 1.0

Calcium binding site 3 out of 20 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1205 b:0.1 occ:1.00 OE2 B:GLU136 2.1 0.1 1.0 O16 B:GHE1207 2.2 0.2 1.0 OD1 B:ASN59 2.3 98.3 1.0 OD1 B:ASP58 2.4 0.8 1.0 OD1 B:ASP138 2.4 0.8 1.0 O B:GLN137 2.5 0.8 1.0 OD2 B:ASP58 2.5 0.8 1.0 CG B:ASP58 2.8 1.0 1.0 CD B:GLU136 2.8 0.1 1.0 OE1 B:GLU136 2.9 0.7 1.0 CG B:ASN59 3.2 99.6 1.0 CG B:ASP138 3.3 0.2 1.0 C16 B:GHE1207 3.4 0.2 1.0 ND2 B:ASN59 3.4 0.1 1.0 C B:GLN137 3.5 0.3 1.0 CA B:ASP138 3.6 0.3 1.0 CB B:ASP138 4.0 0.1 1.0 N B:ASP138 4.0 0.2 1.0 O17 B:GHE1207 4.1 0.2 1.0 OD2 B:ASP138 4.1 0.1 1.0 CG B:GLU136 4.3 0.5 1.0 CB B:ASP58 4.4 0.7 1.0 CA B:CA1206 4.4 0.2 1.0 C15 B:GHE1207 4.4 0.2 1.0 N B:ASN59 4.5 0.5 1.0 C14 B:GHE1207 4.5 0.2 1.0 CB B:ASN59 4.6 0.0 1.0 CA B:GLN137 4.8 0.7 1.0 N B:GLN137 4.9 0.3 1.0 C B:ASP138 4.9 0.2 1.0 CA B:ASN59 4.9 0.1 1.0

Calcium binding site 4 out of 20 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1206 b:0.2 occ:1.00 OD2 B:ASP138 2.0 0.1 1.0 OE1 B:GLN148 2.2 92.4 1.0 OE1 B:GLU136 2.6 0.7 1.0 OD1 B:ASP138 2.6 0.8 1.0 CG B:ASP138 2.7 0.2 1.0 O17 B:GHE1207 2.7 0.2 1.0 CD B:GLN148 3.4 89.3 1.0 C16 B:GHE1207 3.7 0.2 1.0 CB B:ASP145 3.7 0.0 1.0 O16 B:GHE1207 3.8 0.2 1.0 CD B:GLU136 3.8 0.1 1.0 NE2 B:GLN148 3.9 86.6 1.0 OD2 B:ASP145 4.1 0.3 1.0 CB B:ASP138 4.2 0.1 1.0 CA B:CA1205 4.4 0.1 1.0 CG B:ASP145 4.4 0.3 1.0 O B:GLU136 4.4 98.0 1.0 O6 B:GHE1207 4.4 0.2 1.0 CG B:GLN148 4.6 88.3 1.0 OE2 B:GLU136 4.7 0.1 1.0 CG B:GLU136 4.7 0.5 1.0 CB B:GLU136 4.8 96.8 1.0 N B:ASP145 4.9 98.3 1.0 CA B:ASP145 4.9 0.4 1.0

Calcium binding site 5 out of 20 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1205 b:0.1 occ:1.00 OE2 C:GLU136 2.1 76.7 1.0 O2 C:GHE1207 2.3 0.1 1.0 OD1 C:ASN59 2.4 82.2 1.0 OD1 C:ASP58 2.4 81.9 1.0 O C:GLN137 2.4 75.0 1.0 OD1 C:ASP138 2.5 86.6 1.0 OD2 C:ASP58 2.6 82.9 1.0 CD C:GLU136 2.8 76.7 1.0 CG C:ASP58 2.9 83.1 1.0 OE1 C:GLU136 2.9 77.2 1.0 CG C:ASN59 3.3 82.4 1.0 CG C:ASP138 3.3 86.7 1.0 C1 C:GHE1207 3.4 0.1 1.0 C C:GLN137 3.5 74.7 1.0 ND2 C:ASN59 3.5 82.9 1.0 CA C:ASP138 3.6 85.2 1.0 O1 C:GHE1207 3.9 0.1 1.0 N C:ASP138 4.0 84.6 1.0 CB C:ASP138 4.0 87.7 1.0 OD2 C:ASP138 4.1 87.5 1.0 CG C:GLU136 4.3 76.5 1.0 CA C:CA1206 4.3 0.2 1.0 CB C:ASP58 4.4 85.1 1.0 N C:ASN59 4.5 85.2 1.0 C2 C:GHE1207 4.5 0.1 1.0 CB C:ASN59 4.6 82.5 1.0 C3 C:GHE1207 4.7 0.1 1.0 CA C:GLN137 4.7 74.7 1.0 N C:GLN137 4.8 73.9 1.0 C C:ASP138 4.9 86.2 1.0 CA C:ASN59 4.9 83.2 1.0

Calcium binding site 6 out of 20 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1206 b:0.2 occ:1.00 OD2 C:ASP138 2.1 87.5 1.0 OE1 C:GLN148 2.1 70.8 1.0 O1 C:GHE1207 2.5 0.1 1.0 OE1 C:GLU136 2.5 77.2 1.0 OD1 C:ASP138 2.6 86.6 1.0 CG C:ASP138 2.7 86.7 1.0 CD C:GLN148 3.2 69.2 1.0 C1 C:GHE1207 3.5 0.1 1.0 CD C:GLU136 3.7 76.7 1.0 NE2 C:GLN148 3.8 68.7 1.0 CB C:ASP145 3.8 95.4 1.0 O2 C:GHE1207 3.8 0.1 1.0 OD2 C:ASP145 4.2 97.0 1.0 CB C:ASP138 4.2 87.7 1.0 CA C:CA1205 4.3 0.1 1.0 O C:GLU136 4.4 77.5 1.0 CG C:GLN148 4.5 68.2 1.0 CG C:ASP145 4.5 96.6 1.0 OE2 C:GLU136 4.6 76.7 1.0 CG C:GLU136 4.6 76.5 1.0 CB C:GLU136 4.7 75.9 1.0 C9 C:GHE1207 4.7 0.1 1.0 C2 C:GHE1207 4.8 0.1 1.0 N C:ASP145 5.0 96.3 1.0

Calcium binding site 7 out of 20 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1205 b:0.0 occ:1.00 OE2 D:GLU136 2.1 84.4 1.0 OD1 D:ASN59 2.4 88.7 1.0 OD1 D:ASP58 2.4 92.8 1.0 O16 C:GHE1207 2.4 0.1 1.0 O D:GLN137 2.4 83.1 1.0 OD1 D:ASP138 2.5 93.1 1.0 OD2 D:ASP58 2.7 93.9 1.0 CD D:GLU136 2.8 83.4 1.0 OE1 D:GLU136 2.9 83.7 1.0 CG D:ASP58 2.9 94.2 1.0 CG D:ASP138 3.2 92.8 1.0 CG D:ASN59 3.3 88.4 1.0 C16 C:GHE1207 3.4 0.1 1.0 C D:GLN137 3.5 82.7 1.0 ND2 D:ASN59 3.5 88.7 1.0 CA D:ASP138 3.6 93.6 1.0 O17 C:GHE1207 3.9 0.1 1.0 CB D:ASP138 3.9 93.7 1.0 N D:ASP138 3.9 92.2 1.0 OD2 D:ASP138 4.0 92.3 1.0 CA D:CA1206 4.2 0.7 1.0 CG D:GLU136 4.3 82.4 1.0 CB D:ASP58 4.4 96.6 1.0 C15 C:GHE1207 4.5 0.1 1.0 N D:ASN59 4.5 91.9 1.0 C14 C:GHE1207 4.6 0.1 1.0 CB D:ASN59 4.7 88.2 1.0 CA D:GLN137 4.8 82.0 1.0 N D:GLN137 4.9 81.0 1.0 C D:ASP138 4.9 95.1 1.0 CA D:ASN59 5.0 89.2 1.0

Calcium binding site 8 out of 20 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1206 b:0.7 occ:1.00 OD2 D:ASP138 2.0 92.3 1.0 OE1 D:GLN148 2.2 81.9 1.0 OE1 D:GLU136 2.4 83.7 1.0 O17 C:GHE1207 2.5 0.1 1.0 OD1 D:ASP138 2.6 93.1 1.0 CG D:ASP138 2.6 92.8 1.0 CD D:GLN148 3.3 83.4 1.0 C16 C:GHE1207 3.6 0.1 1.0 CD D:GLU136 3.6 83.4 1.0 O16 C:GHE1207 3.7 0.1 1.0 NE2 D:GLN148 3.8 83.3 1.0 CB D:ASP145 3.8 0.6 1.0 CB D:ASP138 4.2 93.7 1.0 CA D:CA1205 4.2 0.0 1.0 OD2 D:ASP145 4.2 0.1 1.0 O D:GLU136 4.3 84.0 1.0 OE2 D:GLU136 4.4 84.4 1.0 CG D:GLN148 4.5 85.7 1.0 CG D:GLU136 4.6 82.4 1.0 CG D:ASP145 4.6 0.5 1.0 CB D:GLU136 4.6 82.4 1.0 C15 C:GHE1207 4.9 0.1 1.0 O D:GLN137 5.0 83.1 1.0 C D:GLU136 5.0 83.2 1.0

Calcium binding site 9 out of 20 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1205 b:0.1 occ:1.00 O2 E:GHE1207 2.1 0.4 1.0 OE2 E:GLU136 2.1 80.8 1.0 OD1 E:ASN59 2.3 77.4 1.0 OD1 E:ASP58 2.4 91.4 1.0 OD1 E:ASP138 2.4 99.2 1.0 O E:GLN137 2.4 75.8 1.0 OD2 E:ASP58 2.6 91.7 1.0 CG E:ASP58 2.8 92.8 1.0 CD E:GLU136 2.9 79.3 1.0 OE1 E:GLU136 2.9 77.9 1.0 CG E:ASP138 3.2 97.2 1.0 CG E:ASN59 3.2 81.7 1.0 C1 E:GHE1207 3.3 0.4 1.0 C E:GLN137 3.5 73.4 1.0 ND2 E:ASN59 3.5 81.9 1.0 CA E:ASP138 3.6 98.5 1.0 O1 E:GHE1207 3.8 0.4 1.0 CB E:ASP138 3.9 97.3 1.0 N E:ASP138 3.9 97.0 1.0 OD2 E:ASP138 4.0 95.6 1.0 CA E:CA1206 4.3 0.2 1.0 CG E:GLU136 4.3 79.5 1.0 CB E:ASP58 4.4 96.4 1.0 N E:ASN59 4.5 85.4 1.0 C2 E:GHE1207 4.5 0.4 1.0 CB E:ASN59 4.6 88.0 1.0 CA E:GLN137 4.7 71.6 1.0 C E:ASP138 4.8 99.5 1.0 C3 E:GHE1207 4.9 0.4 1.0 N E:GLN137 4.9 71.5 1.0 CA E:ASN59 5.0 88.2 1.0

Calcium binding site 10 out of 20 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1206 b:0.2 occ:1.00 OE1 E:GLN148 2.1 66.0 1.0 OD2 E:ASP138 2.1 95.6 1.0 OE1 E:GLU136 2.5 77.9 1.0 O1 E:GHE1207 2.5 0.4 1.0 OD1 E:ASP138 2.6 99.2 1.0 CG E:ASP138 2.7 97.2 1.0 CD E:GLN148 3.2 66.2 1.0 C1 E:GHE1207 3.5 0.4 1.0 CD E:GLU136 3.7 79.3 1.0 NE2 E:GLN148 3.7 66.2 1.0 O2 E:GHE1207 3.8 0.4 1.0 CB E:ASP145 3.8 90.2 1.0 OD2 E:ASP145 4.1 93.6 1.0 CB E:ASP138 4.2 97.3 1.0 CA E:CA1205 4.3 0.1 1.0 C9 E:GHE1207 4.3 0.4 1.0 C10 E:GHE1207 4.4 0.4 1.0 CG E:ASP145 4.5 92.0 1.0 CG E:GLN148 4.5 67.0 1.0 O E:GLU136 4.5 71.8 1.0 OE2 E:GLU136 4.6 80.8 1.0 CG E:GLU136 4.7 79.5 1.0 CB E:GLU136 4.8 76.7 1.0 C2 E:GHE1207 4.9 0.4 1.0

S.E.Kolstoe, M.C.Jenvey, A.Purvis, M.E.Light, D.Thompson, P.Hughes, M.B.Pepys, S.P.Wood. Interaction of Serum Amyloid P Component with Hexanoyl Bis(D-Proline) (Cphpc) Acta Crystallogr.,Sect.D V. 70 2232 2014.
ISSN: ISSN 0907-4449
PubMed: 25084341
DOI: 10.1107/S1399004714013455