Calcium in PDB 2a3x: Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine

The structure of Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine, PDB code: 2a3x was solved by J.G.Ho, P.I.Kitov, E.Paszkiewicz, J.Sadowska, D.R.Bundle, K.K.Ng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.861, 95.054, 164.257, 90.00, 98.74, 90.00
R / Rfree (%)	22.8 / 28.2

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine (pdb code 2a3x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 20 binding sites of Calcium where determined in the Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine, PDB code: 2a3x:
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 Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:0.0 occ:1.00 OE2 A:GLU136 2.0 10.0 1.0 O A:GLN137 2.3 12.0 1.0 OD1 A:ASN59 2.4 12.7 1.0 OD1 A:ASP58 2.7 8.5 1.0 OD1 A:ASP138 2.7 10.2 1.0 OD2 A:ASP58 2.7 11.9 1.0 CG A:ASP58 3.1 11.9 1.0 CD A:GLU136 3.2 10.1 1.0 CG A:ASN59 3.4 12.7 1.0 C A:GLN137 3.4 11.5 1.0 CG A:ASP138 3.6 14.0 1.0 CA A:ASP138 3.8 11.1 1.0 OE1 A:GLU136 3.8 3.5 1.0 ND2 A:ASN59 3.8 11.5 1.0 N A:ASP138 4.0 11.1 1.0 CG A:GLU136 4.3 10.7 1.0 OD2 A:ASP138 4.3 13.7 1.0 CB A:ASP138 4.3 13.0 1.0 CA A:CA302 4.4 0.3 1.0 N A:ASN59 4.6 9.3 1.0 CA A:GLN137 4.6 10.8 1.0 CB A:ASN59 4.6 11.9 1.0 CB A:ASP58 4.6 12.2 1.0 N A:GLN137 4.6 11.3 1.0 ND2 A:ASN53 4.9 13.0 1.0 CD1 A:LEU62 5.0 13.6 1.0 CA A:ASN59 5.0 9.9 1.0 C A:ASP138 5.0 10.9 1.0

Calcium binding site 2 out of 20 in the Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:0.3 occ:1.00 OD2 A:ASP138 2.4 13.7 1.0 OE1 A:GLU136 2.6 3.5 1.0 OE1 A:GLN148 3.0 7.1 1.0 OD1 A:ASP138 3.0 10.2 1.0 CG A:ASP138 3.1 14.0 1.0 CD A:GLU136 3.2 10.1 1.0 NE2 A:GLN148 3.3 11.3 1.0 OE2 A:GLU136 3.4 10.0 1.0 CD A:GLN148 3.6 9.7 1.0 OD2 A:ASP145 4.2 12.0 1.0 CA A:CA301 4.4 0.0 1.0 CG A:GLU136 4.4 10.7 1.0 CB A:ASP138 4.6 13.0 1.0 CB A:ASP145 4.7 11.4 1.0 CG A:ASP145 4.9 11.4 1.0

Calcium binding site 3 out of 20 in the Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:0.4 occ:1.00 OE2 B:GLU136 2.7 10.1 1.0 OD1 B:ASP58 2.8 8.0 1.0 O B:GLN137 2.8 11.8 1.0 OE1 B:GLU136 3.1 10.2 1.0 ND2 B:ASN59 3.2 10.3 1.0 OD1 B:ASN59 3.2 6.0 1.0 CD B:GLU136 3.3 13.3 1.0 OD1 B:ASP138 3.3 10.3 1.0 CG B:ASP138 3.4 12.8 1.0 CA B:CA304 3.4 0.8 1.0 OD2 B:ASP58 3.4 9.0 1.0 CA B:ASP138 3.5 11.0 1.0 CG B:ASN59 3.5 8.1 1.0 CG B:ASP58 3.5 12.0 1.0 OD2 B:ASP138 3.6 9.8 1.0 C B:GLN137 3.6 11.4 1.0 N B:ASP138 3.9 11.2 1.0 CB B:ASP138 4.0 12.2 1.0 C B:ASP138 4.6 10.8 1.0 CG B:GLU136 4.8 9.9 1.0 O B:ASP138 4.9 11.9 1.0 CA B:GLN137 4.9 10.7 1.0 CB B:ASN59 4.9 7.4 1.0 N B:GLN137 5.0 11.8 1.0

Calcium binding site 4 out of 20 in the Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:0.8 occ:1.00 OE1 B:GLU136 2.4 10.2 1.0 NE2 B:GLN148 2.7 12.4 1.0 OD2 B:ASP138 3.0 9.8 1.0 OD2 B:ASP145 3.0 15.9 1.0 CA B:CA303 3.4 0.4 1.0 CD B:GLU136 3.5 13.3 1.0 CD B:GLN148 3.5 13.0 1.0 OE1 B:GLN148 3.6 11.4 1.0 OD1 B:ASP138 3.6 10.3 1.0 CG B:ASP138 3.7 12.8 1.0 CG B:ASP145 4.1 16.7 1.0 OE2 B:GLU136 4.2 10.1 1.0 OD1 B:ASP145 4.5 16.4 1.0 CG B:GLU136 4.5 9.9 1.0 CG B:GLN148 5.0 11.8 1.0

Calcium binding site 5 out of 20 in the Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca305 b:84.3 occ:1.00 O31 C:CPK402 2.2 75.5 1.0 O C:GLN137 2.4 12.0 1.0 OD1 C:ASP138 2.4 12.8 1.0 OE1 C:GLU136 2.5 9.8 1.0 OD1 C:ASN59 2.5 3.3 1.0 OE2 C:GLU136 2.5 8.2 1.0 OD1 C:ASP58 2.7 6.8 1.0 CD C:GLU136 2.9 16.6 1.0 OD2 C:ASP58 3.0 15.0 1.0 C29 C:CPK402 3.3 81.1 1.0 CG C:ASP58 3.3 13.6 1.0 CG C:ASN59 3.3 5.7 1.0 ND2 C:ASN59 3.5 7.3 1.0 C C:GLN137 3.5 11.3 1.0 CG C:ASP138 3.6 13.7 1.0 O30 C:CPK402 3.9 77.3 1.0 CA C:ASP138 3.9 10.7 1.0 CA C:CA306 3.9 81.0 1.0 N C:ASP138 4.1 10.3 1.0 CB C:ASP138 4.3 10.3 1.0 C32 C:CPK402 4.4 85.9 1.0 C26 C:CPK402 4.4 85.7 1.0 CG C:GLU136 4.4 7.2 1.0 OD2 C:ASP138 4.5 15.5 1.0 CA C:GLN137 4.7 10.5 1.0 N C:GLN137 4.7 11.5 1.0 CB C:ASN59 4.7 2.6 1.0 N C:ASN59 4.8 8.9 1.0 CB C:ASP58 4.8 11.4 1.0 O25 C:CPK402 4.8 79.2 1.0 ND2 C:ASN53 4.9 5.9 1.0

Calcium binding site 6 out of 20 in the Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca306 b:81.0 occ:1.00 OE1 C:GLN148 2.3 7.9 1.0 OE1 C:GLU136 2.4 9.8 1.0 OD1 C:ASP138 2.4 12.8 1.0 OD2 C:ASP138 2.8 15.5 1.0 CG C:ASP138 2.9 13.7 1.0 O30 C:CPK402 3.0 77.3 1.0 CD C:GLN148 3.6 11.9 1.0 CD C:GLU136 3.6 16.6 1.0 C29 C:CPK402 3.7 81.1 1.0 CA C:CA305 3.9 84.3 1.0 O31 C:CPK402 3.9 75.5 1.0 O C:GLU136 4.0 13.2 1.0 CB C:ASP145 4.0 9.5 1.0 CB C:GLU136 4.2 10.4 1.0 CB C:ASP138 4.3 10.3 1.0 CG C:GLU136 4.3 7.2 1.0 C C:GLU136 4.4 12.6 1.0 CG C:GLN148 4.5 12.8 1.0 OE2 C:GLU136 4.5 8.2 1.0 NE2 C:GLN148 4.5 11.1 1.0 O C:GLN137 4.5 12.0 1.0 O C:LYS143 4.6 12.5 1.0 C C:GLN137 4.6 11.3 1.0 N C:ASP138 4.7 10.3 1.0 N C:ASP145 4.9 13.2 1.0 OD2 C:ASP145 4.9 17.9 1.0 CA C:ASP138 4.9 10.7 1.0 C26 C:CPK402 4.9 85.7 1.0 N C:GLN137 4.9 11.5 1.0 CA C:GLU136 4.9 10.2 1.0 CG C:ASP145 5.0 16.8 1.0

Calcium binding site 7 out of 20 in the Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca307 b:44.6 occ:1.00 O31 I:CPK401 2.2 73.9 1.0 OD1 D:ASP58 2.4 2.0 1.0 O D:GLN137 2.4 11.8 1.0 OD1 D:ASP138 2.5 9.9 1.0 OE1 D:GLU136 2.5 2.0 1.0 OD1 D:ASN59 2.6 20.0 1.0 OD2 D:ASP58 2.9 9.9 1.0 OE2 D:GLU136 3.0 9.9 1.0 CG D:ASP58 3.1 9.4 1.0 CD D:GLU136 3.1 7.2 1.0 C29 I:CPK401 3.3 83.3 1.0 CG D:ASN59 3.3 13.0 1.0 C D:GLN137 3.5 11.2 1.0 ND2 D:ASN59 3.6 10.8 1.0 CG D:ASP138 3.6 11.9 1.0 CA D:ASP138 3.7 10.6 1.0 O30 I:CPK401 3.9 88.7 1.0 N D:ASP138 4.0 10.0 1.0 CB D:ASP138 4.2 12.8 1.0 C32 I:CPK401 4.3 85.4 1.0 C26 I:CPK401 4.3 79.8 1.0 CA D:CA308 4.3 65.1 1.0 N D:ASN59 4.4 7.6 1.0 OD2 D:ASP138 4.5 11.0 1.0 CB D:ASP58 4.5 10.7 1.0 CB D:ASN59 4.6 2.0 1.0 CG D:GLU136 4.6 8.5 1.0 O25 I:CPK401 4.7 78.1 1.0 CA D:GLN137 4.7 10.1 1.0 ND2 D:ASN53 4.8 5.4 1.0 CA D:ASN59 4.8 9.1 1.0 N D:GLN137 4.9 11.3 1.0 C D:ASP138 4.9 10.7 1.0

Calcium binding site 8 out of 20 in the Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca308 b:65.1 occ:1.00 OD2 D:ASP138 2.4 11.0 1.0 O30 I:CPK401 2.4 88.7 1.0 OD1 D:ASP138 2.5 9.9 1.0 OE1 D:GLN148 2.6 9.4 1.0 CG D:ASP138 2.8 11.9 1.0 OE1 D:GLU136 3.1 2.0 1.0 C29 I:CPK401 3.4 83.3 1.0 CD D:GLN148 3.6 5.3 1.0 O31 I:CPK401 3.7 73.9 1.0 CB D:ASP145 3.8 10.2 1.0 NE2 D:GLN148 3.8 3.2 1.0 OD2 D:ASP145 4.2 10.4 1.0 CD D:GLU136 4.2 7.2 1.0 O D:GLU136 4.2 14.8 1.0 CB D:ASP138 4.2 12.8 1.0 CA D:CA307 4.3 44.6 1.0 CB D:GLU136 4.4 2.0 1.0 CG D:ASP145 4.5 15.2 1.0 CG D:GLU136 4.7 8.5 1.0 C26 I:CPK401 4.7 79.8 1.0 O D:GLN137 4.7 11.8 1.0 O D:LYS143 4.8 13.4 1.0 C D:GLU136 4.8 12.0 1.0 O27 I:CPK401 4.9 81.1 1.0 N D:ASP138 4.9 10.0 1.0 C D:GLN137 4.9 11.2 1.0 CG D:GLN148 4.9 11.3 1.0 CA D:ASP138 5.0 10.6 1.0

Calcium binding site 9 out of 20 in the Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca309 b:76.9 occ:1.00 O E:GLN137 2.2 10.9 1.0 O31 H:CPK403 2.2 78.2 1.0 OD1 E:ASN59 2.3 4.4 1.0 OE1 E:GLU136 2.7 2.0 1.0 OD1 E:ASP58 2.8 4.8 1.0 OE2 E:GLU136 2.8 13.5 1.0 OD1 E:ASP138 2.9 14.1 1.0 OD2 E:ASP58 3.0 12.7 1.0 CD E:GLU136 3.1 12.9 1.0 CG E:ASP58 3.3 9.4 1.0 C E:GLN137 3.3 10.8 1.0 CG E:ASN59 3.3 6.0 1.0 C29 H:CPK403 3.4 80.5 1.0 CG E:ASP138 3.5 13.1 1.0 CA E:ASP138 3.8 11.2 1.0 ND2 E:ASN59 3.8 2.0 1.0 N E:ASP138 3.9 11.2 1.0 OD2 E:ASP138 4.0 16.6 1.0 O30 H:CPK403 4.1 83.3 1.0 CA E:CA310 4.2 74.3 1.0 CB E:ASP138 4.2 12.2 1.0 C32 H:CPK403 4.3 82.0 1.0 C26 H:CPK403 4.4 80.4 1.0 CA E:GLN137 4.5 10.4 1.0 N E:ASN59 4.5 9.6 1.0 N E:GLN137 4.5 11.0 1.0 O25 H:CPK403 4.6 63.9 1.0 CG E:GLU136 4.6 11.9 1.0 ND2 E:ASN53 4.6 10.2 1.0 CB E:ASN59 4.7 10.7 1.0 CB E:ASP58 4.8 14.1 1.0 CA E:ASN59 5.0 9.9 1.0

Calcium binding site 10 out of 20 in the Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Decameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY- 2-Methyl-1,3-Dioxane]- 5-Yloxycarbonyl}- Piperazine within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca310 b:74.3 occ:1.00 OD1 E:ASP138 2.1 14.1 1.0 OE1 E:GLN148 2.3 12.9 1.0 O30 H:CPK403 2.5 83.3 1.0 OE1 E:GLU136 2.7 2.0 1.0 CG E:ASP138 3.1 13.1 1.0 C29 H:CPK403 3.3 80.5 1.0 CD E:GLN148 3.4 18.1 1.0 O31 H:CPK403 3.5 78.2 1.0 OD2 E:ASP138 3.7 16.6 1.0 NE2 E:GLN148 3.7 17.7 1.0 CB E:ASP145 3.8 14.9 1.0 CD E:GLU136 3.9 12.9 1.0 O E:GLU136 4.0 13.9 1.0 CB E:ASP138 4.2 12.2 1.0 CA E:CA309 4.2 76.9 1.0 CB E:GLU136 4.4 6.8 1.0 OD2 E:ASP145 4.4 15.0 1.0 O E:LYS143 4.5 12.2 1.0 CG E:GLU136 4.5 11.9 1.0 CG E:ASP145 4.5 15.2 1.0 C E:GLU136 4.6 11.7 1.0 C26 H:CPK403 4.6 80.4 1.0 O E:GLN137 4.7 10.9 1.0 CG E:GLN148 4.7 15.3 1.0 C E:GLN137 4.8 10.8 1.0 N E:ASP138 4.8 11.2 1.0 OE2 E:GLU136 4.9 13.5 1.0 N E:ASP145 4.9 12.3 1.0 O27 H:CPK403 4.9 94.5 1.0 CA E:ASP138 5.0 11.2 1.0 CA E:ASP145 5.0 10.6 1.0 C32 H:CPK403 5.0 82.0 1.0

J.G.Ho, P.I.Kitov, E.Paszkiewicz, J.Sadowska, D.R.Bundle, K.K.Ng. Ligand-Assisted Aggregation of Proteins: Dimerization of Serum Amyloid P Component By Bivalent Ligands. J.Biol.Chem. V. 280 31999 2005.
ISSN: ISSN 0021-9258
PubMed: 16036920
DOI: 10.1074/JBC.M504403200