Calcium in PDB 2a3y: Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane.
Protein crystallography data
The structure of Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane., PDB code: 2a3y
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)
|
50.60 /
2.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.715,
69.956,
101.367,
90.00,
97.09,
90.00
|
R / Rfree (%)
|
21.6 /
25
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane.
(pdb code 2a3y). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the
Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane., PDB code: 2a3y:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 10 in 2a3y
Go back to
Calcium Binding Sites List in 2a3y
Calcium binding site 1 out
of 10 in the Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca600
b:16.3
occ:1.00
|
OD1
|
A:ASP138
|
2.3
|
7.0
|
1.0
|
O
|
A:GLN137
|
2.3
|
7.9
|
1.0
|
OD1
|
A:ASN59
|
2.4
|
7.3
|
1.0
|
OD1
|
A:ASP58
|
2.4
|
7.9
|
1.0
|
OE1
|
A:GLU136
|
2.5
|
9.6
|
1.0
|
OE2
|
A:GLU136
|
2.6
|
9.2
|
1.0
|
OD2
|
A:ASP58
|
2.7
|
6.3
|
1.0
|
O9
|
A:CPJ610
|
2.9
|
91.4
|
1.0
|
CD
|
A:GLU136
|
2.9
|
9.2
|
1.0
|
CG
|
A:ASP58
|
3.0
|
7.5
|
1.0
|
CG
|
A:ASN59
|
3.4
|
6.2
|
1.0
|
C
|
A:GLN137
|
3.4
|
7.1
|
1.0
|
CG
|
A:ASP138
|
3.5
|
4.8
|
1.0
|
C7
|
A:CPJ610
|
3.7
|
92.3
|
1.0
|
CA
|
A:ASP138
|
3.7
|
7.9
|
1.0
|
CA
|
A:CA601
|
3.8
|
17.2
|
1.0
|
ND2
|
A:ASN59
|
3.8
|
6.8
|
1.0
|
O8
|
A:CPJ610
|
3.9
|
91.3
|
1.0
|
N
|
A:ASP138
|
4.0
|
7.7
|
1.0
|
O
|
A:HOH673
|
4.1
|
20.8
|
1.0
|
CB
|
A:ASP138
|
4.2
|
8.4
|
1.0
|
N
|
A:ASN59
|
4.4
|
8.4
|
1.0
|
CG
|
A:GLU136
|
4.4
|
8.2
|
1.0
|
OD2
|
A:ASP138
|
4.4
|
5.9
|
1.0
|
CB
|
A:ASP58
|
4.5
|
9.2
|
1.0
|
CA
|
A:GLN137
|
4.7
|
7.7
|
1.0
|
N
|
A:GLN137
|
4.7
|
7.9
|
1.0
|
CB
|
A:ASN59
|
4.7
|
7.8
|
1.0
|
ND2
|
A:ASN53
|
4.8
|
5.4
|
1.0
|
O
|
A:HOH687
|
4.9
|
25.6
|
1.0
|
C
|
A:ASP138
|
4.9
|
9.1
|
1.0
|
CA
|
A:ASN59
|
4.9
|
8.2
|
1.0
|
C6
|
A:CPJ610
|
5.0
|
92.8
|
1.0
|
|
Calcium binding site 2 out
of 10 in 2a3y
Go back to
Calcium Binding Sites List in 2a3y
Calcium binding site 2 out
of 10 in the Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca601
b:17.2
occ:1.00
|
O
|
A:HOH687
|
2.2
|
25.6
|
1.0
|
OE1
|
A:GLU136
|
2.4
|
9.6
|
1.0
|
O
|
A:HOH688
|
2.4
|
17.0
|
1.0
|
OD2
|
A:ASP138
|
2.4
|
5.9
|
1.0
|
OE1
|
A:GLN148
|
2.5
|
6.6
|
1.0
|
OD1
|
A:ASP138
|
2.5
|
7.0
|
1.0
|
O8
|
A:CPJ610
|
2.6
|
91.3
|
1.0
|
CG
|
A:ASP138
|
2.8
|
4.8
|
1.0
|
CD
|
A:GLN148
|
3.4
|
8.9
|
1.0
|
CD
|
A:GLU136
|
3.6
|
9.2
|
1.0
|
C7
|
A:CPJ610
|
3.7
|
92.3
|
1.0
|
NE2
|
A:GLN148
|
3.7
|
7.2
|
1.0
|
CA
|
A:CA600
|
3.8
|
16.3
|
1.0
|
O9
|
A:CPJ610
|
4.0
|
91.4
|
1.0
|
CB
|
A:ASP145
|
4.2
|
10.5
|
1.0
|
CB
|
A:ASP138
|
4.2
|
8.4
|
1.0
|
CB
|
A:GLU136
|
4.2
|
8.4
|
1.0
|
O
|
A:GLU136
|
4.3
|
8.1
|
1.0
|
CG
|
A:GLU136
|
4.3
|
8.2
|
1.0
|
O
|
A:GLN137
|
4.4
|
7.9
|
1.0
|
OE2
|
A:GLU136
|
4.5
|
9.2
|
1.0
|
OD2
|
A:ASP145
|
4.6
|
16.4
|
1.0
|
C
|
A:GLN137
|
4.7
|
7.1
|
1.0
|
C
|
A:GLU136
|
4.7
|
7.8
|
1.0
|
O
|
A:LYS143
|
4.8
|
9.0
|
1.0
|
N
|
A:ASP138
|
4.8
|
7.7
|
1.0
|
CG
|
A:GLN148
|
4.8
|
6.4
|
1.0
|
CA
|
A:ASP138
|
4.9
|
7.9
|
1.0
|
CG
|
A:ASP145
|
4.9
|
12.4
|
1.0
|
C6
|
A:CPJ610
|
4.9
|
92.8
|
1.0
|
|
Calcium binding site 3 out
of 10 in 2a3y
Go back to
Calcium Binding Sites List in 2a3y
Calcium binding site 3 out
of 10 in the Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca602
b:25.8
occ:1.00
|
OD1
|
B:ASN59
|
2.3
|
12.0
|
1.0
|
OD1
|
B:ASP138
|
2.4
|
8.3
|
1.0
|
OE2
|
B:GLU136
|
2.4
|
14.7
|
1.0
|
O
|
B:GLN137
|
2.4
|
12.9
|
1.0
|
OD1
|
B:ASP58
|
2.5
|
11.3
|
1.0
|
OD2
|
B:ASP58
|
2.7
|
13.7
|
1.0
|
OE1
|
B:GLU136
|
2.7
|
10.9
|
1.0
|
O9
|
B:CPJ611
|
2.7
|
0.2
|
1.0
|
CD
|
B:GLU136
|
2.9
|
13.2
|
1.0
|
CG
|
B:ASP58
|
3.0
|
12.8
|
1.0
|
CG
|
B:ASN59
|
3.3
|
11.1
|
1.0
|
C
|
B:GLN137
|
3.6
|
13.1
|
1.0
|
CG
|
B:ASP138
|
3.6
|
12.8
|
1.0
|
C7
|
B:CPJ611
|
3.6
|
0.8
|
1.0
|
ND2
|
B:ASN59
|
3.6
|
11.9
|
1.0
|
CA
|
B:ASP138
|
3.8
|
13.9
|
1.0
|
CA
|
B:CA603
|
3.9
|
22.4
|
1.0
|
O8
|
B:CPJ611
|
3.9
|
0.9
|
1.0
|
O
|
B:HOH631
|
4.0
|
34.1
|
1.0
|
N
|
B:ASP138
|
4.1
|
13.5
|
1.0
|
CB
|
B:ASP138
|
4.3
|
13.4
|
1.0
|
N
|
B:ASN59
|
4.4
|
12.5
|
1.0
|
CG
|
B:GLU136
|
4.4
|
10.9
|
1.0
|
CB
|
B:ASP58
|
4.5
|
13.3
|
1.0
|
OD2
|
B:ASP138
|
4.5
|
9.7
|
1.0
|
CB
|
B:ASN59
|
4.6
|
12.3
|
1.0
|
CA
|
B:GLN137
|
4.8
|
12.2
|
1.0
|
ND2
|
B:ASN53
|
4.8
|
8.7
|
1.0
|
CD2
|
B:LEU62
|
4.8
|
11.8
|
1.0
|
CA
|
B:ASN59
|
4.8
|
12.2
|
1.0
|
N
|
B:GLN137
|
4.8
|
11.6
|
1.0
|
C6
|
B:CPJ611
|
4.9
|
0.3
|
1.0
|
C
|
B:ASP138
|
5.0
|
14.8
|
1.0
|
|
Calcium binding site 4 out
of 10 in 2a3y
Go back to
Calcium Binding Sites List in 2a3y
Calcium binding site 4 out
of 10 in the Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca603
b:22.4
occ:1.00
|
OE1
|
B:GLU136
|
2.1
|
10.9
|
1.0
|
O
|
B:HOH656
|
2.2
|
14.3
|
1.0
|
O
|
B:HOH657
|
2.3
|
21.4
|
1.0
|
OE1
|
B:GLN148
|
2.3
|
8.1
|
1.0
|
OD2
|
B:ASP138
|
2.4
|
9.7
|
1.0
|
O8
|
B:CPJ611
|
2.5
|
0.9
|
1.0
|
OD1
|
B:ASP138
|
2.5
|
8.3
|
1.0
|
CG
|
B:ASP138
|
2.8
|
12.8
|
1.0
|
CD
|
B:GLU136
|
3.3
|
13.2
|
1.0
|
CD
|
B:GLN148
|
3.4
|
10.7
|
1.0
|
C7
|
B:CPJ611
|
3.5
|
0.8
|
1.0
|
NE2
|
B:GLN148
|
3.8
|
11.3
|
1.0
|
CA
|
B:CA602
|
3.9
|
25.8
|
1.0
|
O9
|
B:CPJ611
|
3.9
|
0.2
|
1.0
|
CG
|
B:GLU136
|
4.0
|
10.9
|
1.0
|
CB
|
B:GLU136
|
4.0
|
12.3
|
1.0
|
CB
|
B:ASP138
|
4.1
|
13.4
|
1.0
|
OE2
|
B:GLU136
|
4.2
|
14.7
|
1.0
|
O
|
B:GLU136
|
4.2
|
10.9
|
1.0
|
CB
|
B:ASP145
|
4.2
|
14.1
|
1.0
|
O
|
B:GLN137
|
4.4
|
12.9
|
1.0
|
C
|
B:GLU136
|
4.6
|
11.7
|
1.0
|
C
|
B:GLN137
|
4.7
|
13.1
|
1.0
|
OD2
|
B:ASP145
|
4.7
|
18.3
|
1.0
|
CG
|
B:GLN148
|
4.7
|
10.2
|
1.0
|
N
|
B:ASP138
|
4.7
|
13.5
|
1.0
|
C6
|
B:CPJ611
|
4.8
|
0.3
|
1.0
|
CA
|
B:ASP138
|
4.8
|
13.9
|
1.0
|
O
|
B:LYS143
|
4.9
|
15.3
|
1.0
|
CA
|
B:GLU136
|
5.0
|
11.7
|
1.0
|
CG
|
B:ASP145
|
5.0
|
15.0
|
1.0
|
|
Calcium binding site 5 out
of 10 in 2a3y
Go back to
Calcium Binding Sites List in 2a3y
Calcium binding site 5 out
of 10 in the Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca604
b:14.2
occ:1.00
|
OD1
|
C:ASN59
|
2.3
|
3.8
|
1.0
|
O
|
C:GLN137
|
2.4
|
5.4
|
1.0
|
OD1
|
C:ASP58
|
2.4
|
2.9
|
1.0
|
OE2
|
C:GLU136
|
2.4
|
5.9
|
1.0
|
OD1
|
C:ASP138
|
2.5
|
2.0
|
1.0
|
OD2
|
C:ASP58
|
2.6
|
2.0
|
1.0
|
O9
|
C:CPJ612
|
2.6
|
82.2
|
1.0
|
OE1
|
C:GLU136
|
2.6
|
2.0
|
1.0
|
CG
|
C:ASP58
|
2.9
|
3.9
|
1.0
|
CD
|
C:GLU136
|
2.9
|
5.3
|
1.0
|
CG
|
C:ASN59
|
3.3
|
4.3
|
1.0
|
C
|
C:GLN137
|
3.5
|
4.2
|
1.0
|
C7
|
C:CPJ612
|
3.6
|
83.7
|
1.0
|
CG
|
C:ASP138
|
3.7
|
5.8
|
1.0
|
ND2
|
C:ASN59
|
3.7
|
3.9
|
1.0
|
CA
|
C:ASP138
|
3.8
|
4.9
|
1.0
|
CA
|
C:CA605
|
3.9
|
14.2
|
1.0
|
O8
|
C:CPJ612
|
3.9
|
82.4
|
1.0
|
O
|
C:HOH622
|
4.0
|
11.9
|
1.0
|
N
|
C:ASP138
|
4.1
|
4.8
|
1.0
|
N
|
C:ASN59
|
4.3
|
5.6
|
1.0
|
CB
|
C:ASP58
|
4.4
|
3.6
|
1.0
|
CB
|
C:ASP138
|
4.4
|
4.8
|
1.0
|
CG
|
C:GLU136
|
4.4
|
7.0
|
1.0
|
OD2
|
C:ASP138
|
4.6
|
7.0
|
1.0
|
CB
|
C:ASN59
|
4.6
|
4.6
|
1.0
|
CA
|
C:GLN137
|
4.7
|
6.1
|
1.0
|
ND2
|
C:ASN53
|
4.7
|
4.1
|
1.0
|
N
|
C:GLN137
|
4.8
|
5.4
|
1.0
|
CA
|
C:ASN59
|
4.8
|
6.0
|
1.0
|
OD1
|
C:ASN53
|
4.8
|
5.2
|
1.0
|
C6
|
C:CPJ612
|
4.9
|
84.8
|
1.0
|
CD2
|
C:LEU62
|
4.9
|
4.1
|
1.0
|
CA
|
C:ASP58
|
5.0
|
5.0
|
1.0
|
C
|
C:ASP58
|
5.0
|
5.7
|
1.0
|
|
Calcium binding site 6 out
of 10 in 2a3y
Go back to
Calcium Binding Sites List in 2a3y
Calcium binding site 6 out
of 10 in the Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca605
b:14.2
occ:1.00
|
O
|
C:HOH710
|
2.2
|
18.0
|
1.0
|
OE1
|
C:GLU136
|
2.3
|
2.0
|
1.0
|
OE1
|
C:GLN148
|
2.4
|
4.0
|
1.0
|
O
|
C:HOH709
|
2.4
|
14.0
|
1.0
|
OD2
|
C:ASP138
|
2.4
|
7.0
|
1.0
|
O8
|
C:CPJ612
|
2.4
|
82.4
|
1.0
|
OD1
|
C:ASP138
|
2.6
|
2.0
|
1.0
|
CG
|
C:ASP138
|
2.8
|
5.8
|
1.0
|
CD
|
C:GLN148
|
3.4
|
5.8
|
1.0
|
C7
|
C:CPJ612
|
3.5
|
83.7
|
1.0
|
CD
|
C:GLU136
|
3.5
|
5.3
|
1.0
|
O9
|
C:CPJ612
|
3.8
|
82.2
|
1.0
|
NE2
|
C:GLN148
|
3.8
|
4.2
|
1.0
|
CA
|
C:CA604
|
3.9
|
14.2
|
1.0
|
CB
|
C:ASP145
|
4.2
|
7.8
|
1.0
|
CB
|
C:ASP138
|
4.2
|
4.8
|
1.0
|
CB
|
C:GLU136
|
4.2
|
5.2
|
1.0
|
CG
|
C:GLU136
|
4.3
|
7.0
|
1.0
|
O
|
C:GLU136
|
4.3
|
8.5
|
1.0
|
OE2
|
C:GLU136
|
4.4
|
5.9
|
1.0
|
O
|
C:GLN137
|
4.5
|
5.4
|
1.0
|
OD2
|
C:ASP145
|
4.6
|
9.0
|
1.0
|
C
|
C:GLU136
|
4.7
|
6.8
|
1.0
|
C
|
C:GLN137
|
4.7
|
4.2
|
1.0
|
CG
|
C:GLN148
|
4.8
|
5.3
|
1.0
|
C6
|
C:CPJ612
|
4.8
|
84.8
|
1.0
|
N
|
C:ASP138
|
4.8
|
4.8
|
1.0
|
O
|
C:LYS143
|
4.8
|
7.6
|
1.0
|
CA
|
C:ASP138
|
4.9
|
4.9
|
1.0
|
CG
|
C:ASP145
|
4.9
|
10.3
|
1.0
|
|
Calcium binding site 7 out
of 10 in 2a3y
Go back to
Calcium Binding Sites List in 2a3y
Calcium binding site 7 out
of 10 in the Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca606
b:9.9
occ:1.00
|
O
|
D:GLN137
|
2.3
|
6.1
|
1.0
|
OD1
|
D:ASP138
|
2.3
|
4.1
|
1.0
|
OD1
|
D:ASN59
|
2.4
|
4.5
|
1.0
|
OE2
|
D:GLU136
|
2.4
|
5.5
|
1.0
|
OD1
|
D:ASP58
|
2.4
|
10.2
|
1.0
|
OE1
|
D:GLU136
|
2.5
|
4.4
|
1.0
|
O9
|
D:CPJ614
|
2.5
|
71.2
|
1.0
|
OD2
|
D:ASP58
|
2.7
|
7.8
|
1.0
|
CD
|
D:GLU136
|
2.8
|
4.4
|
1.0
|
CG
|
D:ASP58
|
2.9
|
8.0
|
1.0
|
CG
|
D:ASN59
|
3.4
|
7.0
|
1.0
|
C
|
D:GLN137
|
3.4
|
6.0
|
1.0
|
C7
|
D:CPJ614
|
3.5
|
73.1
|
1.0
|
CG
|
D:ASP138
|
3.5
|
8.2
|
1.0
|
ND2
|
D:ASN59
|
3.7
|
4.2
|
1.0
|
CA
|
D:ASP138
|
3.7
|
6.8
|
1.0
|
CA
|
D:CA607
|
3.8
|
11.9
|
1.0
|
O8
|
D:CPJ614
|
3.9
|
70.5
|
1.0
|
N
|
D:ASP138
|
4.0
|
6.4
|
1.0
|
CB
|
D:ASP138
|
4.2
|
7.0
|
1.0
|
O
|
D:HOH620
|
4.2
|
9.2
|
1.0
|
CG
|
D:GLU136
|
4.3
|
5.4
|
1.0
|
N
|
D:ASN59
|
4.4
|
5.6
|
1.0
|
CB
|
D:ASP58
|
4.4
|
8.2
|
1.0
|
OD2
|
D:ASP138
|
4.5
|
4.3
|
1.0
|
CA
|
D:GLN137
|
4.6
|
5.5
|
1.0
|
N
|
D:GLN137
|
4.6
|
5.0
|
1.0
|
CB
|
D:ASN59
|
4.7
|
6.0
|
1.0
|
C6
|
D:CPJ614
|
4.7
|
75.0
|
1.0
|
ND2
|
D:ASN53
|
4.8
|
2.0
|
1.0
|
CA
|
D:ASN59
|
4.9
|
5.9
|
1.0
|
O
|
D:HOH753
|
4.9
|
10.2
|
1.0
|
OD1
|
D:ASN53
|
4.9
|
3.7
|
1.0
|
C
|
D:ASP138
|
5.0
|
7.8
|
1.0
|
|
Calcium binding site 8 out
of 10 in 2a3y
Go back to
Calcium Binding Sites List in 2a3y
Calcium binding site 8 out
of 10 in the Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca607
b:11.9
occ:1.00
|
O
|
D:HOH753
|
2.3
|
10.2
|
1.0
|
OE1
|
D:GLU136
|
2.3
|
4.4
|
1.0
|
OE1
|
D:GLN148
|
2.4
|
5.3
|
1.0
|
O8
|
D:CPJ614
|
2.4
|
70.5
|
1.0
|
OD2
|
D:ASP138
|
2.4
|
4.3
|
1.0
|
OD1
|
D:ASP138
|
2.5
|
4.1
|
1.0
|
O
|
D:HOH752
|
2.5
|
10.8
|
1.0
|
CG
|
D:ASP138
|
2.8
|
8.2
|
1.0
|
C7
|
D:CPJ614
|
3.4
|
73.1
|
1.0
|
CD
|
D:GLN148
|
3.4
|
5.3
|
1.0
|
CD
|
D:GLU136
|
3.5
|
4.4
|
1.0
|
O9
|
D:CPJ614
|
3.6
|
71.2
|
1.0
|
NE2
|
D:GLN148
|
3.7
|
5.4
|
1.0
|
CA
|
D:CA606
|
3.8
|
9.9
|
1.0
|
O
|
D:HOH756
|
4.1
|
29.8
|
1.0
|
CB
|
D:ASP138
|
4.2
|
7.0
|
1.0
|
CB
|
D:ASP145
|
4.2
|
5.7
|
1.0
|
CB
|
D:GLU136
|
4.3
|
5.3
|
1.0
|
CG
|
D:GLU136
|
4.3
|
5.4
|
1.0
|
O
|
D:GLU136
|
4.3
|
5.2
|
1.0
|
OE2
|
D:GLU136
|
4.5
|
5.5
|
1.0
|
O
|
D:GLN137
|
4.5
|
6.1
|
1.0
|
OD2
|
D:ASP145
|
4.6
|
8.3
|
1.0
|
O
|
D:HOH684
|
4.7
|
32.3
|
1.0
|
C6
|
D:CPJ614
|
4.7
|
75.0
|
1.0
|
C
|
D:GLU136
|
4.7
|
5.3
|
1.0
|
C
|
D:GLN137
|
4.7
|
6.0
|
1.0
|
O
|
D:HOH728
|
4.7
|
28.7
|
1.0
|
CG
|
D:GLN148
|
4.8
|
5.1
|
1.0
|
N
|
D:ASP138
|
4.8
|
6.4
|
1.0
|
O
|
D:LYS143
|
4.8
|
5.2
|
1.0
|
CA
|
D:ASP138
|
4.9
|
6.8
|
1.0
|
CG
|
D:ASP145
|
4.9
|
9.3
|
1.0
|
|
Calcium binding site 9 out
of 10 in 2a3y
Go back to
Calcium Binding Sites List in 2a3y
Calcium binding site 9 out
of 10 in the Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca608
b:20.4
occ:1.00
|
OD1
|
E:ASN59
|
2.3
|
15.7
|
1.0
|
OD1
|
E:ASP58
|
2.3
|
15.3
|
1.0
|
O
|
E:GLN137
|
2.3
|
9.0
|
1.0
|
OD1
|
E:ASP138
|
2.4
|
15.7
|
1.0
|
OE2
|
E:GLU136
|
2.5
|
12.9
|
1.0
|
OD2
|
E:ASP58
|
2.5
|
14.4
|
1.0
|
OE1
|
E:GLU136
|
2.6
|
12.3
|
1.0
|
O9
|
E:CPJ613
|
2.7
|
93.2
|
1.0
|
CG
|
E:ASP58
|
2.8
|
16.1
|
1.0
|
CD
|
E:GLU136
|
2.9
|
12.9
|
1.0
|
CG
|
E:ASN59
|
3.3
|
12.6
|
1.0
|
C
|
E:GLN137
|
3.4
|
11.3
|
1.0
|
CG
|
E:ASP138
|
3.6
|
14.3
|
1.0
|
ND2
|
E:ASN59
|
3.7
|
12.9
|
1.0
|
C7
|
E:CPJ613
|
3.7
|
93.8
|
1.0
|
CA
|
E:ASP138
|
3.7
|
13.4
|
1.0
|
CA
|
E:CA609
|
3.9
|
22.3
|
1.0
|
N
|
E:ASP138
|
4.0
|
11.9
|
1.0
|
O8
|
E:CPJ613
|
4.1
|
93.1
|
1.0
|
CB
|
E:ASP138
|
4.2
|
13.4
|
1.0
|
CB
|
E:ASP58
|
4.3
|
15.8
|
1.0
|
N
|
E:ASN59
|
4.3
|
12.4
|
1.0
|
O
|
E:HOH713
|
4.3
|
20.4
|
1.0
|
CG
|
E:GLU136
|
4.4
|
10.3
|
1.0
|
OD2
|
E:ASP138
|
4.5
|
14.3
|
1.0
|
CB
|
E:ASN59
|
4.6
|
11.0
|
1.0
|
CA
|
E:GLN137
|
4.6
|
11.1
|
1.0
|
N
|
E:GLN137
|
4.7
|
10.3
|
1.0
|
ND2
|
E:ASN53
|
4.8
|
7.7
|
1.0
|
CA
|
E:ASN59
|
4.8
|
11.6
|
1.0
|
C6
|
E:CPJ613
|
4.9
|
94.2
|
1.0
|
CA
|
E:ASP58
|
4.9
|
14.7
|
1.0
|
OD1
|
E:ASN53
|
4.9
|
10.6
|
1.0
|
C
|
E:ASP138
|
4.9
|
13.5
|
1.0
|
C
|
E:ASP58
|
5.0
|
13.6
|
1.0
|
|
Calcium binding site 10 out
of 10 in 2a3y
Go back to
Calcium Binding Sites List in 2a3y
Calcium binding site 10 out
of 10 in the Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Pentameric Crystal Structure of Human Serum Amyloid P-Component Bound to Bis-1,2-{[(Z)-2CARBOXY-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}- Ethane. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca609
b:22.3
occ:1.00
|
O
|
E:HOH708
|
2.2
|
30.3
|
1.0
|
OE1
|
E:GLU136
|
2.4
|
12.3
|
1.0
|
OE1
|
E:GLN148
|
2.4
|
12.4
|
1.0
|
OD2
|
E:ASP138
|
2.4
|
14.3
|
1.0
|
O
|
E:HOH707
|
2.4
|
16.3
|
1.0
|
OD1
|
E:ASP138
|
2.5
|
15.7
|
1.0
|
O8
|
E:CPJ613
|
2.6
|
93.1
|
1.0
|
CG
|
E:ASP138
|
2.8
|
14.3
|
1.0
|
CD
|
E:GLN148
|
3.4
|
12.6
|
1.0
|
C7
|
E:CPJ613
|
3.5
|
93.8
|
1.0
|
CD
|
E:GLU136
|
3.6
|
12.9
|
1.0
|
NE2
|
E:GLN148
|
3.6
|
12.3
|
1.0
|
O9
|
E:CPJ613
|
3.7
|
93.2
|
1.0
|
CA
|
E:CA608
|
3.9
|
20.4
|
1.0
|
CB
|
E:ASP145
|
4.2
|
13.4
|
1.0
|
CB
|
E:ASP138
|
4.2
|
13.4
|
1.0
|
CB
|
E:GLU136
|
4.3
|
10.1
|
1.0
|
O
|
E:GLU136
|
4.4
|
10.6
|
1.0
|
CG
|
E:GLU136
|
4.4
|
10.3
|
1.0
|
O
|
E:HOH649
|
4.4
|
38.4
|
1.0
|
O
|
E:GLN137
|
4.4
|
9.0
|
1.0
|
OE2
|
E:GLU136
|
4.5
|
12.9
|
1.0
|
OD2
|
E:ASP145
|
4.6
|
17.9
|
1.0
|
CG
|
E:GLN148
|
4.7
|
12.3
|
1.0
|
C
|
E:GLN137
|
4.8
|
11.3
|
1.0
|
C
|
E:GLU136
|
4.8
|
10.1
|
1.0
|
C6
|
E:CPJ613
|
4.8
|
94.2
|
1.0
|
N
|
E:ASP138
|
4.9
|
11.9
|
1.0
|
O
|
E:LYS143
|
4.9
|
13.6
|
1.0
|
CA
|
E:ASP138
|
4.9
|
13.4
|
1.0
|
CG
|
E:ASP145
|
4.9
|
15.3
|
1.0
|
|
Reference:
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
Page generated: Fri Jul 12 08:33:42 2024
|