Calcium in PDB 2a3w: Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}-Ethane
Protein crystallography data
The structure of Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}-Ethane, PDB code: 2a3w
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)
|
100.00 /
2.20
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
96.712,
105.325,
146.007,
86.53,
78.15,
76.78
|
R / Rfree (%)
|
18.8 /
22.9
|
Calcium Binding Sites:
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 Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}-Ethane
(pdb code 2a3w). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 40 binding sites of Calcium where determined in the
Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}-Ethane, PDB code: 2a3w:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 40 in 2a3w
Go back to
Calcium Binding Sites List in 2a3w
Calcium binding site 1 out
of 40 in the Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-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 Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}-Ethane within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:19.4
occ:1.00
|
O8
|
A:CPJ341
|
2.2
|
19.5
|
1.0
|
OE1
|
A:GLN148
|
2.2
|
10.4
|
1.0
|
O
|
A:HOH638
|
2.2
|
25.0
|
1.0
|
OE1
|
A:GLU136
|
2.3
|
10.2
|
1.0
|
O
|
A:HOH639
|
2.3
|
21.5
|
1.0
|
OD1
|
A:ASP138
|
2.4
|
10.4
|
1.0
|
OD2
|
A:ASP138
|
2.5
|
10.7
|
1.0
|
CG
|
A:ASP138
|
2.8
|
11.5
|
1.0
|
CD
|
A:GLN148
|
3.2
|
10.9
|
1.0
|
C7
|
A:CPJ341
|
3.2
|
22.3
|
1.0
|
CD
|
A:GLU136
|
3.5
|
12.6
|
1.0
|
NE2
|
A:GLN148
|
3.5
|
10.3
|
1.0
|
O9
|
A:CPJ341
|
3.6
|
25.1
|
1.0
|
CA
|
A:CA302
|
3.9
|
20.3
|
1.0
|
CG
|
A:GLU136
|
4.2
|
13.7
|
1.0
|
CB
|
A:ASP145
|
4.2
|
13.6
|
1.0
|
CB
|
A:ASP138
|
4.2
|
10.2
|
1.0
|
CB
|
A:GLU136
|
4.3
|
11.6
|
1.0
|
O
|
A:GLU136
|
4.4
|
12.4
|
1.0
|
OE2
|
A:GLU136
|
4.4
|
11.1
|
1.0
|
O
|
A:GLN137
|
4.5
|
10.4
|
1.0
|
C6
|
A:CPJ341
|
4.5
|
26.9
|
1.0
|
OD2
|
A:ASP145
|
4.6
|
14.7
|
1.0
|
CG
|
A:GLN148
|
4.6
|
11.7
|
1.0
|
O
|
A:HOH1512
|
4.6
|
35.8
|
1.0
|
O5
|
A:CPJ341
|
4.7
|
25.1
|
1.0
|
C
|
A:GLN137
|
4.7
|
10.8
|
1.0
|
C
|
A:GLU136
|
4.8
|
11.8
|
1.0
|
O
|
A:LYS143
|
4.8
|
13.4
|
1.0
|
N
|
A:ASP138
|
4.8
|
9.8
|
1.0
|
CA
|
A:ASP138
|
4.9
|
11.3
|
1.0
|
CG
|
A:ASP145
|
4.9
|
14.3
|
1.0
|
|
Calcium binding site 2 out
of 40 in 2a3w
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Calcium Binding Sites List in 2a3w
Calcium binding site 2 out
of 40 in the Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-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 Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}-Ethane within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca302
b:20.3
occ:1.00
|
O9
|
A:CPJ341
|
2.3
|
25.1
|
1.0
|
OE2
|
A:GLU136
|
2.3
|
11.1
|
1.0
|
O
|
A:GLN137
|
2.3
|
10.4
|
1.0
|
OD1
|
A:ASN59
|
2.4
|
13.9
|
1.0
|
OD1
|
A:ASP58
|
2.5
|
14.8
|
1.0
|
OD1
|
A:ASP138
|
2.5
|
10.4
|
1.0
|
OE1
|
A:GLU136
|
2.5
|
10.2
|
1.0
|
OD2
|
A:ASP58
|
2.6
|
13.3
|
1.0
|
CD
|
A:GLU136
|
2.8
|
12.6
|
1.0
|
CG
|
A:ASP58
|
2.9
|
13.8
|
1.0
|
C7
|
A:CPJ341
|
3.3
|
22.3
|
1.0
|
CG
|
A:ASN59
|
3.4
|
13.5
|
1.0
|
C
|
A:GLN137
|
3.5
|
10.8
|
1.0
|
CG
|
A:ASP138
|
3.7
|
11.5
|
1.0
|
O8
|
A:CPJ341
|
3.8
|
19.5
|
1.0
|
ND2
|
A:ASN59
|
3.8
|
12.6
|
1.0
|
CA
|
A:ASP138
|
3.9
|
11.3
|
1.0
|
CA
|
A:CA301
|
3.9
|
19.4
|
1.0
|
N
|
A:ASP138
|
4.1
|
9.8
|
1.0
|
O
|
A:HOH938
|
4.1
|
18.9
|
1.0
|
CG
|
A:GLU136
|
4.3
|
13.7
|
1.0
|
N
|
A:ASN59
|
4.4
|
11.5
|
1.0
|
CB
|
A:ASP138
|
4.4
|
10.2
|
1.0
|
CB
|
A:ASP58
|
4.4
|
12.3
|
1.0
|
C6
|
A:CPJ341
|
4.5
|
26.9
|
1.0
|
OD2
|
A:ASP138
|
4.7
|
10.7
|
1.0
|
CA
|
A:GLN137
|
4.7
|
10.8
|
1.0
|
N
|
A:GLN137
|
4.7
|
10.9
|
1.0
|
CB
|
A:ASN59
|
4.7
|
11.4
|
1.0
|
C10
|
A:CPJ341
|
4.7
|
26.9
|
1.0
|
ND2
|
A:ASN53
|
4.8
|
10.5
|
1.0
|
O1
|
A:CPJ341
|
4.8
|
27.6
|
1.0
|
CA
|
A:ASN59
|
4.9
|
11.7
|
1.0
|
OD1
|
A:ASN53
|
4.9
|
11.9
|
1.0
|
O
|
A:HOH638
|
4.9
|
25.0
|
1.0
|
|
Calcium binding site 3 out
of 40 in 2a3w
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Calcium Binding Sites List in 2a3w
Calcium binding site 3 out
of 40 in the Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-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 Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}-Ethane within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca303
b:23.8
occ:1.00
|
O
|
B:HOH649
|
2.2
|
26.1
|
1.0
|
O8
|
B:CPJ342
|
2.2
|
21.1
|
1.0
|
OE1
|
B:GLN148
|
2.4
|
10.9
|
1.0
|
O
|
B:HOH648
|
2.4
|
23.2
|
1.0
|
OD2
|
B:ASP138
|
2.4
|
13.1
|
1.0
|
OE1
|
B:GLU136
|
2.4
|
12.9
|
1.0
|
OD1
|
B:ASP138
|
2.5
|
12.1
|
1.0
|
CG
|
B:ASP138
|
2.8
|
11.7
|
1.0
|
C7
|
B:CPJ342
|
3.2
|
25.6
|
1.0
|
CD
|
B:GLN148
|
3.3
|
12.3
|
1.0
|
CD
|
B:GLU136
|
3.6
|
14.4
|
1.0
|
O9
|
B:CPJ342
|
3.6
|
21.0
|
1.0
|
NE2
|
B:GLN148
|
3.7
|
10.1
|
1.0
|
CA
|
B:CA304
|
3.9
|
24.0
|
1.0
|
O
|
B:HOH786
|
4.2
|
38.3
|
1.0
|
CB
|
B:ASP138
|
4.2
|
11.9
|
1.0
|
CB
|
B:ASP145
|
4.2
|
15.5
|
1.0
|
CB
|
B:GLU136
|
4.3
|
13.2
|
1.0
|
CG
|
B:GLU136
|
4.4
|
11.9
|
1.0
|
O
|
B:GLU136
|
4.4
|
13.5
|
1.0
|
OE2
|
B:GLU136
|
4.5
|
16.6
|
1.0
|
OD2
|
B:ASP145
|
4.5
|
15.5
|
1.0
|
C6
|
B:CPJ342
|
4.6
|
27.4
|
1.0
|
O
|
B:GLN137
|
4.6
|
9.0
|
1.0
|
O
|
B:HOH2299
|
4.7
|
40.5
|
1.0
|
CG
|
B:GLN148
|
4.7
|
9.8
|
1.0
|
C
|
B:GLN137
|
4.7
|
10.8
|
1.0
|
O5
|
B:CPJ342
|
4.7
|
31.2
|
1.0
|
O
|
B:LYS143
|
4.7
|
13.8
|
1.0
|
N
|
B:ASP138
|
4.8
|
11.0
|
1.0
|
O
|
B:HOH485
|
4.8
|
43.0
|
1.0
|
C
|
B:GLU136
|
4.8
|
12.3
|
1.0
|
CA
|
B:ASP138
|
4.8
|
12.4
|
1.0
|
CG
|
B:ASP145
|
4.9
|
14.7
|
1.0
|
|
Calcium binding site 4 out
of 40 in 2a3w
Go back to
Calcium Binding Sites List in 2a3w
Calcium binding site 4 out
of 40 in the Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-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 Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}-Ethane within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca304
b:24.0
occ:1.00
|
OD1
|
B:ASN59
|
2.3
|
12.4
|
1.0
|
O9
|
B:CPJ342
|
2.3
|
21.0
|
1.0
|
OD1
|
B:ASP58
|
2.4
|
18.2
|
1.0
|
OD1
|
B:ASP138
|
2.4
|
12.1
|
1.0
|
O
|
B:GLN137
|
2.4
|
9.0
|
1.0
|
OE2
|
B:GLU136
|
2.5
|
16.6
|
1.0
|
OD2
|
B:ASP58
|
2.6
|
15.3
|
1.0
|
OE1
|
B:GLU136
|
2.6
|
12.9
|
1.0
|
CG
|
B:ASP58
|
2.9
|
17.0
|
1.0
|
CD
|
B:GLU136
|
2.9
|
14.4
|
1.0
|
CG
|
B:ASN59
|
3.3
|
12.4
|
1.0
|
C7
|
B:CPJ342
|
3.4
|
25.6
|
1.0
|
C
|
B:GLN137
|
3.5
|
10.8
|
1.0
|
CG
|
B:ASP138
|
3.6
|
11.7
|
1.0
|
ND2
|
B:ASN59
|
3.7
|
10.4
|
1.0
|
CA
|
B:ASP138
|
3.8
|
12.4
|
1.0
|
O8
|
B:CPJ342
|
3.8
|
21.1
|
1.0
|
CA
|
B:CA303
|
3.9
|
23.8
|
1.0
|
N
|
B:ASP138
|
4.0
|
11.0
|
1.0
|
N
|
B:ASN59
|
4.3
|
12.9
|
1.0
|
CB
|
B:ASP138
|
4.3
|
11.9
|
1.0
|
CB
|
B:ASP58
|
4.4
|
14.2
|
1.0
|
CG
|
B:GLU136
|
4.4
|
11.9
|
1.0
|
OD2
|
B:ASP138
|
4.5
|
13.1
|
1.0
|
C6
|
B:CPJ342
|
4.6
|
27.4
|
1.0
|
CB
|
B:ASN59
|
4.6
|
12.0
|
1.0
|
ND2
|
B:ASN53
|
4.7
|
10.1
|
1.0
|
CA
|
B:GLN137
|
4.7
|
11.3
|
1.0
|
N
|
B:GLN137
|
4.8
|
11.3
|
1.0
|
C10
|
B:CPJ342
|
4.8
|
27.7
|
1.0
|
CA
|
B:ASN59
|
4.8
|
13.4
|
1.0
|
O1
|
B:CPJ342
|
4.9
|
27.4
|
1.0
|
OD1
|
B:ASN53
|
4.9
|
6.6
|
1.0
|
C
|
B:ASP138
|
5.0
|
12.8
|
1.0
|
CA
|
B:ASP58
|
5.0
|
14.3
|
1.0
|
C
|
B:ASP58
|
5.0
|
13.6
|
1.0
|
|
Calcium binding site 5 out
of 40 in 2a3w
Go back to
Calcium Binding Sites List in 2a3w
Calcium binding site 5 out
of 40 in the Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-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 Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}-Ethane within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca305
b:28.7
occ:1.00
|
O9
|
C:CPJ343
|
2.2
|
27.8
|
1.0
|
O
|
C:GLN137
|
2.3
|
10.7
|
1.0
|
OD1
|
C:ASP58
|
2.3
|
14.8
|
1.0
|
OD1
|
C:ASP138
|
2.4
|
11.2
|
1.0
|
OD1
|
C:ASN59
|
2.4
|
13.9
|
1.0
|
OE2
|
C:GLU136
|
2.5
|
13.2
|
1.0
|
OE1
|
C:GLU136
|
2.6
|
13.8
|
1.0
|
OD2
|
C:ASP58
|
2.6
|
11.2
|
1.0
|
CG
|
C:ASP58
|
2.9
|
13.4
|
1.0
|
CD
|
C:GLU136
|
2.9
|
12.4
|
1.0
|
C7
|
C:CPJ343
|
3.2
|
32.1
|
1.0
|
C
|
C:GLN137
|
3.4
|
11.6
|
1.0
|
CG
|
C:ASN59
|
3.5
|
13.7
|
1.0
|
CG
|
C:ASP138
|
3.6
|
10.9
|
1.0
|
O8
|
C:CPJ343
|
3.6
|
26.8
|
1.0
|
CA
|
C:ASP138
|
3.8
|
11.9
|
1.0
|
ND2
|
C:ASN59
|
3.9
|
15.7
|
1.0
|
CA
|
C:CA306
|
3.9
|
26.7
|
1.0
|
N
|
C:ASP138
|
4.0
|
11.5
|
1.0
|
O
|
C:HOH1223
|
4.1
|
29.6
|
1.0
|
CB
|
C:ASP138
|
4.3
|
12.3
|
1.0
|
N
|
C:ASN59
|
4.4
|
14.0
|
1.0
|
CB
|
C:ASP58
|
4.4
|
13.4
|
1.0
|
CG
|
C:GLU136
|
4.4
|
13.2
|
1.0
|
C6
|
C:CPJ343
|
4.4
|
33.1
|
1.0
|
OD2
|
C:ASP138
|
4.5
|
8.7
|
1.0
|
C10
|
C:CPJ343
|
4.6
|
32.7
|
1.0
|
CA
|
C:GLN137
|
4.6
|
12.0
|
1.0
|
N
|
C:GLN137
|
4.6
|
13.0
|
1.0
|
CB
|
C:ASN59
|
4.7
|
13.6
|
1.0
|
ND2
|
C:ASN53
|
4.9
|
8.2
|
1.0
|
O1
|
C:CPJ343
|
4.9
|
35.5
|
1.0
|
CA
|
C:ASN59
|
4.9
|
14.2
|
1.0
|
OD1
|
C:ASN53
|
4.9
|
10.9
|
1.0
|
O
|
C:HOH650
|
5.0
|
28.9
|
1.0
|
C
|
C:ASP138
|
5.0
|
11.8
|
1.0
|
|
Calcium binding site 6 out
of 40 in 2a3w
Go back to
Calcium Binding Sites List in 2a3w
Calcium binding site 6 out
of 40 in the Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-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 Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}-Ethane within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca306
b:26.7
occ:1.00
|
O
|
C:HOH650
|
2.2
|
28.9
|
1.0
|
O8
|
C:CPJ343
|
2.3
|
26.8
|
1.0
|
OE1
|
C:GLN148
|
2.4
|
10.1
|
1.0
|
OE1
|
C:GLU136
|
2.4
|
13.8
|
1.0
|
OD2
|
C:ASP138
|
2.4
|
8.7
|
1.0
|
O
|
C:HOH651
|
2.5
|
31.3
|
1.0
|
OD1
|
C:ASP138
|
2.6
|
11.2
|
1.0
|
CG
|
C:ASP138
|
2.8
|
10.9
|
1.0
|
C7
|
C:CPJ343
|
3.3
|
32.1
|
1.0
|
CD
|
C:GLN148
|
3.4
|
10.5
|
1.0
|
CD
|
C:GLU136
|
3.6
|
12.4
|
1.0
|
O9
|
C:CPJ343
|
3.7
|
27.8
|
1.0
|
NE2
|
C:GLN148
|
3.8
|
7.0
|
1.0
|
CA
|
C:CA305
|
3.9
|
28.7
|
1.0
|
CB
|
C:ASP145
|
4.1
|
14.2
|
1.0
|
CB
|
C:GLU136
|
4.2
|
13.7
|
1.0
|
CB
|
C:ASP138
|
4.2
|
12.3
|
1.0
|
CG
|
C:GLU136
|
4.3
|
13.2
|
1.0
|
O
|
C:GLU136
|
4.3
|
13.2
|
1.0
|
O
|
C:GLN137
|
4.5
|
10.7
|
1.0
|
OE2
|
C:GLU136
|
4.6
|
13.2
|
1.0
|
O
|
C:HOH726
|
4.6
|
38.5
|
1.0
|
OD2
|
C:ASP145
|
4.6
|
13.3
|
1.0
|
C6
|
C:CPJ343
|
4.6
|
33.1
|
1.0
|
O
|
C:HOH1145
|
4.6
|
35.7
|
1.0
|
C
|
C:GLN137
|
4.7
|
11.6
|
1.0
|
C
|
C:GLU136
|
4.7
|
13.6
|
1.0
|
O
|
C:LYS143
|
4.7
|
12.5
|
1.0
|
O
|
C:HOH3606
|
4.7
|
44.4
|
1.0
|
N
|
C:ASP138
|
4.7
|
11.5
|
1.0
|
CG
|
C:GLN148
|
4.8
|
10.9
|
1.0
|
O5
|
C:CPJ343
|
4.8
|
33.7
|
1.0
|
CG
|
C:ASP145
|
4.9
|
15.6
|
1.0
|
CA
|
C:ASP138
|
4.9
|
11.9
|
1.0
|
|
Calcium binding site 7 out
of 40 in 2a3w
Go back to
Calcium Binding Sites List in 2a3w
Calcium binding site 7 out
of 40 in the Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-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 Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}-Ethane within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca307
b:26.8
occ:1.00
|
O
|
D:GLN137
|
2.3
|
11.5
|
1.0
|
O9
|
D:CPJ344
|
2.3
|
31.2
|
1.0
|
OD1
|
D:ASP138
|
2.3
|
6.1
|
1.0
|
OD1
|
D:ASP58
|
2.4
|
7.7
|
1.0
|
OD1
|
D:ASN59
|
2.4
|
13.0
|
1.0
|
OE2
|
D:GLU136
|
2.5
|
15.2
|
1.0
|
OE1
|
D:GLU136
|
2.6
|
10.3
|
1.0
|
OD2
|
D:ASP58
|
2.6
|
11.5
|
1.0
|
CG
|
D:ASP58
|
2.9
|
11.3
|
1.0
|
CD
|
D:GLU136
|
2.9
|
11.5
|
1.0
|
C7
|
D:CPJ344
|
3.4
|
31.9
|
1.0
|
C
|
D:GLN137
|
3.4
|
11.5
|
1.0
|
CG
|
D:ASN59
|
3.5
|
12.7
|
1.0
|
CG
|
D:ASP138
|
3.5
|
10.3
|
1.0
|
CA
|
D:ASP138
|
3.7
|
10.8
|
1.0
|
CA
|
D:CA308
|
3.8
|
26.7
|
1.0
|
O8
|
D:CPJ344
|
3.9
|
29.9
|
1.0
|
ND2
|
D:ASN59
|
3.9
|
13.3
|
1.0
|
N
|
D:ASP138
|
4.0
|
11.3
|
1.0
|
O
|
D:HOH513
|
4.1
|
24.2
|
1.0
|
CB
|
D:ASP138
|
4.2
|
10.4
|
1.0
|
N
|
D:ASN59
|
4.4
|
12.0
|
1.0
|
CB
|
D:ASP58
|
4.4
|
10.6
|
1.0
|
CG
|
D:GLU136
|
4.4
|
9.7
|
1.0
|
OD2
|
D:ASP138
|
4.5
|
12.1
|
1.0
|
C6
|
D:CPJ344
|
4.5
|
33.8
|
1.0
|
C10
|
D:CPJ344
|
4.6
|
27.6
|
1.0
|
CA
|
D:GLN137
|
4.6
|
11.6
|
1.0
|
N
|
D:GLN137
|
4.7
|
10.8
|
1.0
|
O
|
D:HOH652
|
4.8
|
26.3
|
1.0
|
CB
|
D:ASN59
|
4.8
|
12.8
|
1.0
|
ND2
|
D:ASN53
|
4.8
|
6.1
|
1.0
|
OD1
|
D:ASN53
|
4.9
|
8.2
|
1.0
|
C
|
D:ASP138
|
4.9
|
10.7
|
1.0
|
O1
|
D:CPJ344
|
4.9
|
33.1
|
1.0
|
CA
|
D:ASN59
|
4.9
|
12.9
|
1.0
|
|
Calcium binding site 8 out
of 40 in 2a3w
Go back to
Calcium Binding Sites List in 2a3w
Calcium binding site 8 out
of 40 in the Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-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 Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}-Ethane within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca308
b:26.7
occ:1.00
|
O
|
D:HOH652
|
2.2
|
26.3
|
1.0
|
O
|
D:HOH653
|
2.2
|
27.5
|
1.0
|
O8
|
D:CPJ344
|
2.3
|
29.9
|
1.0
|
OE1
|
D:GLN148
|
2.4
|
6.0
|
1.0
|
OE1
|
D:GLU136
|
2.4
|
10.3
|
1.0
|
OD1
|
D:ASP138
|
2.5
|
6.1
|
1.0
|
OD2
|
D:ASP138
|
2.6
|
12.1
|
1.0
|
CG
|
D:ASP138
|
2.9
|
10.3
|
1.0
|
C7
|
D:CPJ344
|
3.2
|
31.9
|
1.0
|
CD
|
D:GLN148
|
3.3
|
8.9
|
1.0
|
O9
|
D:CPJ344
|
3.5
|
31.2
|
1.0
|
CD
|
D:GLU136
|
3.6
|
11.5
|
1.0
|
NE2
|
D:GLN148
|
3.6
|
6.1
|
1.0
|
CA
|
D:CA307
|
3.8
|
26.8
|
1.0
|
CB
|
D:ASP145
|
4.2
|
13.6
|
1.0
|
CB
|
D:ASP138
|
4.3
|
10.4
|
1.0
|
O
|
D:HOH3388
|
4.3
|
38.6
|
1.0
|
O
|
D:GLU136
|
4.3
|
9.6
|
1.0
|
O
|
D:GLN137
|
4.4
|
11.5
|
1.0
|
CB
|
D:GLU136
|
4.4
|
10.0
|
1.0
|
CG
|
D:GLU136
|
4.4
|
9.7
|
1.0
|
OE2
|
D:GLU136
|
4.5
|
15.2
|
1.0
|
C6
|
D:CPJ344
|
4.5
|
33.8
|
1.0
|
OD2
|
D:ASP145
|
4.6
|
18.1
|
1.0
|
C
|
D:GLN137
|
4.7
|
11.5
|
1.0
|
CG
|
D:GLN148
|
4.7
|
8.2
|
1.0
|
C
|
D:GLU136
|
4.7
|
10.5
|
1.0
|
O5
|
D:CPJ344
|
4.8
|
33.8
|
1.0
|
N
|
D:ASP138
|
4.8
|
11.3
|
1.0
|
O
|
D:LYS143
|
4.8
|
10.8
|
1.0
|
CG
|
D:ASP145
|
4.9
|
15.3
|
1.0
|
CA
|
D:ASP138
|
4.9
|
10.8
|
1.0
|
O
|
D:HOH1189
|
4.9
|
36.1
|
1.0
|
|
Calcium binding site 9 out
of 40 in 2a3w
Go back to
Calcium Binding Sites List in 2a3w
Calcium binding site 9 out
of 40 in the Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-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 Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}-Ethane within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca309
b:24.9
occ:1.00
|
O
|
E:GLN137
|
2.3
|
11.3
|
1.0
|
O9
|
E:CPJ345
|
2.3
|
29.0
|
1.0
|
OD1
|
E:ASN59
|
2.3
|
14.9
|
1.0
|
OE2
|
E:GLU136
|
2.3
|
11.6
|
1.0
|
OD1
|
E:ASP138
|
2.3
|
10.1
|
1.0
|
OD1
|
E:ASP58
|
2.5
|
9.8
|
1.0
|
OD2
|
E:ASP58
|
2.6
|
10.7
|
1.0
|
OE1
|
E:GLU136
|
2.8
|
11.2
|
1.0
|
CD
|
E:GLU136
|
2.9
|
12.1
|
1.0
|
CG
|
E:ASP58
|
2.9
|
13.4
|
1.0
|
CG
|
E:ASN59
|
3.3
|
14.7
|
1.0
|
C7
|
E:CPJ345
|
3.4
|
32.9
|
1.0
|
C
|
E:GLN137
|
3.4
|
12.2
|
1.0
|
CG
|
E:ASP138
|
3.5
|
13.0
|
1.0
|
ND2
|
E:ASN59
|
3.8
|
11.0
|
1.0
|
CA
|
E:ASP138
|
3.8
|
13.3
|
1.0
|
O8
|
E:CPJ345
|
3.9
|
33.4
|
1.0
|
CA
|
E:CA310
|
3.9
|
23.0
|
1.0
|
N
|
E:ASP138
|
4.0
|
12.4
|
1.0
|
CB
|
E:ASP138
|
4.3
|
11.8
|
1.0
|
N
|
E:ASN59
|
4.3
|
13.2
|
1.0
|
CG
|
E:GLU136
|
4.4
|
8.9
|
1.0
|
CB
|
E:ASP58
|
4.4
|
10.9
|
1.0
|
OD2
|
E:ASP138
|
4.4
|
13.3
|
1.0
|
C6
|
E:CPJ345
|
4.6
|
33.5
|
1.0
|
CA
|
E:GLN137
|
4.6
|
12.0
|
1.0
|
CB
|
E:ASN59
|
4.6
|
11.6
|
1.0
|
N
|
E:GLN137
|
4.7
|
12.2
|
1.0
|
C10
|
E:CPJ345
|
4.7
|
33.7
|
1.0
|
ND2
|
E:ASN53
|
4.8
|
9.1
|
1.0
|
OD1
|
E:ASN53
|
4.8
|
9.7
|
1.0
|
CA
|
E:ASN59
|
4.8
|
13.2
|
1.0
|
O1
|
E:CPJ345
|
5.0
|
34.0
|
1.0
|
O
|
E:HOH655
|
5.0
|
23.6
|
1.0
|
C
|
E:ASP138
|
5.0
|
12.7
|
1.0
|
|
Calcium binding site 10 out
of 40 in 2a3w
Go back to
Calcium Binding Sites List in 2a3w
Calcium binding site 10 out
of 40 in the Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-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 Decameric Structure of Human Serum Amyloid P-Component Bound to Bis-1, 2-{[(Z)-2-Carboxy-2-Methyl-1,3-Dioxane]-5-Yloxycarbamoyl}-Ethane within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca310
b:23.0
occ:1.00
|
OE1
|
E:GLU136
|
2.1
|
11.2
|
1.0
|
O8
|
E:CPJ345
|
2.3
|
33.4
|
1.0
|
O
|
E:HOH654
|
2.3
|
17.0
|
1.0
|
OE1
|
E:GLN148
|
2.4
|
8.6
|
1.0
|
O
|
E:HOH655
|
2.4
|
23.6
|
1.0
|
OD2
|
E:ASP138
|
2.4
|
13.3
|
1.0
|
OD1
|
E:ASP138
|
2.7
|
10.1
|
1.0
|
CG
|
E:ASP138
|
2.8
|
13.0
|
1.0
|
C7
|
E:CPJ345
|
3.3
|
32.9
|
1.0
|
CD
|
E:GLU136
|
3.3
|
12.1
|
1.0
|
CD
|
E:GLN148
|
3.4
|
10.1
|
1.0
|
O9
|
E:CPJ345
|
3.6
|
29.0
|
1.0
|
NE2
|
E:GLN148
|
3.7
|
5.7
|
1.0
|
CA
|
E:CA309
|
3.9
|
24.9
|
1.0
|
CB
|
E:ASP145
|
4.1
|
12.7
|
1.0
|
CG
|
E:GLU136
|
4.2
|
8.9
|
1.0
|
CB
|
E:GLU136
|
4.2
|
10.6
|
1.0
|
CB
|
E:ASP138
|
4.2
|
11.8
|
1.0
|
OE2
|
E:GLU136
|
4.2
|
11.6
|
1.0
|
O
|
E:GLU136
|
4.3
|
12.3
|
1.0
|
O
|
E:GLN137
|
4.4
|
11.3
|
1.0
|
OD2
|
E:ASP145
|
4.5
|
13.9
|
1.0
|
O
|
E:HOH2150
|
4.5
|
35.6
|
1.0
|
C6
|
E:CPJ345
|
4.6
|
33.5
|
1.0
|
CG
|
E:GLN148
|
4.7
|
10.6
|
1.0
|
C
|
E:GLU136
|
4.7
|
12.2
|
1.0
|
C
|
E:GLN137
|
4.7
|
12.2
|
1.0
|
O5
|
E:CPJ345
|
4.8
|
34.2
|
1.0
|
CG
|
E:ASP145
|
4.8
|
15.2
|
1.0
|
O
|
E:LYS143
|
4.8
|
14.0
|
1.0
|
N
|
E:ASP138
|
4.9
|
12.4
|
1.0
|
O
|
E:HOH1221
|
4.9
|
41.2
|
1.0
|
CA
|
E:ASP138
|
4.9
|
13.3
|
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 08:33:43 2024
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