Calcium in PDB 4ayu: Structure of N-Acetyl-D-Proline Bound to Serum Amyloid P Component
Protein crystallography data
The structure of Structure of N-Acetyl-D-Proline Bound to Serum Amyloid P Component, PDB code: 4ayu
was solved by
P.Hughes,
S.E.Kolstoe,
S.P.Wood,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
28.663 /
1.50
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.420,
70.555,
99.055,
90.00,
96.90,
90.00
|
|
R / Rfree (%)
|
15.47 /
16.76
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of N-Acetyl-D-Proline Bound to Serum Amyloid P Component
(pdb code 4ayu). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the
Structure of N-Acetyl-D-Proline Bound to Serum Amyloid P Component, PDB code: 4ayu:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 10 in 4ayu
Go back to
Calcium Binding Sites List in 4ayu
Calcium binding site 1 out
of 10 in the Structure of N-Acetyl-D-Proline 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 N-Acetyl-D-Proline Bound to Serum Amyloid P Component within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca205
b:10.3
occ:1.00
|
OE1
|
A:GLU136
|
2.4
|
8.7
|
1.0
|
|
O
|
A:N8P499
|
2.4
|
12.3
|
1.0
|
|
O
|
A:HOH2256
|
2.4
|
13.0
|
1.0
|
|
OE1
|
A:GLN148
|
2.4
|
9.2
|
1.0
|
|
O
|
A:HOH2252
|
2.4
|
9.8
|
1.0
|
|
OD1
|
A:ASP138
|
2.5
|
9.1
|
1.0
|
|
OD2
|
A:ASP138
|
2.6
|
11.3
|
1.0
|
|
O
|
A:HOH2254
|
2.7
|
24.6
|
1.0
|
|
CG
|
A:ASP138
|
2.9
|
8.3
|
1.0
|
|
C
|
A:N8P499
|
3.3
|
10.8
|
1.0
|
|
CD
|
A:GLN148
|
3.4
|
8.4
|
1.0
|
|
OXT
|
A:N8P499
|
3.5
|
10.5
|
1.0
|
|
CD
|
A:GLU136
|
3.6
|
9.4
|
1.0
|
|
NE2
|
A:GLN148
|
3.8
|
12.6
|
1.0
|
|
CA
|
A:CA206
|
3.8
|
9.2
|
1.0
|
|
CB
|
A:ASP138
|
4.3
|
9.1
|
1.0
|
|
CG
|
A:GLU136
|
4.3
|
9.8
|
1.0
|
|
CB
|
A:ASP145
|
4.4
|
11.1
|
1.0
|
|
CB
|
A:GLU136
|
4.4
|
8.8
|
1.0
|
|
O
|
A:GLU136
|
4.4
|
9.8
|
1.0
|
|
OE2
|
A:GLU136
|
4.5
|
8.3
|
1.0
|
|
O
|
A:HOH2149
|
4.5
|
30.2
|
1.0
|
|
O
|
A:GLN137
|
4.6
|
8.6
|
1.0
|
|
OD2
|
A:ASP145
|
4.6
|
15.9
|
1.0
|
|
CA
|
A:N8P499
|
4.7
|
9.6
|
1.0
|
|
CG
|
A:GLN148
|
4.8
|
7.9
|
1.0
|
|
C
|
A:GLN137
|
4.9
|
11.5
|
1.0
|
|
O
|
A:LYS143
|
4.9
|
9.4
|
1.0
|
|
C
|
A:GLU136
|
4.9
|
8.3
|
1.0
|
|
N
|
A:ASP138
|
4.9
|
8.5
|
1.0
|
|
O
|
A:HOH2255
|
4.9
|
19.3
|
1.0
|
|
CA
|
A:ASP138
|
5.0
|
9.4
|
1.0
|
|
Calcium binding site 2 out
of 10 in 4ayu
Go back to
Calcium Binding Sites List in 4ayu
Calcium binding site 2 out
of 10 in the Structure of N-Acetyl-D-Proline 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 N-Acetyl-D-Proline Bound to Serum Amyloid P Component within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca206
b:9.2
occ:1.00
|
OD1
|
A:ASP138
|
2.4
|
9.1
|
1.0
|
|
OXT
|
A:N8P499
|
2.4
|
10.5
|
1.0
|
|
O
|
A:GLN137
|
2.4
|
8.6
|
1.0
|
|
OD1
|
A:ASN59
|
2.4
|
8.6
|
1.0
|
|
OE2
|
A:GLU136
|
2.5
|
8.3
|
1.0
|
|
OD1
|
A:ASP58
|
2.5
|
9.8
|
1.0
|
|
OE1
|
A:GLU136
|
2.6
|
8.7
|
1.0
|
|
OD2
|
A:ASP58
|
2.7
|
10.9
|
1.0
|
|
CD
|
A:GLU136
|
2.9
|
9.4
|
1.0
|
|
CG
|
A:ASP58
|
2.9
|
9.3
|
1.0
|
|
C
|
A:N8P499
|
3.4
|
10.8
|
1.0
|
|
CG
|
A:ASN59
|
3.4
|
9.7
|
1.0
|
|
C
|
A:GLN137
|
3.5
|
11.5
|
1.0
|
|
CG
|
A:ASP138
|
3.6
|
8.3
|
1.0
|
|
CA
|
A:ASP138
|
3.8
|
9.4
|
1.0
|
|
ND2
|
A:ASN59
|
3.8
|
11.2
|
1.0
|
|
CA
|
A:CA205
|
3.8
|
10.3
|
1.0
|
|
O
|
A:N8P499
|
3.9
|
12.3
|
1.0
|
|
N
|
A:ASP138
|
4.0
|
8.5
|
1.0
|
|
O
|
A:HOH2125
|
4.2
|
9.5
|
1.0
|
|
CB
|
A:ASP138
|
4.2
|
9.1
|
1.0
|
|
O
|
A:HOH2149
|
4.4
|
30.2
|
1.0
|
|
N
|
A:ASN59
|
4.4
|
8.8
|
1.0
|
|
CG
|
A:GLU136
|
4.4
|
9.8
|
1.0
|
|
CB
|
A:ASP58
|
4.4
|
9.1
|
1.0
|
|
OD2
|
A:ASP138
|
4.6
|
11.3
|
1.0
|
|
CA
|
A:N8P499
|
4.6
|
9.6
|
1.0
|
|
CB
|
A:N8P499
|
4.7
|
10.7
|
1.0
|
|
CA
|
A:GLN137
|
4.7
|
9.5
|
1.0
|
|
CB
|
A:ASN59
|
4.7
|
9.9
|
1.0
|
|
N
|
A:GLN137
|
4.7
|
8.2
|
1.0
|
|
O
|
A:HOH2254
|
4.8
|
24.6
|
1.0
|
|
ND2
|
A:ASN53
|
4.8
|
9.1
|
1.0
|
|
CA
|
A:ASN59
|
4.9
|
9.3
|
1.0
|
|
O
|
A:HOH2148
|
4.9
|
26.8
|
1.0
|
|
C
|
A:ASP138
|
5.0
|
12.6
|
1.0
|
|
O
|
A:HOH2252
|
5.0
|
9.8
|
1.0
|
|
Calcium binding site 3 out
of 10 in 4ayu
Go back to
Calcium Binding Sites List in 4ayu
Calcium binding site 3 out
of 10 in the Structure of N-Acetyl-D-Proline 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 N-Acetyl-D-Proline Bound to Serum Amyloid P Component within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca205
b:12.3
occ:1.00
|
OE1
|
B:GLU136
|
2.3
|
11.1
|
1.0
|
|
OE1
|
B:GLN148
|
2.4
|
12.6
|
1.0
|
|
O
|
B:N8P499
|
2.4
|
13.9
|
1.0
|
|
O
|
B:HOH2221
|
2.5
|
12.5
|
1.0
|
|
O
|
B:HOH2223
|
2.5
|
15.5
|
1.0
|
|
OD1
|
B:ASP138
|
2.5
|
13.2
|
1.0
|
|
OD2
|
B:ASP138
|
2.6
|
14.7
|
1.0
|
|
O
|
B:HOH2222
|
2.8
|
29.4
|
1.0
|
|
CG
|
B:ASP138
|
2.9
|
13.5
|
1.0
|
|
C
|
B:N8P499
|
3.4
|
13.1
|
1.0
|
|
CD
|
B:GLN148
|
3.4
|
10.5
|
1.0
|
|
CD
|
B:GLU136
|
3.5
|
12.2
|
1.0
|
|
OXT
|
B:N8P499
|
3.6
|
11.8
|
1.0
|
|
O
|
B:HOH2110
|
3.7
|
35.6
|
1.0
|
|
NE2
|
B:GLN148
|
3.7
|
15.2
|
1.0
|
|
CA
|
B:CA206
|
3.8
|
11.8
|
1.0
|
|
CG
|
B:GLU136
|
4.3
|
11.4
|
1.0
|
|
CB
|
B:ASP138
|
4.3
|
13.8
|
1.0
|
|
CB
|
B:GLU136
|
4.4
|
10.3
|
1.0
|
|
CB
|
B:ASP145
|
4.4
|
11.8
|
1.0
|
|
OE2
|
B:GLU136
|
4.4
|
11.0
|
1.0
|
|
O
|
B:GLU136
|
4.4
|
11.6
|
1.0
|
|
O
|
B:HOH2134
|
4.5
|
34.9
|
1.0
|
|
OD2
|
B:ASP145
|
4.6
|
15.6
|
1.0
|
|
O
|
B:GLN137
|
4.7
|
11.6
|
1.0
|
|
CG
|
B:GLN148
|
4.8
|
11.8
|
1.0
|
|
CA
|
B:N8P499
|
4.8
|
12.1
|
1.0
|
|
C
|
B:GLN137
|
4.8
|
13.4
|
1.0
|
|
C
|
B:GLU136
|
4.8
|
10.5
|
1.0
|
|
O
|
B:LYS143
|
4.9
|
13.2
|
1.0
|
|
N
|
B:ASP138
|
4.9
|
13.1
|
1.0
|
|
O
|
B:HOH2224
|
4.9
|
21.7
|
1.0
|
|
CA
|
B:ASP138
|
4.9
|
15.3
|
1.0
|
|
Calcium binding site 4 out
of 10 in 4ayu
Go back to
Calcium Binding Sites List in 4ayu
Calcium binding site 4 out
of 10 in the Structure of N-Acetyl-D-Proline 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 N-Acetyl-D-Proline Bound to Serum Amyloid P Component within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca206
b:11.8
occ:1.00
|
OD1
|
B:ASP138
|
2.3
|
13.2
|
1.0
|
|
OXT
|
B:N8P499
|
2.4
|
11.8
|
1.0
|
|
OE2
|
B:GLU136
|
2.4
|
11.0
|
1.0
|
|
OD1
|
B:ASN59
|
2.4
|
12.4
|
1.0
|
|
O
|
B:GLN137
|
2.4
|
11.6
|
1.0
|
|
OD1
|
B:ASP58
|
2.5
|
12.3
|
1.0
|
|
OE1
|
B:GLU136
|
2.6
|
11.1
|
1.0
|
|
OD2
|
B:ASP58
|
2.7
|
14.1
|
1.0
|
|
CD
|
B:GLU136
|
2.8
|
12.2
|
1.0
|
|
CG
|
B:ASP58
|
2.9
|
13.0
|
1.0
|
|
CG
|
B:ASN59
|
3.4
|
11.3
|
1.0
|
|
C
|
B:N8P499
|
3.4
|
13.1
|
1.0
|
|
C
|
B:GLN137
|
3.5
|
13.4
|
1.0
|
|
CG
|
B:ASP138
|
3.5
|
13.5
|
1.0
|
|
CA
|
B:ASP138
|
3.8
|
15.3
|
1.0
|
|
ND2
|
B:ASN59
|
3.8
|
14.8
|
1.0
|
|
CA
|
B:CA205
|
3.8
|
12.3
|
1.0
|
|
O
|
B:N8P499
|
3.8
|
13.9
|
1.0
|
|
N
|
B:ASP138
|
4.0
|
13.1
|
1.0
|
|
O
|
B:HOH2116
|
4.1
|
12.1
|
1.0
|
|
CB
|
B:ASP138
|
4.2
|
13.8
|
1.0
|
|
O
|
B:HOH2134
|
4.3
|
34.9
|
1.0
|
|
CG
|
B:GLU136
|
4.4
|
11.4
|
1.0
|
|
CB
|
B:ASP58
|
4.4
|
12.5
|
1.0
|
|
N
|
B:ASN59
|
4.4
|
11.5
|
1.0
|
|
OD2
|
B:ASP138
|
4.5
|
14.7
|
1.0
|
|
CA
|
B:N8P499
|
4.6
|
12.1
|
1.0
|
|
CA
|
B:GLN137
|
4.7
|
10.1
|
1.0
|
|
N
|
B:GLN137
|
4.7
|
11.5
|
1.0
|
|
CB
|
B:ASN59
|
4.7
|
11.2
|
1.0
|
|
ND2
|
B:ASN53
|
4.7
|
12.8
|
1.0
|
|
CB
|
B:N8P499
|
4.8
|
11.6
|
1.0
|
|
CA
|
B:ASN59
|
4.9
|
11.4
|
1.0
|
|
O
|
B:HOH2133
|
4.9
|
27.9
|
1.0
|
|
OD1
|
B:ASN53
|
4.9
|
12.3
|
1.0
|
|
C
|
B:ASP138
|
5.0
|
15.6
|
1.0
|
|
O
|
B:HOH2222
|
5.0
|
29.4
|
1.0
|
|
Calcium binding site 5 out
of 10 in 4ayu
Go back to
Calcium Binding Sites List in 4ayu
Calcium binding site 5 out
of 10 in the Structure of N-Acetyl-D-Proline 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 N-Acetyl-D-Proline Bound to Serum Amyloid P Component within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca205
b:14.1
occ:1.00
|
O
|
C:HOH2183
|
2.4
|
18.1
|
1.0
|
|
OE1
|
C:GLU136
|
2.4
|
14.7
|
1.0
|
|
O
|
C:N8P499
|
2.4
|
16.4
|
1.0
|
|
OE1
|
C:GLN148
|
2.4
|
13.1
|
1.0
|
|
O
|
C:HOH2180
|
2.5
|
14.2
|
1.0
|
|
OD2
|
C:ASP138
|
2.6
|
15.4
|
1.0
|
|
O
|
C:HOH2182
|
2.6
|
28.2
|
1.0
|
|
OD1
|
C:ASP138
|
2.6
|
14.6
|
1.0
|
|
CG
|
C:ASP138
|
2.9
|
15.7
|
1.0
|
|
C
|
C:N8P499
|
3.4
|
14.4
|
1.0
|
|
CD
|
C:GLN148
|
3.4
|
12.0
|
1.0
|
|
OXT
|
C:N8P499
|
3.5
|
14.6
|
1.0
|
|
CD
|
C:GLU136
|
3.6
|
15.0
|
1.0
|
|
NE2
|
C:GLN148
|
3.8
|
15.3
|
1.0
|
|
CA
|
C:CA206
|
3.9
|
13.6
|
1.0
|
|
CG
|
C:GLU136
|
4.3
|
11.0
|
1.0
|
|
CB
|
C:ASP145
|
4.3
|
15.1
|
1.0
|
|
CB
|
C:ASP138
|
4.3
|
16.9
|
1.0
|
|
CB
|
C:GLU136
|
4.4
|
12.7
|
1.0
|
|
OE2
|
C:GLU136
|
4.4
|
11.7
|
1.0
|
|
O
|
C:HOH2106
|
4.5
|
32.5
|
1.0
|
|
O
|
C:GLU136
|
4.5
|
13.1
|
1.0
|
|
OD2
|
C:ASP145
|
4.6
|
19.9
|
1.0
|
|
O
|
C:GLN137
|
4.7
|
14.1
|
1.0
|
|
CG
|
C:GLN148
|
4.8
|
13.6
|
1.0
|
|
CA
|
C:N8P499
|
4.8
|
14.2
|
1.0
|
|
C8
|
C:N8P499
|
4.9
|
15.7
|
1.0
|
|
C
|
C:GLN137
|
4.9
|
13.7
|
1.0
|
|
O
|
C:HOH2184
|
4.9
|
26.4
|
1.0
|
|
C
|
C:GLU136
|
4.9
|
12.1
|
1.0
|
|
N
|
C:ASP138
|
4.9
|
14.9
|
1.0
|
|
O
|
C:LYS143
|
4.9
|
15.0
|
1.0
|
|
CA
|
C:ASP138
|
5.0
|
15.2
|
1.0
|
|
Calcium binding site 6 out
of 10 in 4ayu
Go back to
Calcium Binding Sites List in 4ayu
Calcium binding site 6 out
of 10 in the Structure of N-Acetyl-D-Proline 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 N-Acetyl-D-Proline Bound to Serum Amyloid P Component within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca206
b:13.6
occ:1.00
|
OD1
|
C:ASP138
|
2.4
|
14.6
|
1.0
|
|
O
|
C:GLN137
|
2.4
|
14.1
|
1.0
|
|
OE2
|
C:GLU136
|
2.4
|
11.7
|
1.0
|
|
OD1
|
C:ASN59
|
2.4
|
13.5
|
1.0
|
|
OXT
|
C:N8P499
|
2.4
|
14.6
|
1.0
|
|
OD1
|
C:ASP58
|
2.5
|
14.9
|
1.0
|
|
OE1
|
C:GLU136
|
2.6
|
14.7
|
1.0
|
|
OD2
|
C:ASP58
|
2.7
|
17.4
|
1.0
|
|
CD
|
C:GLU136
|
2.9
|
15.0
|
1.0
|
|
CG
|
C:ASP58
|
2.9
|
14.1
|
1.0
|
|
CG
|
C:ASN59
|
3.4
|
12.7
|
1.0
|
|
C
|
C:GLN137
|
3.5
|
13.7
|
1.0
|
|
C
|
C:N8P499
|
3.5
|
14.4
|
1.0
|
|
CG
|
C:ASP138
|
3.6
|
15.7
|
1.0
|
|
CA
|
C:ASP138
|
3.8
|
15.2
|
1.0
|
|
ND2
|
C:ASN59
|
3.8
|
16.6
|
1.0
|
|
O
|
C:N8P499
|
3.8
|
16.4
|
1.0
|
|
CA
|
C:CA205
|
3.9
|
14.1
|
1.0
|
|
N
|
C:ASP138
|
4.0
|
14.9
|
1.0
|
|
O
|
C:HOH2088
|
4.2
|
13.8
|
1.0
|
|
O
|
C:HOH2106
|
4.2
|
32.5
|
1.0
|
|
CB
|
C:ASP138
|
4.3
|
16.9
|
1.0
|
|
N
|
C:ASN59
|
4.4
|
13.1
|
1.0
|
|
CG
|
C:GLU136
|
4.4
|
11.0
|
1.0
|
|
CB
|
C:ASP58
|
4.4
|
15.1
|
1.0
|
|
OD2
|
C:ASP138
|
4.5
|
15.4
|
1.0
|
|
CA
|
C:GLN137
|
4.7
|
13.8
|
1.0
|
|
CA
|
C:N8P499
|
4.7
|
14.2
|
1.0
|
|
ND2
|
C:ASN53
|
4.7
|
14.0
|
1.0
|
|
N
|
C:GLN137
|
4.7
|
12.3
|
1.0
|
|
CB
|
C:ASN59
|
4.7
|
14.2
|
1.0
|
|
O
|
C:HOH2182
|
4.8
|
28.2
|
1.0
|
|
CB
|
C:N8P499
|
4.9
|
15.2
|
1.0
|
|
CA
|
C:ASN59
|
4.9
|
11.2
|
1.0
|
|
C
|
C:ASP138
|
5.0
|
18.5
|
1.0
|
|
OD1
|
C:ASN53
|
5.0
|
13.1
|
1.0
|
|
O
|
C:HOH2180
|
5.0
|
14.2
|
1.0
|
|
Calcium binding site 7 out
of 10 in 4ayu
Go back to
Calcium Binding Sites List in 4ayu
Calcium binding site 7 out
of 10 in the Structure of N-Acetyl-D-Proline 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 N-Acetyl-D-Proline Bound to Serum Amyloid P Component within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca205
b:16.5
occ:1.00
|
OE1
|
D:GLU136
|
2.4
|
16.4
|
1.0
|
|
O
|
D:N8P499
|
2.4
|
16.8
|
1.0
|
|
O
|
D:HOH2203
|
2.4
|
16.1
|
1.0
|
|
OE1
|
D:GLN148
|
2.4
|
17.1
|
1.0
|
|
O
|
D:HOH2206
|
2.5
|
20.1
|
1.0
|
|
OD2
|
D:ASP138
|
2.5
|
16.4
|
1.0
|
|
OD1
|
D:ASP138
|
2.6
|
17.6
|
1.0
|
|
CG
|
D:ASP138
|
2.9
|
15.2
|
1.0
|
|
O
|
D:HOH2205
|
2.9
|
35.8
|
1.0
|
|
C
|
D:N8P499
|
3.4
|
14.5
|
1.0
|
|
CD
|
D:GLN148
|
3.4
|
17.8
|
1.0
|
|
OXT
|
D:N8P499
|
3.5
|
16.3
|
1.0
|
|
CD
|
D:GLU136
|
3.6
|
12.6
|
1.0
|
|
NE2
|
D:GLN148
|
3.8
|
18.4
|
1.0
|
|
CA
|
D:CA206
|
3.8
|
15.4
|
1.0
|
|
CB
|
D:ASP138
|
4.3
|
20.0
|
1.0
|
|
CG
|
D:GLU136
|
4.3
|
13.8
|
1.0
|
|
CB
|
D:ASP145
|
4.4
|
18.1
|
1.0
|
|
O
|
D:GLU136
|
4.4
|
16.1
|
1.0
|
|
CB
|
D:GLU136
|
4.4
|
14.3
|
1.0
|
|
OE2
|
D:GLU136
|
4.4
|
13.6
|
1.0
|
|
O
|
D:HOH2125
|
4.6
|
38.9
|
1.0
|
|
O
|
D:GLN137
|
4.6
|
13.9
|
1.0
|
|
OD2
|
D:ASP145
|
4.6
|
21.9
|
1.0
|
|
O2
|
D:GOL1206
|
4.7
|
46.2
|
1.0
|
|
CA
|
D:N8P499
|
4.8
|
17.4
|
1.0
|
|
CG
|
D:GLN148
|
4.8
|
14.2
|
1.0
|
|
C
|
D:GLN137
|
4.8
|
14.3
|
1.0
|
|
C
|
D:GLU136
|
4.8
|
12.2
|
1.0
|
|
N
|
D:ASP138
|
4.9
|
16.8
|
1.0
|
|
O
|
D:LYS143
|
4.9
|
18.5
|
1.0
|
|
CA
|
D:ASP138
|
5.0
|
16.7
|
1.0
|
|
O3
|
D:GOL1206
|
5.0
|
27.6
|
1.0
|
|
Calcium binding site 8 out
of 10 in 4ayu
Go back to
Calcium Binding Sites List in 4ayu
Calcium binding site 8 out
of 10 in the Structure of N-Acetyl-D-Proline 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 N-Acetyl-D-Proline Bound to Serum Amyloid P Component within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca206
b:15.4
occ:1.00
|
OD1
|
D:ASP138
|
2.4
|
17.6
|
1.0
|
|
O
|
D:GLN137
|
2.4
|
13.9
|
1.0
|
|
OE2
|
D:GLU136
|
2.4
|
13.6
|
1.0
|
|
OD1
|
D:ASN59
|
2.4
|
14.5
|
1.0
|
|
OXT
|
D:N8P499
|
2.5
|
16.3
|
1.0
|
|
OD1
|
D:ASP58
|
2.5
|
17.4
|
1.0
|
|
OE1
|
D:GLU136
|
2.6
|
16.4
|
1.0
|
|
OD2
|
D:ASP58
|
2.7
|
17.7
|
1.0
|
|
CD
|
D:GLU136
|
2.9
|
12.6
|
1.0
|
|
CG
|
D:ASP58
|
3.0
|
17.4
|
1.0
|
|
CG
|
D:ASN59
|
3.4
|
14.4
|
1.0
|
|
C
|
D:GLN137
|
3.4
|
14.3
|
1.0
|
|
C
|
D:N8P499
|
3.5
|
14.5
|
1.0
|
|
CG
|
D:ASP138
|
3.6
|
15.2
|
1.0
|
|
CA
|
D:ASP138
|
3.8
|
16.7
|
1.0
|
|
ND2
|
D:ASN59
|
3.8
|
15.6
|
1.0
|
|
CA
|
D:CA205
|
3.8
|
16.5
|
1.0
|
|
O
|
D:N8P499
|
3.8
|
16.8
|
1.0
|
|
N
|
D:ASP138
|
4.0
|
16.8
|
1.0
|
|
O
|
D:HOH2109
|
4.1
|
14.4
|
1.0
|
|
CB
|
D:ASP138
|
4.3
|
20.0
|
1.0
|
|
O
|
D:HOH2125
|
4.3
|
38.9
|
1.0
|
|
N
|
D:ASN59
|
4.4
|
14.8
|
1.0
|
|
CG
|
D:GLU136
|
4.4
|
13.8
|
1.0
|
|
CB
|
D:ASP58
|
4.4
|
17.1
|
1.0
|
|
OD2
|
D:ASP138
|
4.5
|
16.4
|
1.0
|
|
CA
|
D:N8P499
|
4.6
|
17.4
|
1.0
|
|
CA
|
D:GLN137
|
4.7
|
12.9
|
1.0
|
|
CB
|
D:ASN59
|
4.7
|
14.4
|
1.0
|
|
N
|
D:GLN137
|
4.7
|
13.3
|
1.0
|
|
ND2
|
D:ASN53
|
4.7
|
15.6
|
1.0
|
|
CB
|
D:N8P499
|
4.8
|
14.6
|
1.0
|
|
CA
|
D:ASN59
|
4.9
|
14.7
|
1.0
|
|
OD1
|
D:ASN53
|
4.9
|
16.0
|
1.0
|
|
O
|
D:HOH2203
|
5.0
|
16.1
|
1.0
|
|
Calcium binding site 9 out
of 10 in 4ayu
Go back to
Calcium Binding Sites List in 4ayu
Calcium binding site 9 out
of 10 in the Structure of N-Acetyl-D-Proline 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 N-Acetyl-D-Proline Bound to Serum Amyloid P Component within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca205
b:16.0
occ:1.00
|
O
|
E:N8P499
|
2.4
|
16.4
|
1.0
|
|
OE1
|
E:GLU136
|
2.4
|
16.0
|
1.0
|
|
OE1
|
E:GLN148
|
2.4
|
16.5
|
1.0
|
|
O
|
E:HOH2163
|
2.4
|
20.4
|
1.0
|
|
O
|
E:HOH2160
|
2.5
|
17.2
|
1.0
|
|
OD1
|
E:ASP138
|
2.6
|
17.6
|
1.0
|
|
OD2
|
E:ASP138
|
2.6
|
19.2
|
1.0
|
|
CG
|
E:ASP138
|
2.8
|
19.2
|
1.0
|
|
C
|
E:N8P499
|
3.4
|
16.6
|
1.0
|
|
CD
|
E:GLN148
|
3.4
|
15.9
|
1.0
|
|
CD
|
E:GLU136
|
3.6
|
15.6
|
1.0
|
|
OXT
|
E:N8P499
|
3.6
|
15.3
|
1.0
|
|
NE2
|
E:GLN148
|
3.7
|
19.6
|
1.0
|
|
CA
|
E:CA206
|
3.9
|
16.4
|
1.0
|
|
CB
|
E:ASP138
|
4.3
|
17.5
|
1.0
|
|
CB
|
E:ASP145
|
4.3
|
17.7
|
1.0
|
|
O
|
E:HOH2081
|
4.3
|
34.6
|
1.0
|
|
CG
|
E:GLU136
|
4.3
|
17.6
|
1.0
|
|
CB
|
E:GLU136
|
4.4
|
12.9
|
1.0
|
|
O
|
E:GLU136
|
4.4
|
15.2
|
1.0
|
|
OE2
|
E:GLU136
|
4.5
|
15.5
|
1.0
|
|
OD2
|
E:ASP145
|
4.5
|
22.6
|
1.0
|
|
O
|
E:GLN137
|
4.6
|
15.7
|
1.0
|
|
CA
|
E:N8P499
|
4.7
|
16.5
|
1.0
|
|
CG
|
E:GLN148
|
4.8
|
13.7
|
1.0
|
|
C
|
E:GLN137
|
4.8
|
18.0
|
1.0
|
|
N
|
E:ASP138
|
4.8
|
17.5
|
1.0
|
|
C
|
E:GLU136
|
4.9
|
13.5
|
1.0
|
|
CA
|
E:ASP138
|
4.9
|
16.7
|
1.0
|
|
O
|
E:LYS143
|
4.9
|
18.2
|
1.0
|
|
CG
|
E:ASP145
|
5.0
|
21.6
|
1.0
|
|
Calcium binding site 10 out
of 10 in 4ayu
Go back to
Calcium Binding Sites List in 4ayu
Calcium binding site 10 out
of 10 in the Structure of N-Acetyl-D-Proline 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 N-Acetyl-D-Proline Bound to Serum Amyloid P Component within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca206
b:16.4
occ:1.00
|
OD1
|
E:ASN59
|
2.4
|
14.7
|
1.0
|
|
OXT
|
E:N8P499
|
2.4
|
15.3
|
1.0
|
|
OD1
|
E:ASP138
|
2.4
|
17.6
|
1.0
|
|
O
|
E:GLN137
|
2.4
|
15.7
|
1.0
|
|
OE2
|
E:GLU136
|
2.5
|
15.5
|
1.0
|
|
OD1
|
E:ASP58
|
2.6
|
19.4
|
1.0
|
|
OE1
|
E:GLU136
|
2.7
|
16.0
|
1.0
|
|
OD2
|
E:ASP58
|
2.7
|
18.6
|
1.0
|
|
CD
|
E:GLU136
|
2.9
|
15.6
|
1.0
|
|
CG
|
E:ASP58
|
3.0
|
18.6
|
1.0
|
|
CG
|
E:ASN59
|
3.4
|
13.7
|
1.0
|
|
C
|
E:N8P499
|
3.4
|
16.6
|
1.0
|
|
C
|
E:GLN137
|
3.5
|
18.0
|
1.0
|
|
CG
|
E:ASP138
|
3.6
|
19.2
|
1.0
|
|
ND2
|
E:ASN59
|
3.7
|
15.9
|
1.0
|
|
CA
|
E:ASP138
|
3.7
|
16.7
|
1.0
|
|
O
|
E:N8P499
|
3.8
|
16.4
|
1.0
|
|
CA
|
E:CA205
|
3.9
|
16.0
|
1.0
|
|
N
|
E:ASP138
|
4.0
|
17.5
|
1.0
|
|
O
|
E:HOH2086
|
4.2
|
16.2
|
1.0
|
|
CB
|
E:ASP138
|
4.3
|
17.5
|
1.0
|
|
N
|
E:ASN59
|
4.4
|
16.8
|
1.0
|
|
CG
|
E:GLU136
|
4.4
|
17.6
|
1.0
|
|
CB
|
E:ASP58
|
4.5
|
21.1
|
1.0
|
|
OD2
|
E:ASP138
|
4.6
|
19.2
|
1.0
|
|
CA
|
E:N8P499
|
4.6
|
16.5
|
1.0
|
|
CB
|
E:ASN59
|
4.7
|
14.5
|
1.0
|
|
CA
|
E:GLN137
|
4.7
|
15.1
|
1.0
|
|
CB
|
E:N8P499
|
4.7
|
15.8
|
1.0
|
|
N
|
E:GLN137
|
4.8
|
15.0
|
1.0
|
|
ND2
|
E:ASN53
|
4.8
|
17.5
|
1.0
|
|
CA
|
E:ASN59
|
4.9
|
16.6
|
1.0
|
|
C
|
E:ASP138
|
4.9
|
25.1
|
1.0
|
|
O
|
E:HOH2160
|
5.0
|
17.2
|
1.0
|
|
Reference:
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
Page generated: Tue Jul 8 18:47:55 2025
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