Calcium in PDB 3kqr: The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine
Protein crystallography data
The structure of The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine, PDB code: 3kqr
was solved by
H.Mikolajek,
S.E.Kolstoe,
S.P.Wood,
M.B.Pepys,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
36.81 /
1.50
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.860,
69.860,
102.270,
90.00,
96.95,
90.00
|
|
R / Rfree (%)
|
14.1 /
16.1
|
Calcium Binding Sites:
The binding sites of Calcium atom in the The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine
(pdb code 3kqr). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the
The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine, PDB code: 3kqr:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 10 in 3kqr
Go back to
Calcium Binding Sites List in 3kqr
Calcium binding site 1 out
of 10 in the The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca205
b:19.3
occ:1.00
|
O1
|
A:OPE700
|
2.3
|
23.2
|
1.0
|
|
OE1
|
A:GLU136
|
2.3
|
19.4
|
1.0
|
|
OE1
|
A:GLN148
|
2.4
|
19.8
|
1.0
|
|
O
|
A:HOH227
|
2.4
|
21.4
|
1.0
|
|
O
|
A:HOH226
|
2.5
|
20.5
|
1.0
|
|
OD2
|
A:ASP138
|
2.5
|
24.9
|
1.0
|
|
OD1
|
A:ASP138
|
2.6
|
20.7
|
1.0
|
|
CG
|
A:ASP138
|
2.8
|
25.0
|
1.0
|
|
HE21
|
A:GLN148
|
3.3
|
26.3
|
1.0
|
|
CD
|
A:GLN148
|
3.4
|
18.2
|
1.0
|
|
P
|
A:OPE700
|
3.4
|
24.5
|
1.0
|
|
HB3
|
A:GLU136
|
3.5
|
19.9
|
1.0
|
|
CD
|
A:GLU136
|
3.6
|
18.5
|
1.0
|
|
O3
|
A:OPE700
|
3.6
|
19.0
|
1.0
|
|
NE2
|
A:GLN148
|
3.7
|
21.9
|
1.0
|
|
HB3
|
A:ASP145
|
3.7
|
23.9
|
1.0
|
|
HB2
|
A:ASP145
|
3.8
|
23.9
|
1.0
|
|
CA
|
A:CA206
|
3.9
|
19.3
|
1.0
|
|
CB
|
A:ASP138
|
4.2
|
23.0
|
1.0
|
|
CB
|
A:ASP145
|
4.2
|
19.9
|
1.0
|
|
O4
|
A:OPE700
|
4.2
|
26.4
|
1.0
|
|
CB
|
A:GLU136
|
4.4
|
16.6
|
1.0
|
|
O
|
A:HOH605
|
4.4
|
30.8
|
1.0
|
|
O
|
A:GLU136
|
4.4
|
16.4
|
1.0
|
|
CG
|
A:GLU136
|
4.4
|
15.4
|
1.0
|
|
HG3
|
A:GLU136
|
4.4
|
18.5
|
1.0
|
|
HB2
|
A:ASP138
|
4.4
|
27.6
|
1.0
|
|
OE2
|
A:GLU136
|
4.5
|
17.8
|
1.0
|
|
OD2
|
A:ASP145
|
4.5
|
25.3
|
1.0
|
|
HE22
|
A:GLN148
|
4.6
|
26.3
|
1.0
|
|
O
|
A:GLN137
|
4.6
|
18.4
|
1.0
|
|
CG
|
A:GLN148
|
4.7
|
19.7
|
1.0
|
|
O2
|
A:OPE700
|
4.7
|
29.7
|
1.0
|
|
HA
|
A:ASP138
|
4.8
|
28.2
|
1.0
|
|
HG3
|
A:GLN148
|
4.8
|
23.6
|
1.0
|
|
O
|
A:LYS143
|
4.8
|
24.2
|
1.0
|
|
C
|
A:GLU136
|
4.8
|
15.9
|
1.0
|
|
HB2
|
A:GLN148
|
4.8
|
17.8
|
1.0
|
|
HB3
|
A:ASP138
|
4.8
|
27.6
|
1.0
|
|
C
|
A:GLN137
|
4.9
|
16.9
|
1.0
|
|
N
|
A:ASP138
|
4.9
|
19.7
|
1.0
|
|
O
|
A:HOH1398
|
4.9
|
35.4
|
1.0
|
|
CA
|
A:ASP138
|
4.9
|
23.5
|
1.0
|
|
CG
|
A:ASP145
|
4.9
|
22.2
|
1.0
|
|
HB2
|
A:GLU136
|
4.9
|
19.9
|
1.0
|
|
Calcium binding site 2 out
of 10 in 3kqr
Go back to
Calcium Binding Sites List in 3kqr
Calcium binding site 2 out
of 10 in the The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca206
b:19.3
occ:1.00
|
O3
|
A:OPE700
|
2.3
|
19.0
|
1.0
|
|
OD1
|
A:ASP138
|
2.4
|
20.7
|
1.0
|
|
OE2
|
A:GLU136
|
2.4
|
17.8
|
1.0
|
|
O
|
A:GLN137
|
2.4
|
18.4
|
1.0
|
|
OD1
|
A:ASN59
|
2.4
|
18.3
|
1.0
|
|
OD1
|
A:ASP58
|
2.5
|
24.3
|
1.0
|
|
OD2
|
A:ASP58
|
2.7
|
23.8
|
1.0
|
|
OE1
|
A:GLU136
|
2.7
|
19.4
|
1.0
|
|
CD
|
A:GLU136
|
2.9
|
18.5
|
1.0
|
|
CG
|
A:ASP58
|
3.0
|
26.4
|
1.0
|
|
HA
|
A:ASP138
|
3.0
|
28.2
|
1.0
|
|
HD21
|
A:ASN59
|
3.4
|
21.9
|
1.0
|
|
CG
|
A:ASN59
|
3.4
|
17.4
|
1.0
|
|
C
|
A:GLN137
|
3.5
|
16.9
|
1.0
|
|
CG
|
A:ASP138
|
3.6
|
25.0
|
1.0
|
|
P
|
A:OPE700
|
3.7
|
24.5
|
1.0
|
|
ND2
|
A:ASN59
|
3.8
|
18.3
|
1.0
|
|
CA
|
A:ASP138
|
3.8
|
23.5
|
1.0
|
|
HD21
|
A:ASN53
|
3.8
|
25.2
|
1.0
|
|
H
|
A:ASN59
|
3.9
|
22.4
|
1.0
|
|
CA
|
A:CA205
|
3.9
|
19.3
|
1.0
|
|
N
|
A:ASP138
|
4.1
|
19.7
|
1.0
|
|
O
|
A:HOH225
|
4.1
|
16.6
|
1.0
|
|
O1
|
A:OPE700
|
4.2
|
23.2
|
1.0
|
|
HD22
|
A:LEU62
|
4.3
|
14.8
|
1.0
|
|
CB
|
A:ASP138
|
4.3
|
23.0
|
1.0
|
|
CG
|
A:GLU136
|
4.4
|
15.4
|
1.0
|
|
N
|
A:ASN59
|
4.4
|
18.7
|
1.0
|
|
CB
|
A:ASP58
|
4.5
|
26.3
|
1.0
|
|
O
|
A:HOH847
|
4.5
|
37.5
|
1.0
|
|
OD2
|
A:ASP138
|
4.5
|
24.9
|
1.0
|
|
O4
|
A:OPE700
|
4.6
|
26.4
|
1.0
|
|
N
|
A:GLN137
|
4.6
|
16.4
|
1.0
|
|
CA
|
A:GLN137
|
4.7
|
17.1
|
1.0
|
|
CA
|
A:OPE700
|
4.7
|
24.4
|
1.0
|
|
HG2
|
A:GLU136
|
4.7
|
18.5
|
1.0
|
|
HA
|
A:ASN59
|
4.7
|
24.2
|
1.0
|
|
CB
|
A:ASN59
|
4.7
|
17.7
|
1.0
|
|
HD22
|
A:ASN59
|
4.7
|
21.9
|
1.0
|
|
H
|
A:GLN137
|
4.7
|
19.7
|
1.0
|
|
HG3
|
A:GLU136
|
4.7
|
18.5
|
1.0
|
|
HB3
|
A:ASP138
|
4.8
|
27.6
|
1.0
|
|
ND2
|
A:ASN53
|
4.8
|
21.0
|
1.0
|
|
O2
|
A:OPE700
|
4.8
|
29.7
|
1.0
|
|
HB3
|
A:ASP58
|
4.9
|
31.6
|
1.0
|
|
H
|
A:ASP138
|
4.9
|
23.7
|
1.0
|
|
CA
|
A:ASN59
|
4.9
|
20.2
|
1.0
|
|
HA
|
A:ASP58
|
4.9
|
25.7
|
1.0
|
|
HB2
|
A:GLN137
|
5.0
|
22.5
|
1.0
|
|
HB3
|
A:GLU136
|
5.0
|
19.9
|
1.0
|
|
HB2
|
A:ASP58
|
5.0
|
31.6
|
1.0
|
|
C
|
A:GLU136
|
5.0
|
15.9
|
1.0
|
|
Calcium binding site 3 out
of 10 in 3kqr
Go back to
Calcium Binding Sites List in 3kqr
Calcium binding site 3 out
of 10 in the The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca205
b:7.8
occ:1.00
|
O1
|
B:OPE1700
|
2.3
|
9.1
|
1.0
|
|
OD1
|
B:ASP138
|
2.3
|
7.6
|
1.0
|
|
OE2
|
B:GLU136
|
2.4
|
8.7
|
1.0
|
|
OD1
|
B:ASN59
|
2.4
|
7.8
|
1.0
|
|
O
|
B:GLN137
|
2.4
|
7.2
|
1.0
|
|
OD1
|
B:ASP58
|
2.5
|
8.3
|
1.0
|
|
OE1
|
B:GLU136
|
2.6
|
8.9
|
1.0
|
|
OD2
|
B:ASP58
|
2.6
|
9.9
|
1.0
|
|
CD
|
B:GLU136
|
2.9
|
8.5
|
1.0
|
|
CG
|
B:ASP58
|
2.9
|
8.6
|
1.0
|
|
HA
|
B:ASP138
|
3.0
|
9.1
|
1.0
|
|
HD21
|
B:ASN59
|
3.3
|
11.2
|
1.0
|
|
CG
|
B:ASN59
|
3.4
|
8.0
|
1.0
|
|
C
|
B:GLN137
|
3.5
|
8.5
|
1.0
|
|
CG
|
B:ASP138
|
3.6
|
7.9
|
1.0
|
|
P
|
B:OPE1700
|
3.6
|
10.9
|
1.0
|
|
ND2
|
B:ASN59
|
3.7
|
9.3
|
1.0
|
|
CA
|
B:ASP138
|
3.8
|
7.6
|
1.0
|
|
HD21
|
B:ASN53
|
3.9
|
8.6
|
1.0
|
|
CA
|
B:CA206
|
3.9
|
8.2
|
1.0
|
|
H
|
B:ASN59
|
3.9
|
9.8
|
1.0
|
|
O2
|
B:OPE1700
|
4.0
|
9.8
|
1.0
|
|
N
|
B:ASP138
|
4.0
|
7.0
|
1.0
|
|
O
|
B:HOH224
|
4.2
|
9.3
|
1.0
|
|
O
|
B:HOH1374
|
4.2
|
31.0
|
1.0
|
|
CB
|
B:ASP138
|
4.3
|
7.7
|
1.0
|
|
HD22
|
B:LEU62
|
4.3
|
9.5
|
1.0
|
|
CG
|
B:GLU136
|
4.4
|
8.4
|
1.0
|
|
CB
|
B:ASP58
|
4.4
|
10.0
|
1.0
|
|
N
|
B:ASN59
|
4.4
|
8.1
|
1.0
|
|
O4
|
B:OPE1700
|
4.4
|
10.9
|
1.0
|
|
OD2
|
B:ASP138
|
4.5
|
9.2
|
1.0
|
|
CA
|
B:OPE1700
|
4.7
|
12.1
|
1.0
|
|
HD22
|
B:ASN59
|
4.7
|
11.2
|
1.0
|
|
HB3
|
B:ASP138
|
4.7
|
9.2
|
1.0
|
|
CB
|
B:ASN59
|
4.7
|
8.7
|
1.0
|
|
CA
|
B:GLN137
|
4.7
|
6.7
|
1.0
|
|
HG2
|
B:GLU136
|
4.7
|
10.0
|
1.0
|
|
HG3
|
B:GLU136
|
4.7
|
10.0
|
1.0
|
|
HA
|
B:ASN59
|
4.7
|
9.4
|
1.0
|
|
N
|
B:GLN137
|
4.8
|
6.5
|
1.0
|
|
O3
|
B:OPE1700
|
4.8
|
13.9
|
1.0
|
|
HB3
|
B:ASP58
|
4.8
|
12.0
|
1.0
|
|
ND2
|
B:ASN53
|
4.8
|
7.2
|
1.0
|
|
H
|
B:ASP138
|
4.9
|
8.4
|
1.0
|
|
HB2
|
B:ASP58
|
4.9
|
12.0
|
1.0
|
|
H
|
B:GLN137
|
4.9
|
7.8
|
1.0
|
|
CA
|
B:ASN59
|
4.9
|
7.8
|
1.0
|
|
HA
|
B:ASP58
|
4.9
|
11.1
|
1.0
|
|
O
|
B:HOH235
|
5.0
|
21.2
|
1.0
|
|
O
|
B:HOH234
|
5.0
|
9.0
|
1.0
|
|
Calcium binding site 4 out
of 10 in 3kqr
Go back to
Calcium Binding Sites List in 3kqr
Calcium binding site 4 out
of 10 in the The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca206
b:8.2
occ:1.00
|
O2
|
B:OPE1700
|
2.3
|
9.8
|
1.0
|
|
OE1
|
B:GLU136
|
2.4
|
8.9
|
1.0
|
|
OE1
|
B:GLN148
|
2.4
|
8.0
|
1.0
|
|
O
|
B:HOH232
|
2.4
|
11.0
|
1.0
|
|
O
|
B:HOH234
|
2.4
|
9.0
|
1.0
|
|
OD2
|
B:ASP138
|
2.5
|
9.2
|
1.0
|
|
OD1
|
B:ASP138
|
2.5
|
7.6
|
1.0
|
|
CG
|
B:ASP138
|
2.8
|
7.9
|
1.0
|
|
HE21
|
B:GLN148
|
3.4
|
12.7
|
1.0
|
|
CD
|
B:GLN148
|
3.4
|
8.0
|
1.0
|
|
P
|
B:OPE1700
|
3.5
|
10.9
|
1.0
|
|
CD
|
B:GLU136
|
3.6
|
8.5
|
1.0
|
|
HB3
|
B:GLU136
|
3.6
|
7.9
|
1.0
|
|
O1
|
B:OPE1700
|
3.7
|
9.1
|
1.0
|
|
NE2
|
B:GLN148
|
3.8
|
10.6
|
1.0
|
|
HB3
|
B:ASP145
|
3.9
|
12.3
|
1.0
|
|
HB2
|
B:ASP145
|
3.9
|
12.3
|
1.0
|
|
CA
|
B:CA205
|
3.9
|
7.8
|
1.0
|
|
O4
|
B:OPE1700
|
4.2
|
10.9
|
1.0
|
|
CB
|
B:ASP138
|
4.3
|
7.7
|
1.0
|
|
O
|
B:HOH457
|
4.3
|
15.6
|
1.0
|
|
CB
|
B:ASP145
|
4.3
|
10.3
|
1.0
|
|
HG3
|
B:GLU136
|
4.3
|
10.0
|
1.0
|
|
CG
|
B:GLU136
|
4.3
|
8.4
|
1.0
|
|
CB
|
B:GLU136
|
4.4
|
6.6
|
1.0
|
|
O
|
B:GLU136
|
4.4
|
8.4
|
1.0
|
|
OE2
|
B:GLU136
|
4.5
|
8.7
|
1.0
|
|
HB2
|
B:ASP138
|
4.5
|
9.2
|
1.0
|
|
OD2
|
B:ASP145
|
4.6
|
11.9
|
1.0
|
|
O
|
B:GLN137
|
4.6
|
7.2
|
1.0
|
|
O
|
B:HOH1368
|
4.7
|
40.6
|
1.0
|
|
HE22
|
B:GLN148
|
4.7
|
12.7
|
1.0
|
|
O3
|
B:OPE1700
|
4.7
|
13.9
|
1.0
|
|
O
|
B:LYS143
|
4.7
|
6.4
|
0.4
|
|
CG
|
B:GLN148
|
4.8
|
8.0
|
1.0
|
|
O
|
B:HOH644
|
4.8
|
21.1
|
1.0
|
|
O
|
B:LYS143
|
4.8
|
9.1
|
0.6
|
|
HA
|
B:ASP138
|
4.8
|
9.1
|
1.0
|
|
C
|
B:GLN137
|
4.8
|
8.5
|
1.0
|
|
N
|
B:ASP138
|
4.9
|
7.0
|
1.0
|
|
O
|
B:HOH1374
|
4.9
|
31.0
|
1.0
|
|
C
|
B:GLU136
|
4.9
|
7.7
|
1.0
|
|
HB3
|
B:ASP138
|
4.9
|
9.2
|
1.0
|
|
HG3
|
B:GLN148
|
4.9
|
9.6
|
1.0
|
|
CA
|
B:ASP138
|
4.9
|
7.6
|
1.0
|
|
HB2
|
B:GLN148
|
4.9
|
8.8
|
1.0
|
|
HB2
|
B:GLU136
|
5.0
|
7.9
|
1.0
|
|
Calcium binding site 5 out
of 10 in 3kqr
Go back to
Calcium Binding Sites List in 3kqr
Calcium binding site 5 out
of 10 in the The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca205
b:10.9
occ:1.00
|
O2
|
C:OPE2700
|
2.3
|
12.1
|
1.0
|
|
OE2
|
C:GLU136
|
2.3
|
10.0
|
1.0
|
|
OE1
|
C:GLN148
|
2.4
|
12.0
|
1.0
|
|
O
|
C:HOH228
|
2.4
|
13.5
|
1.0
|
|
O
|
C:HOH250
|
2.4
|
11.3
|
1.0
|
|
OD2
|
C:ASP138
|
2.5
|
12.6
|
1.0
|
|
OD1
|
C:ASP138
|
2.6
|
10.4
|
1.0
|
|
CG
|
C:ASP138
|
2.8
|
8.0
|
1.0
|
|
HE21
|
C:GLN148
|
3.3
|
13.8
|
1.0
|
|
CD
|
C:GLN148
|
3.4
|
10.0
|
1.0
|
|
P
|
C:OPE2700
|
3.5
|
12.4
|
1.0
|
|
CD
|
C:GLU136
|
3.6
|
9.3
|
1.0
|
|
HB3
|
C:GLU136
|
3.6
|
12.5
|
1.0
|
|
NE2
|
C:GLN148
|
3.7
|
11.5
|
1.0
|
|
O1
|
C:OPE2700
|
3.7
|
10.8
|
1.0
|
|
HB3
|
C:ASP145
|
3.8
|
15.1
|
1.0
|
|
HB2
|
C:ASP145
|
3.9
|
15.1
|
1.0
|
|
CA
|
C:CA206
|
3.9
|
9.8
|
1.0
|
|
CB
|
C:ASP138
|
4.2
|
10.6
|
1.0
|
|
O4
|
C:OPE2700
|
4.3
|
12.5
|
1.0
|
|
CB
|
C:ASP145
|
4.3
|
12.6
|
1.0
|
|
O
|
C:HOH229
|
4.3
|
18.4
|
1.0
|
|
O
|
C:HOH1114
|
4.3
|
36.6
|
1.0
|
|
CG
|
C:GLU136
|
4.3
|
8.9
|
1.0
|
|
HG3
|
C:GLU136
|
4.3
|
10.6
|
1.0
|
|
O
|
C:GLU136
|
4.4
|
10.1
|
1.0
|
|
CB
|
C:GLU136
|
4.4
|
10.5
|
1.0
|
|
HB2
|
C:ASP138
|
4.5
|
12.7
|
1.0
|
|
OE1
|
C:GLU136
|
4.5
|
10.2
|
1.0
|
|
O
|
C:GLN137
|
4.6
|
10.2
|
1.0
|
|
OD2
|
C:ASP145
|
4.6
|
17.0
|
1.0
|
|
HE22
|
C:GLN148
|
4.6
|
13.8
|
1.0
|
|
CG
|
C:GLN148
|
4.7
|
10.6
|
1.0
|
|
O3
|
C:OPE2700
|
4.7
|
14.9
|
1.0
|
|
O
|
C:HOH679
|
4.8
|
22.6
|
1.0
|
|
O
|
C:LYS143
|
4.8
|
12.7
|
1.0
|
|
HA
|
C:ASP138
|
4.8
|
13.7
|
1.0
|
|
C
|
C:GLN137
|
4.8
|
10.3
|
1.0
|
|
HG3
|
C:GLN148
|
4.8
|
12.8
|
1.0
|
|
N
|
C:ASP138
|
4.8
|
10.4
|
1.0
|
|
HB3
|
C:ASP138
|
4.8
|
12.7
|
1.0
|
|
C
|
C:GLU136
|
4.9
|
8.3
|
1.0
|
|
CA
|
C:ASP138
|
4.9
|
11.4
|
1.0
|
|
HB2
|
C:GLN148
|
4.9
|
12.2
|
1.0
|
|
CG
|
C:ASP145
|
5.0
|
16.9
|
1.0
|
|
Calcium binding site 6 out
of 10 in 3kqr
Go back to
Calcium Binding Sites List in 3kqr
Calcium binding site 6 out
of 10 in the The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca206
b:9.8
occ:1.00
|
OD1
|
C:ASP138
|
2.3
|
10.4
|
1.0
|
|
O1
|
C:OPE2700
|
2.3
|
10.8
|
1.0
|
|
O
|
C:GLN137
|
2.4
|
10.2
|
1.0
|
|
OE1
|
C:GLU136
|
2.4
|
10.2
|
1.0
|
|
OD1
|
C:ASN59
|
2.4
|
9.9
|
1.0
|
|
OD1
|
C:ASP58
|
2.5
|
11.1
|
1.0
|
|
OE2
|
C:GLU136
|
2.6
|
10.0
|
1.0
|
|
CD
|
C:GLU136
|
2.8
|
9.3
|
1.0
|
|
OD2
|
C:ASP58
|
2.9
|
12.8
|
1.0
|
|
HA
|
C:ASP138
|
3.0
|
13.7
|
1.0
|
|
CG
|
C:ASP58
|
3.0
|
12.8
|
1.0
|
|
HD21
|
C:ASN59
|
3.4
|
13.5
|
1.0
|
|
CG
|
C:ASN59
|
3.4
|
9.8
|
1.0
|
|
C
|
C:GLN137
|
3.5
|
10.3
|
1.0
|
|
CG
|
C:ASP138
|
3.6
|
8.0
|
1.0
|
|
P
|
C:OPE2700
|
3.7
|
12.4
|
1.0
|
|
ND2
|
C:ASN59
|
3.8
|
11.2
|
1.0
|
|
HD21
|
C:ASN53
|
3.8
|
11.3
|
1.0
|
|
CA
|
C:ASP138
|
3.8
|
11.4
|
1.0
|
|
CA
|
C:CA205
|
3.9
|
10.9
|
1.0
|
|
H
|
C:ASN59
|
3.9
|
11.1
|
1.0
|
|
N
|
C:ASP138
|
4.0
|
10.4
|
1.0
|
|
O
|
C:HOH259
|
4.1
|
11.4
|
1.0
|
|
O2
|
C:OPE2700
|
4.1
|
12.1
|
1.0
|
|
CB
|
C:ASP138
|
4.3
|
10.6
|
1.0
|
|
O
|
C:HOH608
|
4.3
|
20.9
|
1.0
|
|
CG
|
C:GLU136
|
4.3
|
8.9
|
1.0
|
|
HD22
|
C:LEU62
|
4.4
|
11.1
|
1.0
|
|
N
|
C:ASN59
|
4.4
|
9.2
|
1.0
|
|
OD2
|
C:ASP138
|
4.5
|
12.6
|
1.0
|
|
O4
|
C:OPE2700
|
4.5
|
12.5
|
1.0
|
|
CB
|
C:ASP58
|
4.5
|
11.1
|
1.0
|
|
HB3
|
C:ASP138
|
4.7
|
12.7
|
1.0
|
|
CA
|
C:OPE2700
|
4.7
|
12.5
|
1.0
|
|
HG2
|
C:GLU136
|
4.7
|
10.6
|
1.0
|
|
CA
|
C:GLN137
|
4.7
|
8.1
|
1.0
|
|
CB
|
C:ASN59
|
4.7
|
12.0
|
1.0
|
|
HG3
|
C:GLU136
|
4.7
|
10.6
|
1.0
|
|
HA
|
C:ASN59
|
4.7
|
13.4
|
1.0
|
|
HH22
|
C:ARG77
|
4.7
|
18.6
|
1.0
|
|
HD22
|
C:ASN59
|
4.7
|
13.5
|
1.0
|
|
O3
|
C:OPE2700
|
4.8
|
14.9
|
1.0
|
|
N
|
C:GLN137
|
4.8
|
7.7
|
1.0
|
|
ND2
|
C:ASN53
|
4.8
|
9.4
|
1.0
|
|
H
|
C:ASP138
|
4.8
|
12.4
|
1.0
|
|
HB2
|
C:ASP58
|
4.9
|
13.3
|
1.0
|
|
CA
|
C:ASN59
|
4.9
|
11.2
|
1.0
|
|
H
|
C:GLN137
|
4.9
|
9.2
|
1.0
|
|
HB2
|
C:GLN137
|
5.0
|
10.3
|
1.0
|
|
HB3
|
C:ASP58
|
5.0
|
13.3
|
1.0
|
|
O
|
C:HOH250
|
5.0
|
11.3
|
1.0
|
|
Calcium binding site 7 out
of 10 in 3kqr
Go back to
Calcium Binding Sites List in 3kqr
Calcium binding site 7 out
of 10 in the The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca205
b:9.8
occ:1.00
|
O1
|
D:OPE3700
|
2.3
|
15.2
|
1.0
|
|
OE1
|
D:GLU136
|
2.4
|
9.7
|
1.0
|
|
OE1
|
D:GLN148
|
2.4
|
11.0
|
1.0
|
|
O
|
D:HOH235
|
2.4
|
13.2
|
1.0
|
|
O
|
D:HOH230
|
2.4
|
10.9
|
1.0
|
|
OD2
|
D:ASP138
|
2.5
|
13.0
|
1.0
|
|
OD1
|
D:ASP138
|
2.6
|
10.0
|
1.0
|
|
CG
|
D:ASP138
|
2.9
|
9.5
|
1.0
|
|
HE21
|
D:GLN148
|
3.4
|
16.2
|
1.0
|
|
CD
|
D:GLN148
|
3.4
|
9.4
|
1.0
|
|
P
|
D:OPE3700
|
3.5
|
17.7
|
1.0
|
|
CD
|
D:GLU136
|
3.6
|
9.0
|
1.0
|
|
HB3
|
D:GLU136
|
3.6
|
11.8
|
1.0
|
|
O3
|
D:OPE3700
|
3.7
|
12.1
|
1.0
|
|
NE2
|
D:GLN148
|
3.8
|
13.5
|
1.0
|
|
HB2
|
D:ASP145
|
3.9
|
13.1
|
1.0
|
|
HB3
|
D:ASP145
|
3.9
|
13.1
|
1.0
|
|
CA
|
D:CA206
|
3.9
|
8.9
|
1.0
|
|
O
|
D:HOH931
|
4.1
|
28.0
|
1.0
|
|
CB
|
D:ASP138
|
4.2
|
11.1
|
1.0
|
|
HG3
|
D:GLU136
|
4.2
|
11.8
|
1.0
|
|
O
|
D:HOH252
|
4.2
|
19.0
|
1.0
|
|
CG
|
D:GLU136
|
4.3
|
9.8
|
1.0
|
|
CB
|
D:ASP145
|
4.3
|
10.9
|
1.0
|
|
O4
|
D:OPE3700
|
4.3
|
18.1
|
1.0
|
|
CB
|
D:GLU136
|
4.4
|
9.9
|
1.0
|
|
O
|
D:GLU136
|
4.4
|
10.2
|
1.0
|
|
HB2
|
D:ASP138
|
4.4
|
13.3
|
1.0
|
|
OE2
|
D:GLU136
|
4.5
|
8.9
|
1.0
|
|
OD2
|
D:ASP145
|
4.6
|
14.8
|
1.0
|
|
HE22
|
D:GLN148
|
4.6
|
16.2
|
1.0
|
|
O
|
D:GLN137
|
4.6
|
8.5
|
1.0
|
|
O
|
D:HOH1401
|
4.7
|
33.6
|
1.0
|
|
CG
|
D:GLN148
|
4.7
|
9.5
|
1.0
|
|
O2
|
D:OPE3700
|
4.8
|
23.1
|
1.0
|
|
HA
|
D:ASP138
|
4.8
|
11.3
|
1.0
|
|
N
|
D:ASP138
|
4.8
|
9.1
|
1.0
|
|
C
|
D:GLN137
|
4.8
|
8.9
|
1.0
|
|
O
|
D:LYS143
|
4.8
|
12.7
|
1.0
|
|
HB3
|
D:ASP138
|
4.8
|
13.3
|
1.0
|
|
C
|
D:GLU136
|
4.9
|
8.9
|
1.0
|
|
HG3
|
D:GLN148
|
4.9
|
11.4
|
1.0
|
|
CA
|
D:ASP138
|
4.9
|
9.5
|
1.0
|
|
HB2
|
D:GLN148
|
4.9
|
10.4
|
1.0
|
|
HB2
|
D:GLU136
|
5.0
|
11.8
|
1.0
|
|
Calcium binding site 8 out
of 10 in 3kqr
Go back to
Calcium Binding Sites List in 3kqr
Calcium binding site 8 out
of 10 in the The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca206
b:8.9
occ:1.00
|
OD1
|
D:ASP138
|
2.3
|
10.0
|
1.0
|
|
O3
|
D:OPE3700
|
2.4
|
12.1
|
1.0
|
|
OD1
|
D:ASN59
|
2.4
|
8.5
|
1.0
|
|
OE2
|
D:GLU136
|
2.4
|
8.9
|
1.0
|
|
O
|
D:GLN137
|
2.4
|
8.5
|
1.0
|
|
OD1
|
D:ASP58
|
2.5
|
11.1
|
1.0
|
|
OE1
|
D:GLU136
|
2.6
|
9.7
|
1.0
|
|
OD2
|
D:ASP58
|
2.7
|
11.2
|
1.0
|
|
CD
|
D:GLU136
|
2.9
|
9.0
|
1.0
|
|
CG
|
D:ASP58
|
2.9
|
8.5
|
1.0
|
|
HA
|
D:ASP138
|
3.0
|
11.3
|
1.0
|
|
HD21
|
D:ASN59
|
3.3
|
13.0
|
1.0
|
|
CG
|
D:ASN59
|
3.3
|
8.1
|
1.0
|
|
C
|
D:GLN137
|
3.5
|
8.9
|
1.0
|
|
CG
|
D:ASP138
|
3.6
|
9.5
|
1.0
|
|
P
|
D:OPE3700
|
3.7
|
17.7
|
1.0
|
|
ND2
|
D:ASN59
|
3.7
|
10.8
|
1.0
|
|
HD21
|
D:ASN53
|
3.8
|
11.2
|
1.0
|
|
CA
|
D:ASP138
|
3.8
|
9.5
|
1.0
|
|
CA
|
D:CA205
|
3.9
|
9.8
|
1.0
|
|
H
|
D:ASN59
|
4.0
|
9.7
|
1.0
|
|
N
|
D:ASP138
|
4.0
|
9.1
|
1.0
|
|
O1
|
D:OPE3700
|
4.1
|
15.2
|
1.0
|
|
O
|
D:HOH225
|
4.2
|
9.9
|
1.0
|
|
HD22
|
D:LEU62
|
4.2
|
9.8
|
1.0
|
|
CB
|
D:ASP138
|
4.3
|
11.1
|
1.0
|
|
O
|
D:HOH906
|
4.3
|
32.0
|
1.0
|
|
CG
|
D:GLU136
|
4.4
|
9.8
|
1.0
|
|
CB
|
D:ASP58
|
4.4
|
9.2
|
1.0
|
|
N
|
D:ASN59
|
4.4
|
8.1
|
1.0
|
|
OD2
|
D:ASP138
|
4.5
|
13.0
|
1.0
|
|
HD22
|
D:ASN59
|
4.6
|
13.0
|
1.0
|
|
O4
|
D:OPE3700
|
4.6
|
18.1
|
1.0
|
|
CB
|
D:ASN59
|
4.6
|
8.0
|
1.0
|
|
HB3
|
D:ASP138
|
4.7
|
13.3
|
1.0
|
|
N
|
D:GLN137
|
4.7
|
7.6
|
1.0
|
|
CA
|
D:GLN137
|
4.7
|
6.7
|
1.0
|
|
HG3
|
D:GLU136
|
4.7
|
11.8
|
1.0
|
|
ND2
|
D:ASN53
|
4.7
|
9.3
|
1.0
|
|
HA
|
D:ASN59
|
4.7
|
11.4
|
1.0
|
|
HG2
|
D:GLU136
|
4.8
|
11.8
|
1.0
|
|
H
|
D:GLN137
|
4.8
|
9.2
|
1.0
|
|
O2
|
D:OPE3700
|
4.8
|
23.1
|
1.0
|
|
H
|
D:ASP138
|
4.8
|
10.9
|
1.0
|
|
HA
|
D:ASP58
|
4.8
|
11.5
|
1.0
|
|
HB3
|
D:ASP58
|
4.9
|
11.0
|
1.0
|
|
HB2
|
D:ASP58
|
4.9
|
11.0
|
1.0
|
|
CA
|
D:OPE3700
|
4.9
|
19.7
|
1.0
|
|
CA
|
D:ASN59
|
4.9
|
9.5
|
1.0
|
|
OD1
|
D:ASN53
|
4.9
|
9.6
|
1.0
|
|
O
|
D:HOH528
|
4.9
|
31.2
|
1.0
|
|
HB2
|
D:GLN137
|
5.0
|
10.2
|
1.0
|
|
Calcium binding site 9 out
of 10 in 3kqr
Go back to
Calcium Binding Sites List in 3kqr
Calcium binding site 9 out
of 10 in the The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca205
b:8.2
occ:1.00
|
O2
|
E:OPE4700
|
2.3
|
11.8
|
1.0
|
|
OE1
|
E:GLU136
|
2.3
|
7.9
|
1.0
|
|
OE1
|
E:GLN148
|
2.4
|
7.9
|
1.0
|
|
O
|
E:HOH226
|
2.4
|
9.4
|
1.0
|
|
O
|
E:HOH225
|
2.4
|
10.1
|
1.0
|
|
OD1
|
E:ASP138
|
2.5
|
8.6
|
1.0
|
|
OD2
|
E:ASP138
|
2.5
|
10.3
|
1.0
|
|
CG
|
E:ASP138
|
2.8
|
8.7
|
1.0
|
|
HE21
|
E:GLN148
|
3.4
|
14.1
|
1.0
|
|
CD
|
E:GLN148
|
3.4
|
7.4
|
1.0
|
|
P
|
E:OPE4700
|
3.5
|
14.2
|
1.0
|
|
CD
|
E:GLU136
|
3.6
|
8.3
|
1.0
|
|
HB3
|
E:GLU136
|
3.6
|
7.9
|
1.0
|
|
O1
|
E:OPE4700
|
3.7
|
10.7
|
1.0
|
|
NE2
|
E:GLN148
|
3.8
|
11.8
|
1.0
|
|
HB3
|
E:ASP145
|
3.8
|
9.0
|
1.0
|
|
CA
|
E:CA206
|
3.9
|
8.3
|
1.0
|
|
O
|
E:HOH1243
|
3.9
|
33.9
|
1.0
|
|
HB2
|
E:ASP145
|
3.9
|
9.0
|
1.0
|
|
O4
|
E:OPE4700
|
4.2
|
15.9
|
1.0
|
|
CB
|
E:ASP138
|
4.3
|
8.5
|
1.0
|
|
HG3
|
E:GLU136
|
4.3
|
7.8
|
1.0
|
|
CG
|
E:GLU136
|
4.3
|
6.6
|
1.0
|
|
CB
|
E:ASP145
|
4.3
|
7.5
|
1.0
|
|
O
|
E:GLU136
|
4.4
|
8.3
|
1.0
|
|
O
|
E:HOH649
|
4.4
|
23.2
|
1.0
|
|
CB
|
E:GLU136
|
4.4
|
6.6
|
1.0
|
|
OE2
|
E:GLU136
|
4.5
|
8.1
|
1.0
|
|
HB2
|
E:ASP138
|
4.5
|
10.2
|
1.0
|
|
OD2
|
E:ASP145
|
4.5
|
11.3
|
1.0
|
|
O
|
E:GLN137
|
4.6
|
7.7
|
1.0
|
|
HE22
|
E:GLN148
|
4.6
|
14.1
|
1.0
|
|
O
|
E:HOH727
|
4.6
|
27.6
|
1.0
|
|
O3
|
E:OPE4700
|
4.7
|
18.0
|
1.0
|
|
CG
|
E:GLN148
|
4.7
|
8.1
|
1.0
|
|
HA
|
E:ASP138
|
4.8
|
10.2
|
1.0
|
|
C
|
E:GLN137
|
4.8
|
8.5
|
1.0
|
|
O
|
E:LYS143
|
4.8
|
10.6
|
1.0
|
|
N
|
E:ASP138
|
4.8
|
8.1
|
1.0
|
|
C
|
E:GLU136
|
4.8
|
6.7
|
1.0
|
|
HB3
|
E:ASP138
|
4.8
|
10.2
|
1.0
|
|
O
|
E:HOH244
|
4.9
|
20.5
|
1.0
|
|
HG3
|
E:GLN148
|
4.9
|
9.8
|
1.0
|
|
CA
|
E:ASP138
|
4.9
|
8.6
|
1.0
|
|
HB2
|
E:GLN148
|
5.0
|
7.4
|
1.0
|
|
Calcium binding site 10 out
of 10 in 3kqr
Go back to
Calcium Binding Sites List in 3kqr
Calcium binding site 10 out
of 10 in the The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of The Structure of Serum Amyloid P Component Bound to Phosphoethanolamine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca206
b:8.3
occ:1.00
|
O1
|
E:OPE4700
|
2.3
|
10.7
|
1.0
|
|
OD1
|
E:ASP138
|
2.4
|
8.6
|
1.0
|
|
OD1
|
E:ASN59
|
2.4
|
8.5
|
1.0
|
|
OE2
|
E:GLU136
|
2.4
|
8.1
|
1.0
|
|
O
|
E:GLN137
|
2.4
|
7.7
|
1.0
|
|
OD1
|
E:ASP58
|
2.5
|
9.0
|
1.0
|
|
OE1
|
E:GLU136
|
2.6
|
7.9
|
1.0
|
|
OD2
|
E:ASP58
|
2.6
|
12.2
|
1.0
|
|
CD
|
E:GLU136
|
2.9
|
8.3
|
1.0
|
|
CG
|
E:ASP58
|
2.9
|
8.9
|
1.0
|
|
HA
|
E:ASP138
|
3.0
|
10.2
|
1.0
|
|
HD21
|
E:ASN59
|
3.3
|
12.5
|
1.0
|
|
CG
|
E:ASN59
|
3.4
|
8.1
|
1.0
|
|
C
|
E:GLN137
|
3.5
|
8.5
|
1.0
|
|
CG
|
E:ASP138
|
3.6
|
8.7
|
1.0
|
|
P
|
E:OPE4700
|
3.7
|
14.2
|
1.0
|
|
ND2
|
E:ASN59
|
3.7
|
10.4
|
1.0
|
|
CA
|
E:ASP138
|
3.8
|
8.6
|
1.0
|
|
HD21
|
E:ASN53
|
3.8
|
9.9
|
1.0
|
|
CA
|
E:CA205
|
3.9
|
8.2
|
1.0
|
|
H
|
E:ASN59
|
4.0
|
9.1
|
1.0
|
|
N
|
E:ASP138
|
4.0
|
8.1
|
1.0
|
|
O2
|
E:OPE4700
|
4.1
|
11.8
|
1.0
|
|
O
|
E:HOH268
|
4.2
|
9.4
|
1.0
|
|
CB
|
E:ASP138
|
4.3
|
8.5
|
1.0
|
|
HD22
|
E:LEU62
|
4.3
|
8.8
|
1.0
|
|
CG
|
E:GLU136
|
4.4
|
6.6
|
1.0
|
|
CB
|
E:ASP58
|
4.4
|
8.8
|
1.0
|
|
N
|
E:ASN59
|
4.4
|
7.6
|
1.0
|
|
O4
|
E:OPE4700
|
4.5
|
15.9
|
1.0
|
|
OD2
|
E:ASP138
|
4.5
|
10.3
|
1.0
|
|
HB3
|
E:ASP138
|
4.6
|
10.2
|
1.0
|
|
CA
|
E:OPE4700
|
4.7
|
17.5
|
1.0
|
|
CB
|
E:ASN59
|
4.7
|
8.5
|
1.0
|
|
HD22
|
E:ASN59
|
4.7
|
12.5
|
1.0
|
|
CA
|
E:GLN137
|
4.7
|
6.3
|
1.0
|
|
HG2
|
E:GLU136
|
4.7
|
7.8
|
1.0
|
|
HG3
|
E:GLU136
|
4.7
|
7.8
|
1.0
|
|
HA
|
E:ASN59
|
4.7
|
9.6
|
1.0
|
|
HB3
|
E:ASP58
|
4.8
|
10.6
|
1.0
|
|
N
|
E:GLN137
|
4.8
|
7.0
|
1.0
|
|
ND2
|
E:ASN53
|
4.8
|
8.3
|
1.0
|
|
O3
|
E:OPE4700
|
4.8
|
18.0
|
1.0
|
|
H
|
E:ASP138
|
4.8
|
9.8
|
1.0
|
|
HB2
|
E:ASP58
|
4.9
|
10.6
|
1.0
|
|
HA
|
E:ASP58
|
4.9
|
12.0
|
1.0
|
|
CA
|
E:ASN59
|
4.9
|
8.0
|
1.0
|
|
H
|
E:GLN137
|
5.0
|
8.3
|
1.0
|
|
Reference:
H.Mikolajek,
S.E.Kolstoe,
V.E.Pye,
P.Mangione,
M.B.Pepys,
S.P.Wood.
Structural Basis of Ligand Specificity in the Human Pentraxins, C-Reactive Protein and Serum Amyloid P Component. J.Mol.Recognit. V. 24 371 2011.
ISSN: ISSN 0952-3499
PubMed: 21360619
DOI: 10.1002/JMR.1090
Page generated: Sat Jul 13 12:38:55 2024
|
