Samarium in PDB 4zhh: Siderocalin-Mediated Recognition and Cellular Uptake of Actinides
Protein crystallography data
The structure of Siderocalin-Mediated Recognition and Cellular Uptake of Actinides, PDB code: 4zhh
was solved by
B.E.Allred,
P.B.Rupert,
S.S.Gauny,
D.D.An,
C.Y.Ralston,
M.Sturzbecher-Hoehne,
R.K.Strong,
R.J.Abergel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.04
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
110.683,
115.320,
120.517,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.4 /
19.9
|
Other elements in 4zhh:
The structure of Siderocalin-Mediated Recognition and Cellular Uptake of Actinides also contains other interesting chemical elements:
Samarium Binding Sites:
The binding sites of Samarium atom in the Siderocalin-Mediated Recognition and Cellular Uptake of Actinides
(pdb code 4zhh). This binding sites where shown within
5.0 Angstroms radius around Samarium atom.
In total 6 binding sites of Samarium where determined in the
Siderocalin-Mediated Recognition and Cellular Uptake of Actinides, PDB code: 4zhh:
Jump to Samarium binding site number:
1;
2;
3;
4;
5;
6;
Samarium binding site 1 out
of 6 in 4zhh
Go back to
Samarium Binding Sites List in 4zhh
Samarium binding site 1 out
of 6 in the Siderocalin-Mediated Recognition and Cellular Uptake of Actinides
Mono view
Stereo pair view
|
A full contact list of Samarium with other atoms in the Sm binding
site number 1 of Siderocalin-Mediated Recognition and Cellular Uptake of Actinides within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Sm201
b:23.6
occ:1.00
|
O10
|
A:4OL202
|
2.0
|
21.2
|
1.0
|
O48
|
A:4OL202
|
2.1
|
24.6
|
1.0
|
O50
|
A:4OL202
|
2.3
|
34.2
|
1.0
|
O51
|
A:4OL202
|
2.4
|
32.9
|
1.0
|
O46
|
A:4OL202
|
2.4
|
24.5
|
1.0
|
O47
|
A:4OL202
|
2.5
|
18.4
|
1.0
|
O49
|
A:4OL202
|
2.5
|
20.8
|
1.0
|
O9
|
A:4OL202
|
2.5
|
20.0
|
1.0
|
N3
|
A:4OL202
|
3.0
|
19.6
|
1.0
|
N27
|
A:4OL202
|
3.1
|
22.0
|
1.0
|
C4
|
A:4OL202
|
3.1
|
16.7
|
1.0
|
C26
|
A:4OL202
|
3.2
|
23.3
|
1.0
|
N45
|
A:4OL202
|
3.2
|
30.3
|
1.0
|
C44
|
A:4OL202
|
3.2
|
33.2
|
1.0
|
N35
|
A:4OL202
|
3.2
|
18.6
|
1.0
|
C36
|
A:4OL202
|
3.2
|
20.2
|
1.0
|
O
|
A:HOH372
|
4.0
|
40.0
|
1.0
|
O
|
A:HOH339
|
4.0
|
19.9
|
1.0
|
C2
|
A:4OL202
|
4.3
|
20.3
|
1.0
|
C22
|
A:4OL202
|
4.4
|
23.9
|
1.0
|
C5
|
A:4OL202
|
4.5
|
20.8
|
1.0
|
OH
|
A:TYR106
|
4.5
|
21.6
|
1.0
|
C37
|
A:4OL202
|
4.5
|
17.7
|
1.0
|
C43
|
A:4OL202
|
4.5
|
34.6
|
1.0
|
C40
|
A:4OL202
|
4.5
|
31.3
|
1.0
|
C25
|
A:4OL202
|
4.6
|
28.8
|
1.0
|
C34
|
A:4OL202
|
4.6
|
19.8
|
1.0
|
NZ
|
A:LYS125
|
4.6
|
30.7
|
1.0
|
NZ
|
A:LYS134
|
4.6
|
22.8
|
1.0
|
N9
|
A:4OL202
|
4.7
|
23.0
|
1.0
|
C29
|
A:4OL202
|
4.8
|
23.0
|
1.0
|
C14
|
A:4OL202
|
4.8
|
27.7
|
1.0
|
CZ3
|
A:TRP79
|
4.8
|
22.4
|
1.0
|
N32
|
A:4OL202
|
4.9
|
32.8
|
1.0
|
C1
|
A:4OL202
|
4.9
|
24.5
|
1.0
|
CH2
|
A:TRP79
|
5.0
|
26.3
|
1.0
|
|
Samarium binding site 2 out
of 6 in 4zhh
Go back to
Samarium Binding Sites List in 4zhh
Samarium binding site 2 out
of 6 in the Siderocalin-Mediated Recognition and Cellular Uptake of Actinides
Mono view
Stereo pair view
|
A full contact list of Samarium with other atoms in the Sm binding
site number 2 of Siderocalin-Mediated Recognition and Cellular Uptake of Actinides within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Sm201
b:21.0
occ:1.00
|
O10
|
B:4OL202
|
1.9
|
18.6
|
1.0
|
O48
|
B:4OL202
|
2.2
|
22.8
|
1.0
|
O50
|
B:4OL202
|
2.3
|
26.9
|
1.0
|
O51
|
B:4OL202
|
2.4
|
23.1
|
1.0
|
O47
|
B:4OL202
|
2.4
|
18.4
|
1.0
|
O46
|
B:4OL202
|
2.4
|
21.9
|
1.0
|
O49
|
B:4OL202
|
2.5
|
18.9
|
1.0
|
O9
|
B:4OL202
|
2.5
|
19.5
|
1.0
|
N3
|
B:4OL202
|
2.9
|
18.6
|
1.0
|
C4
|
B:4OL202
|
3.1
|
18.2
|
1.0
|
N27
|
B:4OL202
|
3.1
|
22.9
|
1.0
|
C36
|
B:4OL202
|
3.2
|
17.7
|
1.0
|
N35
|
B:4OL202
|
3.2
|
14.7
|
1.0
|
C26
|
B:4OL202
|
3.2
|
22.0
|
1.0
|
N45
|
B:4OL202
|
3.2
|
24.2
|
1.0
|
C44
|
B:4OL202
|
3.2
|
25.3
|
1.0
|
O
|
B:HOH340
|
4.0
|
20.4
|
1.0
|
O
|
B:HOH319
|
4.1
|
32.7
|
1.0
|
C2
|
B:4OL202
|
4.2
|
19.1
|
1.0
|
C5
|
B:4OL202
|
4.4
|
23.9
|
1.0
|
OH
|
B:TYR106
|
4.5
|
22.5
|
1.0
|
C22
|
B:4OL202
|
4.5
|
23.4
|
1.0
|
NZ
|
B:LYS125
|
4.5
|
27.9
|
1.0
|
C37
|
B:4OL202
|
4.5
|
16.9
|
1.0
|
C25
|
B:4OL202
|
4.5
|
27.0
|
1.0
|
NZ
|
B:LYS134
|
4.5
|
20.2
|
1.0
|
C43
|
B:4OL202
|
4.5
|
25.5
|
1.0
|
C40
|
B:4OL202
|
4.5
|
27.3
|
1.0
|
C34
|
B:4OL202
|
4.6
|
14.5
|
1.0
|
N9
|
B:4OL202
|
4.6
|
25.5
|
1.0
|
N32
|
B:4OL202
|
4.8
|
25.4
|
1.0
|
C1
|
B:4OL202
|
4.8
|
26.3
|
1.0
|
C29
|
B:4OL202
|
4.9
|
21.6
|
1.0
|
C14
|
B:4OL202
|
4.9
|
23.4
|
1.0
|
CZ3
|
B:TRP79
|
4.9
|
19.1
|
1.0
|
|
Samarium binding site 3 out
of 6 in 4zhh
Go back to
Samarium Binding Sites List in 4zhh
Samarium binding site 3 out
of 6 in the Siderocalin-Mediated Recognition and Cellular Uptake of Actinides
Mono view
Stereo pair view
|
A full contact list of Samarium with other atoms in the Sm binding
site number 3 of Siderocalin-Mediated Recognition and Cellular Uptake of Actinides within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Sm201
b:20.1
occ:1.00
|
O10
|
C:4OL202
|
2.1
|
19.2
|
1.0
|
O51
|
C:4OL202
|
2.2
|
23.5
|
1.0
|
O50
|
C:4OL202
|
2.3
|
23.0
|
1.0
|
O47
|
C:4OL202
|
2.4
|
14.9
|
1.0
|
O48
|
C:4OL202
|
2.4
|
26.2
|
1.0
|
O46
|
C:4OL202
|
2.4
|
23.7
|
1.0
|
O9
|
C:4OL202
|
2.5
|
16.2
|
1.0
|
O49
|
C:4OL202
|
2.5
|
25.4
|
1.0
|
N3
|
C:4OL202
|
3.0
|
17.0
|
1.0
|
C44
|
C:4OL202
|
3.1
|
24.0
|
1.0
|
C4
|
C:4OL202
|
3.1
|
14.7
|
1.0
|
C36
|
C:4OL202
|
3.2
|
17.7
|
1.0
|
N27
|
C:4OL202
|
3.2
|
23.8
|
1.0
|
N45
|
C:4OL202
|
3.2
|
20.1
|
1.0
|
C26
|
C:4OL202
|
3.2
|
22.1
|
1.0
|
N35
|
C:4OL202
|
3.2
|
18.3
|
1.0
|
O
|
C:HOH301
|
3.7
|
44.8
|
1.0
|
O
|
C:HOH342
|
4.0
|
16.1
|
1.0
|
C2
|
C:4OL202
|
4.3
|
16.9
|
1.0
|
C43
|
C:4OL202
|
4.4
|
25.9
|
1.0
|
C5
|
C:4OL202
|
4.5
|
15.2
|
1.0
|
C22
|
C:4OL202
|
4.5
|
24.8
|
1.0
|
C37
|
C:4OL202
|
4.5
|
18.4
|
1.0
|
OH
|
C:TYR106
|
4.5
|
19.2
|
1.0
|
NZ
|
C:LYS134
|
4.5
|
15.7
|
1.0
|
C40
|
C:4OL202
|
4.5
|
27.1
|
1.0
|
C25
|
C:4OL202
|
4.5
|
24.0
|
1.0
|
NZ
|
C:LYS125
|
4.6
|
25.2
|
1.0
|
C34
|
C:4OL202
|
4.6
|
20.9
|
1.0
|
N9
|
C:4OL202
|
4.7
|
19.6
|
1.0
|
C14
|
C:4OL202
|
4.8
|
24.8
|
1.0
|
C29
|
C:4OL202
|
4.8
|
18.5
|
1.0
|
N32
|
C:4OL202
|
4.8
|
22.2
|
1.0
|
CZ3
|
C:TRP79
|
4.9
|
17.6
|
1.0
|
C1
|
C:4OL202
|
5.0
|
22.3
|
1.0
|
|
Samarium binding site 4 out
of 6 in 4zhh
Go back to
Samarium Binding Sites List in 4zhh
Samarium binding site 4 out
of 6 in the Siderocalin-Mediated Recognition and Cellular Uptake of Actinides
Mono view
Stereo pair view
|
A full contact list of Samarium with other atoms in the Sm binding
site number 4 of Siderocalin-Mediated Recognition and Cellular Uptake of Actinides within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Sm201
b:27.0
occ:1.00
|
O48
|
D:4OL202
|
2.0
|
27.8
|
1.0
|
O51
|
D:4OL202
|
2.2
|
29.5
|
1.0
|
O10
|
D:4OL202
|
2.2
|
23.5
|
1.0
|
O50
|
D:4OL202
|
2.3
|
39.6
|
1.0
|
O46
|
D:4OL202
|
2.4
|
27.9
|
1.0
|
O9
|
D:4OL202
|
2.4
|
25.9
|
1.0
|
O47
|
D:4OL202
|
2.5
|
25.1
|
1.0
|
O49
|
D:4OL202
|
2.5
|
22.1
|
1.0
|
N3
|
D:4OL202
|
2.9
|
19.5
|
1.0
|
C4
|
D:4OL202
|
3.0
|
22.8
|
1.0
|
C44
|
D:4OL202
|
3.1
|
31.4
|
1.0
|
N27
|
D:4OL202
|
3.1
|
29.2
|
1.0
|
N45
|
D:4OL202
|
3.1
|
28.5
|
1.0
|
N35
|
D:4OL202
|
3.1
|
23.8
|
1.0
|
C36
|
D:4OL202
|
3.2
|
20.3
|
1.0
|
C26
|
D:4OL202
|
3.2
|
26.4
|
1.0
|
O
|
D:HOH338
|
3.9
|
41.0
|
1.0
|
O
|
D:HOH319
|
4.0
|
21.0
|
1.0
|
C2
|
D:4OL202
|
4.2
|
24.8
|
1.0
|
C5
|
D:4OL202
|
4.3
|
25.8
|
1.0
|
C43
|
D:4OL202
|
4.4
|
36.1
|
1.0
|
C22
|
D:4OL202
|
4.4
|
27.9
|
1.0
|
OH
|
D:TYR106
|
4.4
|
23.3
|
1.0
|
NZ
|
D:LYS134
|
4.5
|
22.1
|
1.0
|
C34
|
D:4OL202
|
4.5
|
24.8
|
1.0
|
C40
|
D:4OL202
|
4.5
|
35.1
|
1.0
|
C37
|
D:4OL202
|
4.5
|
22.3
|
1.0
|
NZ
|
D:LYS125
|
4.6
|
31.8
|
1.0
|
C25
|
D:4OL202
|
4.6
|
29.3
|
1.0
|
C14
|
D:4OL202
|
4.7
|
32.9
|
1.0
|
N9
|
D:4OL202
|
4.7
|
25.9
|
1.0
|
C29
|
D:4OL202
|
4.7
|
26.4
|
1.0
|
CZ3
|
D:TRP79
|
4.8
|
26.9
|
1.0
|
N32
|
D:4OL202
|
4.8
|
31.0
|
1.0
|
C1
|
D:4OL202
|
4.9
|
28.6
|
1.0
|
|
Samarium binding site 5 out
of 6 in 4zhh
Go back to
Samarium Binding Sites List in 4zhh
Samarium binding site 5 out
of 6 in the Siderocalin-Mediated Recognition and Cellular Uptake of Actinides
Mono view
Stereo pair view
|
A full contact list of Samarium with other atoms in the Sm binding
site number 5 of Siderocalin-Mediated Recognition and Cellular Uptake of Actinides within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Sm201
b:24.3
occ:1.00
|
O50
|
E:4OL202
|
2.1
|
31.9
|
1.0
|
O10
|
E:4OL202
|
2.1
|
29.1
|
1.0
|
O49
|
E:4OL202
|
2.3
|
26.2
|
1.0
|
O51
|
E:4OL202
|
2.4
|
22.6
|
1.0
|
O46
|
E:4OL202
|
2.4
|
25.6
|
1.0
|
O47
|
E:4OL202
|
2.4
|
22.7
|
1.0
|
O48
|
E:4OL202
|
2.5
|
29.9
|
1.0
|
O9
|
E:4OL202
|
2.5
|
17.1
|
1.0
|
N3
|
E:4OL202
|
3.0
|
19.2
|
1.0
|
C4
|
E:4OL202
|
3.1
|
19.6
|
1.0
|
N45
|
E:4OL202
|
3.1
|
26.7
|
1.0
|
C44
|
E:4OL202
|
3.1
|
28.2
|
1.0
|
C26
|
E:4OL202
|
3.1
|
27.3
|
1.0
|
C36
|
E:4OL202
|
3.2
|
19.2
|
1.0
|
N27
|
E:4OL202
|
3.2
|
23.5
|
1.0
|
N35
|
E:4OL202
|
3.2
|
20.1
|
1.0
|
O
|
E:HOH321
|
4.1
|
24.6
|
1.0
|
C2
|
E:4OL202
|
4.3
|
24.0
|
1.0
|
C5
|
E:4OL202
|
4.4
|
19.1
|
1.0
|
C25
|
E:4OL202
|
4.4
|
32.4
|
1.0
|
C40
|
E:4OL202
|
4.5
|
31.2
|
1.0
|
C43
|
E:4OL202
|
4.5
|
29.5
|
1.0
|
OH
|
E:TYR106
|
4.5
|
20.9
|
1.0
|
NZ
|
E:LYS125
|
4.5
|
31.0
|
1.0
|
C37
|
E:4OL202
|
4.5
|
16.3
|
1.0
|
C22
|
E:4OL202
|
4.5
|
29.8
|
1.0
|
C34
|
E:4OL202
|
4.6
|
19.6
|
1.0
|
NZ
|
E:LYS134
|
4.6
|
23.0
|
1.0
|
N9
|
E:4OL202
|
4.7
|
26.7
|
1.0
|
N32
|
E:4OL202
|
4.8
|
32.2
|
1.0
|
C29
|
E:4OL202
|
4.8
|
24.9
|
1.0
|
CZ3
|
E:TRP79
|
4.9
|
25.0
|
1.0
|
C14
|
E:4OL202
|
4.9
|
30.1
|
1.0
|
C1
|
E:4OL202
|
4.9
|
27.7
|
1.0
|
|
Samarium binding site 6 out
of 6 in 4zhh
Go back to
Samarium Binding Sites List in 4zhh
Samarium binding site 6 out
of 6 in the Siderocalin-Mediated Recognition and Cellular Uptake of Actinides
Mono view
Stereo pair view
|
A full contact list of Samarium with other atoms in the Sm binding
site number 6 of Siderocalin-Mediated Recognition and Cellular Uptake of Actinides within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Sm201
b:23.0
occ:1.00
|
O10
|
F:4OL202
|
1.9
|
22.1
|
1.0
|
O50
|
F:4OL202
|
2.1
|
26.6
|
1.0
|
O48
|
F:4OL202
|
2.3
|
32.1
|
1.0
|
O9
|
F:4OL202
|
2.4
|
15.2
|
1.0
|
O51
|
F:4OL202
|
2.5
|
21.0
|
1.0
|
O47
|
F:4OL202
|
2.5
|
28.7
|
1.0
|
O49
|
F:4OL202
|
2.5
|
22.2
|
1.0
|
O46
|
F:4OL202
|
2.6
|
25.3
|
1.0
|
N3
|
F:4OL202
|
2.9
|
25.6
|
1.0
|
C4
|
F:4OL202
|
3.0
|
19.7
|
1.0
|
N45
|
F:4OL202
|
3.1
|
29.2
|
1.0
|
N27
|
F:4OL202
|
3.2
|
29.8
|
1.0
|
C44
|
F:4OL202
|
3.2
|
25.1
|
1.0
|
C26
|
F:4OL202
|
3.2
|
27.3
|
1.0
|
C36
|
F:4OL202
|
3.3
|
26.0
|
1.0
|
N35
|
F:4OL202
|
3.3
|
24.8
|
1.0
|
O
|
F:HOH303
|
4.0
|
41.5
|
1.0
|
O
|
F:HOH314
|
4.1
|
21.5
|
1.0
|
C2
|
F:4OL202
|
4.2
|
20.7
|
1.0
|
C5
|
F:4OL202
|
4.4
|
20.0
|
1.0
|
C40
|
F:4OL202
|
4.5
|
26.2
|
1.0
|
OH
|
F:TYR106
|
4.5
|
22.6
|
1.0
|
C22
|
F:4OL202
|
4.5
|
28.6
|
1.0
|
C25
|
F:4OL202
|
4.6
|
27.2
|
1.0
|
C43
|
F:4OL202
|
4.6
|
23.7
|
1.0
|
NZ
|
F:LYS134
|
4.6
|
21.2
|
1.0
|
NZ
|
F:LYS125
|
4.6
|
31.2
|
1.0
|
C37
|
F:4OL202
|
4.6
|
24.8
|
1.0
|
N9
|
F:4OL202
|
4.6
|
26.8
|
1.0
|
C34
|
F:4OL202
|
4.7
|
27.4
|
1.0
|
N32
|
F:4OL202
|
4.8
|
28.8
|
1.0
|
C29
|
F:4OL202
|
4.8
|
28.9
|
1.0
|
C14
|
F:4OL202
|
4.8
|
31.1
|
1.0
|
CZ3
|
F:TRP79
|
4.9
|
23.5
|
1.0
|
C1
|
F:4OL202
|
4.9
|
28.5
|
1.0
|
|
Reference:
B.E.Allred,
P.B.Rupert,
S.S.Gauny,
D.D.An,
C.Y.Ralston,
M.Sturzbecher-Hoehne,
R.K.Strong,
R.J.Abergel.
Siderocalin-Mediated Recognition, Sensitization, and Cellular Uptake of Actinides. Proc.Natl.Acad.Sci.Usa V. 112 10342 2015.
ISSN: ESSN 1091-6490
PubMed: 26240330
DOI: 10.1073/PNAS.1508902112
Page generated: Thu Oct 10 13:52:44 2024
|