Iodine in PDB 5f1t: Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55.
Protein crystallography data
The structure of Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55., PDB code: 5f1t
was solved by
P.J.Salveson,
R.K.Spencer,
J.S.Nowick,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.76 /
1.97
|
Space group
|
P 21 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.518,
77.518,
77.518,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.3 /
22.1
|
Other elements in 5f1t:
The structure of Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55. also contains other interesting chemical elements:
Iodine Binding Sites:
The binding sites of Iodine atom in the Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55.
(pdb code 5f1t). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the
Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55., PDB code: 5f1t:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
Iodine binding site 1 out
of 7 in 5f1t
Go back to
Iodine Binding Sites List in 5f1t
Iodine binding site 1 out
of 7 in the Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I5
b:30.8
occ:1.00
|
I
|
A:PHI5
|
0.0
|
30.8
|
1.0
|
CZ
|
A:PHI5
|
2.1
|
27.6
|
1.0
|
CE2
|
A:PHI5
|
3.0
|
29.3
|
1.0
|
HE2
|
A:PHI5
|
3.1
|
35.2
|
1.0
|
CE1
|
A:PHI5
|
3.1
|
25.7
|
1.0
|
HE1
|
A:PHI5
|
3.2
|
30.9
|
1.0
|
HG23
|
C:MVA13
|
3.6
|
21.6
|
1.0
|
HG21
|
C:THR15
|
3.7
|
22.0
|
1.0
|
HG13
|
C:VAL3
|
3.8
|
14.4
|
1.0
|
HG22
|
C:VAL3
|
3.9
|
14.8
|
1.0
|
HG23
|
C:THR15
|
3.9
|
22.0
|
1.0
|
HG11
|
C:VAL3
|
4.0
|
14.4
|
1.0
|
HG22
|
C:THR15
|
4.1
|
22.0
|
1.0
|
CG2
|
C:THR15
|
4.1
|
18.3
|
1.0
|
HG22
|
C:MVA13
|
4.1
|
21.6
|
1.0
|
HG21
|
C:VAL3
|
4.1
|
14.8
|
1.0
|
CD2
|
A:PHI5
|
4.3
|
28.6
|
1.0
|
CD1
|
A:PHI5
|
4.3
|
24.4
|
1.0
|
CG1
|
C:VAL3
|
4.4
|
12.0
|
1.0
|
CG2
|
C:MVA13
|
4.4
|
18.0
|
1.0
|
HE2
|
F:PHI5
|
4.4
|
36.2
|
0.5
|
CG2
|
C:VAL3
|
4.5
|
12.4
|
1.0
|
I
|
F:PHI5
|
4.8
|
45.9
|
0.5
|
HG12
|
A:MVA13
|
4.8
|
25.2
|
1.0
|
CG
|
A:PHI5
|
4.9
|
25.2
|
1.0
|
CE2
|
F:PHI5
|
4.9
|
30.2
|
0.5
|
|
Iodine binding site 2 out
of 7 in 5f1t
Go back to
Iodine Binding Sites List in 5f1t
Iodine binding site 2 out
of 7 in the Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I5
b:25.4
occ:1.00
|
I
|
B:PHI5
|
0.0
|
25.4
|
1.0
|
CZ
|
B:PHI5
|
2.1
|
23.8
|
1.0
|
CE1
|
B:PHI5
|
3.0
|
23.2
|
1.0
|
HE1
|
B:PHI5
|
3.0
|
27.8
|
1.0
|
CE2
|
B:PHI5
|
3.1
|
22.9
|
1.0
|
HE2
|
B:PHI5
|
3.2
|
27.4
|
1.0
|
HB3
|
D:PHI5
|
3.3
|
30.3
|
1.0
|
HB2
|
E:HIS11
|
3.3
|
24.8
|
1.0
|
HB2
|
B:HIS11
|
3.4
|
18.4
|
1.0
|
CG
|
E:HIS11
|
3.5
|
19.9
|
1.0
|
HB2
|
D:PHI5
|
3.5
|
30.3
|
1.0
|
CD2
|
E:HIS11
|
3.7
|
20.5
|
1.0
|
CB
|
E:HIS11
|
3.7
|
20.6
|
1.0
|
CB
|
D:PHI5
|
3.8
|
25.2
|
1.0
|
HB3
|
E:HIS11
|
3.8
|
24.8
|
1.0
|
CG
|
B:HIS11
|
3.8
|
16.9
|
1.0
|
ND1
|
E:HIS11
|
3.8
|
18.9
|
1.0
|
ND1
|
B:HIS11
|
3.9
|
19.3
|
1.0
|
CB
|
B:HIS11
|
3.9
|
15.4
|
1.0
|
HD2
|
E:HIS11
|
4.0
|
24.6
|
1.0
|
HB3
|
E:PHI5
|
4.0
|
27.8
|
1.0
|
HB3
|
B:HIS11
|
4.0
|
18.4
|
1.0
|
HB2
|
E:PHI5
|
4.1
|
27.8
|
1.0
|
O
|
E:HOH102
|
4.1
|
20.7
|
1.0
|
CG
|
D:PHI5
|
4.1
|
26.6
|
1.0
|
NE2
|
E:HIS11
|
4.1
|
19.7
|
1.0
|
HD2
|
D:PHI5
|
4.2
|
38.5
|
1.0
|
CE1
|
E:HIS11
|
4.2
|
18.8
|
1.0
|
CE1
|
D:HIS11
|
4.3
|
19.1
|
1.0
|
CD1
|
B:PHI5
|
4.3
|
21.5
|
1.0
|
CD2
|
B:HIS11
|
4.3
|
17.2
|
1.0
|
CD2
|
D:PHI5
|
4.3
|
32.1
|
1.0
|
ND1
|
D:HIS11
|
4.3
|
17.5
|
1.0
|
NE2
|
D:HIS11
|
4.3
|
19.6
|
1.0
|
CD2
|
B:PHI5
|
4.4
|
21.8
|
1.0
|
CE1
|
B:HIS11
|
4.4
|
21.1
|
1.0
|
CB
|
E:PHI5
|
4.5
|
23.1
|
1.0
|
CG
|
D:HIS11
|
4.5
|
15.6
|
1.0
|
CD2
|
D:HIS11
|
4.5
|
17.1
|
1.0
|
HE1
|
D:HIS11
|
4.5
|
22.9
|
1.0
|
HE2
|
D:HIS11
|
4.6
|
23.5
|
1.0
|
HE2
|
E:HIS11
|
4.6
|
23.6
|
1.0
|
NE2
|
B:HIS11
|
4.6
|
19.9
|
1.0
|
HD2
|
B:HIS11
|
4.7
|
20.6
|
1.0
|
HE1
|
E:HIS11
|
4.8
|
22.6
|
1.0
|
CG
|
B:PHI5
|
4.8
|
21.9
|
1.0
|
HD2
|
D:HIS11
|
4.9
|
20.5
|
1.0
|
HE1
|
B:HIS11
|
4.9
|
25.3
|
1.0
|
CD1
|
D:PHI5
|
4.9
|
25.8
|
1.0
|
|
Iodine binding site 3 out
of 7 in 5f1t
Go back to
Iodine Binding Sites List in 5f1t
Iodine binding site 3 out
of 7 in the Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:I5
b:25.1
occ:1.00
|
I
|
C:PHI5
|
0.0
|
25.1
|
1.0
|
CZ
|
C:PHI5
|
2.1
|
23.0
|
1.0
|
CE1
|
C:PHI5
|
3.1
|
22.1
|
1.0
|
CE2
|
C:PHI5
|
3.1
|
23.0
|
1.0
|
HE1
|
C:PHI5
|
3.1
|
26.6
|
1.0
|
HE2
|
C:PHI5
|
3.1
|
27.6
|
1.0
|
HB2
|
C:HIS11
|
3.4
|
20.5
|
1.0
|
CG
|
C:HIS11
|
3.8
|
18.7
|
1.0
|
ND1
|
C:HIS11
|
3.8
|
20.9
|
1.0
|
CB
|
C:HIS11
|
4.0
|
17.1
|
1.0
|
HB3
|
C:HIS11
|
4.2
|
20.5
|
1.0
|
O
|
C:HOH202
|
4.2
|
16.9
|
1.0
|
CD1
|
C:PHI5
|
4.3
|
20.9
|
1.0
|
CD2
|
C:PHI5
|
4.4
|
22.1
|
1.0
|
CD2
|
C:HIS11
|
4.4
|
18.7
|
1.0
|
CE1
|
C:HIS11
|
4.4
|
22.4
|
1.0
|
NE2
|
C:HIS11
|
4.7
|
21.0
|
1.0
|
HE1
|
C:HIS11
|
4.8
|
26.9
|
1.0
|
HD2
|
C:HIS11
|
4.8
|
22.4
|
1.0
|
CG
|
C:PHI5
|
4.9
|
20.9
|
1.0
|
|
Iodine binding site 4 out
of 7 in 5f1t
Go back to
Iodine Binding Sites List in 5f1t
Iodine binding site 4 out
of 7 in the Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:I5
b:32.3
occ:1.00
|
I
|
D:PHI5
|
0.0
|
32.3
|
1.0
|
CZ
|
D:PHI5
|
2.1
|
29.4
|
1.0
|
CE1
|
D:PHI5
|
3.1
|
27.0
|
1.0
|
CE2
|
D:PHI5
|
3.1
|
33.6
|
1.0
|
HE1
|
D:PHI5
|
3.1
|
32.5
|
1.0
|
HE2
|
D:PHI5
|
3.2
|
40.3
|
1.0
|
HG12
|
B:MVA13
|
3.5
|
22.9
|
1.0
|
HG13
|
B:MVA13
|
3.9
|
22.9
|
1.0
|
HD2
|
B:PHI5
|
4.0
|
26.2
|
1.0
|
CG1
|
B:MVA13
|
4.1
|
19.1
|
1.0
|
HB3
|
B:PHI5
|
4.3
|
24.9
|
1.0
|
CD1
|
D:PHI5
|
4.3
|
25.8
|
1.0
|
HG11
|
B:MVA13
|
4.4
|
22.9
|
1.0
|
CD2
|
D:PHI5
|
4.4
|
32.1
|
1.0
|
CD2
|
B:PHI5
|
4.5
|
21.8
|
1.0
|
HG13
|
D:MVA13
|
4.5
|
26.8
|
1.0
|
HG12
|
D:MVA13
|
4.5
|
26.8
|
1.0
|
I
|
E:PHI5
|
4.8
|
50.9
|
1.0
|
HE2
|
E:PHI5
|
4.8
|
34.9
|
1.0
|
CG
|
D:PHI5
|
4.9
|
26.6
|
1.0
|
O3
|
B:SO4102
|
4.9
|
69.1
|
0.7
|
O4
|
B:SO4102
|
5.0
|
67.6
|
0.7
|
|
Iodine binding site 5 out
of 7 in 5f1t
Go back to
Iodine Binding Sites List in 5f1t
Iodine binding site 5 out
of 7 in the Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:I5
b:50.9
occ:1.00
|
I
|
E:PHI5
|
0.0
|
50.9
|
1.0
|
CZ
|
E:PHI5
|
2.1
|
30.0
|
1.0
|
CE1
|
E:PHI5
|
3.0
|
28.6
|
1.0
|
O
|
B:HOH212
|
3.1
|
27.6
|
1.0
|
HE1
|
E:PHI5
|
3.1
|
34.3
|
1.0
|
CE2
|
E:PHI5
|
3.1
|
29.1
|
1.0
|
HE2
|
E:PHI5
|
3.2
|
34.9
|
1.0
|
HE2
|
D:PHI5
|
3.4
|
40.3
|
1.0
|
HG11
|
D:VAL3
|
3.6
|
49.2
|
1.0
|
O
|
B:HOH214
|
3.9
|
58.3
|
1.0
|
HG11
|
E:VAL3
|
4.0
|
33.0
|
1.0
|
HG13
|
B:MVA13
|
4.0
|
22.9
|
1.0
|
HG11
|
B:MVA13
|
4.1
|
22.9
|
1.0
|
HG12
|
E:MVA13
|
4.2
|
32.8
|
1.0
|
O
|
B:HOH201
|
4.2
|
41.8
|
1.0
|
O
|
D:HOH219
|
4.2
|
44.4
|
1.0
|
CE2
|
D:PHI5
|
4.3
|
33.6
|
1.0
|
CD1
|
E:PHI5
|
4.3
|
26.2
|
1.0
|
CD2
|
E:PHI5
|
4.4
|
26.8
|
1.0
|
HG12
|
E:VAL3
|
4.4
|
33.0
|
1.0
|
HG12
|
D:VAL3
|
4.4
|
49.2
|
1.0
|
CG1
|
D:VAL3
|
4.4
|
41.0
|
1.0
|
HB
|
D:VAL3
|
4.5
|
53.2
|
1.0
|
CG1
|
B:MVA13
|
4.6
|
19.1
|
1.0
|
HG13
|
E:MVA13
|
4.6
|
32.8
|
1.0
|
CG1
|
E:VAL3
|
4.6
|
27.5
|
1.0
|
I
|
D:PHI5
|
4.8
|
32.3
|
1.0
|
HN1
|
B:MVA13
|
4.8
|
19.5
|
1.0
|
HG13
|
E:VAL3
|
4.8
|
33.0
|
1.0
|
CG1
|
E:MVA13
|
4.8
|
27.4
|
1.0
|
HG21
|
D:VAL3
|
4.8
|
55.9
|
1.0
|
CG
|
E:PHI5
|
4.9
|
25.2
|
1.0
|
O2
|
B:SO4102
|
4.9
|
67.8
|
0.7
|
CB
|
D:VAL3
|
5.0
|
44.3
|
1.0
|
CZ
|
D:PHI5
|
5.0
|
29.4
|
1.0
|
|
Iodine binding site 6 out
of 7 in 5f1t
Go back to
Iodine Binding Sites List in 5f1t
Iodine binding site 6 out
of 7 in the Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:I5
b:45.2
occ:0.51
|
I
|
F:PHI5
|
0.0
|
45.2
|
0.5
|
CZ
|
F:PHI5
|
2.1
|
31.2
|
0.5
|
HE2
|
F:PHI5
|
2.3
|
36.2
|
0.5
|
CE1
|
F:PHI5
|
3.1
|
30.6
|
0.5
|
CE2
|
F:PHI5
|
3.1
|
30.2
|
0.5
|
HE1
|
F:PHI5
|
3.1
|
36.7
|
0.5
|
CE2
|
F:PHI5
|
3.1
|
29.4
|
0.5
|
HE2
|
F:PHI5
|
3.2
|
35.3
|
0.5
|
I
|
F:PHI5
|
3.5
|
45.9
|
0.5
|
CZ
|
F:PHI5
|
3.6
|
32.0
|
0.5
|
O
|
A:HOH217
|
4.1
|
51.2
|
1.0
|
CD2
|
F:PHI5
|
4.1
|
27.5
|
0.5
|
HG12
|
F:VAL3
|
4.2
|
40.6
|
1.0
|
HD2
|
F:PHI5
|
4.3
|
33.0
|
0.5
|
HG11
|
F:VAL3
|
4.3
|
40.6
|
1.0
|
CD1
|
F:PHI5
|
4.3
|
28.1
|
0.5
|
CD2
|
F:PHI5
|
4.4
|
26.7
|
0.5
|
HE2
|
A:PHI5
|
4.5
|
35.2
|
1.0
|
CG1
|
F:VAL3
|
4.8
|
33.8
|
1.0
|
HG12
|
F:MVA13
|
4.9
|
33.0
|
1.0
|
CG
|
F:PHI5
|
4.9
|
25.8
|
0.5
|
CE1
|
F:PHI5
|
4.9
|
30.2
|
0.5
|
|
Iodine binding site 7 out
of 7 in 5f1t
Go back to
Iodine Binding Sites List in 5f1t
Iodine binding site 7 out
of 7 in the Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 7 of Crystal Structure of A Macrocyclic Peptide Containing Fragments From Alpha-Synuclein 36-55. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:I5
b:45.9
occ:0.49
|
I
|
F:PHI5
|
0.0
|
45.9
|
0.5
|
CZ
|
F:PHI5
|
2.1
|
32.0
|
0.5
|
HE1
|
F:PHI5
|
2.2
|
36.7
|
0.5
|
CE1
|
F:PHI5
|
2.9
|
30.6
|
0.5
|
CE1
|
F:PHI5
|
3.1
|
30.2
|
0.5
|
HE1
|
F:PHI5
|
3.1
|
36.3
|
0.5
|
CE2
|
F:PHI5
|
3.1
|
30.2
|
0.5
|
HE2
|
F:PHI5
|
3.2
|
36.2
|
0.5
|
HG13
|
A:VAL3
|
3.4
|
51.8
|
0.7
|
CZ
|
F:PHI5
|
3.4
|
31.2
|
0.5
|
I
|
F:PHI5
|
3.5
|
45.2
|
0.5
|
HG12
|
A:VAL3
|
3.6
|
44.0
|
0.3
|
HG11
|
A:VAL3
|
3.7
|
51.8
|
0.7
|
HG11
|
A:VAL3
|
3.9
|
44.0
|
0.3
|
CD1
|
F:PHI5
|
3.9
|
28.1
|
0.5
|
HE2
|
A:PHI5
|
3.9
|
35.2
|
1.0
|
HG12
|
F:MVA13
|
3.9
|
33.0
|
1.0
|
CG1
|
A:VAL3
|
4.0
|
43.1
|
0.7
|
HD1
|
F:PHI5
|
4.0
|
33.8
|
0.5
|
CE2
|
A:PHI5
|
4.1
|
29.3
|
1.0
|
HG22
|
A:VAL3
|
4.1
|
43.3
|
0.7
|
CG1
|
A:VAL3
|
4.2
|
36.6
|
0.3
|
HG13
|
F:MVA13
|
4.2
|
33.0
|
1.0
|
HG21
|
A:VAL3
|
4.3
|
43.3
|
0.7
|
CD1
|
F:PHI5
|
4.3
|
27.1
|
0.5
|
CD2
|
F:PHI5
|
4.4
|
27.5
|
0.5
|
HB
|
A:VAL3
|
4.4
|
47.2
|
0.3
|
CG1
|
F:MVA13
|
4.5
|
27.5
|
1.0
|
CZ
|
A:PHI5
|
4.5
|
27.6
|
1.0
|
O
|
A:HOH217
|
4.5
|
51.2
|
1.0
|
CG2
|
A:VAL3
|
4.6
|
36.0
|
0.7
|
HG11
|
F:MVA13
|
4.6
|
33.0
|
1.0
|
HG12
|
A:VAL3
|
4.6
|
51.8
|
0.7
|
CD2
|
A:PHI5
|
4.7
|
28.6
|
1.0
|
CE2
|
F:PHI5
|
4.7
|
29.4
|
0.5
|
I
|
A:PHI5
|
4.8
|
30.8
|
1.0
|
HD2
|
A:PHI5
|
4.8
|
34.3
|
1.0
|
CG
|
F:PHI5
|
4.9
|
25.7
|
0.5
|
CB
|
A:VAL3
|
4.9
|
39.3
|
0.3
|
CB
|
A:VAL3
|
4.9
|
39.2
|
0.7
|
O
|
A:HOH216
|
5.0
|
43.7
|
1.0
|
O
|
A:VAL3
|
5.0
|
32.7
|
1.0
|
HG13
|
A:VAL3
|
5.0
|
44.0
|
0.3
|
|
Reference:
P.J.Salveson,
R.K.Spencer,
J.S.Nowick.
X-Ray Crystallographic Structure of Oligomers Formed By A Toxic Beta-Hairpin Derived From Alpha-Synuclein: Trimers and Higher-Order Oligomers. J.Am.Chem.Soc. V. 138 4458 2016.
ISSN: ESSN 1520-5126
PubMed: 26926877
DOI: 10.1021/JACS.5B13261
Page generated: Sun Aug 11 20:57:37 2024
|