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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:

Chlorine (Cl) 3 atoms

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

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