Iodine in PDB 5f1w: Crystal Structure of the Enantiomer of A Macrocyclic Peptide Containing Fragments From Alpha Synuclein 36-55

The structure of Crystal Structure of the Enantiomer of A Macrocyclic Peptide Containing Fragments From Alpha Synuclein 36-55, PDB code: 5f1w 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)	34.84 / 2.16
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	77.910, 77.910, 77.910, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 28.3

The binding sites of Iodine atom in the Crystal Structure of the Enantiomer of A Macrocyclic Peptide Containing Fragments From Alpha Synuclein 36-55 (pdb code 5f1w). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of the Enantiomer of A Macrocyclic Peptide Containing Fragments From Alpha Synuclein 36-55, PDB code: 5f1w:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Crystal Structure of the Enantiomer 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 the Enantiomer 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:85.0 occ:1.00 I1 A:IOY5 0.0 85.0 1.0 CZ A:IOY5 2.1 66.5 1.0 CE1 A:IOY5 3.1 45.9 1.0 CE2 A:IOY5 3.1 44.5 1.0 HE1 A:IOY5 3.1 55.1 1.0 HE2 A:IOY5 3.2 53.4 1.0 HG23 C:DVA3 3.5 38.5 1.0 HG13 C:MV913 3.5 72.0 1.0 HG12 C:DVA3 3.7 36.9 1.0 HG23 C:DTH15 3.8 42.1 1.0 HG21 C:DTH15 3.9 42.1 1.0 HG22 C:DTH15 3.9 42.1 1.0 CG2 C:DTH15 4.1 35.1 1.0 HG12 C:MV913 4.2 72.0 1.0 CD1 A:IOY5 4.4 60.7 1.0 CG1 C:MV913 4.4 60.0 1.0 CD2 A:IOY5 4.4 67.2 1.0 CG2 C:DVA3 4.4 32.1 1.0 CG1 C:DVA3 4.7 30.7 1.0 HG22 A:MV913 4.7 48.7 1.0 HG21 C:DVA3 4.7 38.5 1.0 CG A:IOY5 4.9 41.1 1.0 HG22 C:DVA3 4.9 38.5 1.0 O C:HOH206 4.9 55.7 0.3 HG11 C:MV913 5.0 72.0 1.0

Iodine binding site 2 out of 6 in the Crystal Structure of the Enantiomer 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 the Enantiomer 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:68.8 occ:1.00 I1 B:IOY5 0.0 68.8 1.0 CZ B:IOY5 2.1 41.5 1.0 CE1 B:IOY5 3.0 43.8 1.0 HE1 B:IOY5 3.1 52.6 1.0 CE2 B:IOY5 3.1 45.1 1.0 HE2 B:IOY5 3.2 54.2 1.0 HB2 B:DHI11 3.3 42.8 1.0 CG E:DHI11 3.4 32.9 1.0 HB2 E:DHI11 3.5 34.8 1.0 HB3 D:IOY5 3.5 48.7 1.0 CD2 E:DHI11 3.6 39.7 1.0 HB2 D:IOY5 3.6 48.7 1.0 ND1 E:DHI11 3.7 34.6 1.0 ND1 B:DHI11 3.8 36.5 1.0 CG B:DHI11 3.8 38.9 1.0 CB E:DHI11 3.8 29.0 1.0 O E:HOH102 3.8 34.3 1.0 HB3 E:DHI11 3.8 34.8 1.0 HD2 E:DHI11 3.8 47.7 1.0 NE2 E:DHI11 3.9 40.3 1.0 CB B:DHI11 3.9 35.7 1.0 CB D:IOY5 3.9 40.6 1.0 CE1 E:DHI11 4.0 41.2 1.0 HD1 E:DHI11 4.0 41.5 1.0 HB3 B:DHI11 4.1 42.8 1.0 HB3 E:IOY5 4.2 39.2 1.0 CE1 D:DHI11 4.2 55.7 1.0 CG D:IOY5 4.3 41.5 1.0 HB2 E:IOY5 4.3 39.2 1.0 CE1 B:DHI11 4.3 46.0 1.0 ND1 D:DHI11 4.3 53.1 1.0 CD1 B:IOY5 4.3 43.5 1.0 CD2 B:DHI11 4.3 33.7 1.0 HE1 D:DHI11 4.4 66.8 1.0 CD2 B:IOY5 4.4 55.4 1.0 HD2 D:IOY5 4.4 89.1 1.0 NE2 D:DHI11 4.5 54.8 1.0 HD1 D:DHI11 4.5 63.7 1.0 CD2 D:IOY5 4.5 74.2 1.0 HE1 E:DHI11 4.5 49.4 1.0 CG D:DHI11 4.6 31.6 1.0 NE2 B:DHI11 4.6 46.0 1.0 CB E:IOY5 4.7 32.6 1.0 CD2 D:DHI11 4.7 37.5 1.0 HE1 B:DHI11 4.7 55.1 1.0 HD2 B:DHI11 4.8 40.4 1.0 CG B:IOY5 4.9 30.5 1.0

Iodine binding site 3 out of 6 in the Crystal Structure of the Enantiomer 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 the Enantiomer 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:72.7 occ:1.00 I1 C:IOY5 0.0 72.7 1.0 CZ C:IOY5 2.1 44.6 1.0 CE1 C:IOY5 3.1 40.9 1.0 HE1 C:IOY5 3.1 49.1 1.0 CE2 C:IOY5 3.1 47.3 1.0 HE2 C:IOY5 3.2 56.7 1.0 HB2 C:DHI11 3.3 47.6 1.0 HD1 C:DHI11 3.7 57.6 1.0 ND1 C:DHI11 3.7 48.0 1.0 CG C:DHI11 3.8 50.3 1.0 CB C:DHI11 3.9 39.6 1.0 HB3 C:DHI11 4.1 47.6 1.0 CE1 C:DHI11 4.3 54.1 1.0 CD1 C:IOY5 4.3 50.2 1.0 CD2 C:IOY5 4.4 59.9 1.0 CD2 C:DHI11 4.4 43.7 1.0 NE2 C:DHI11 4.7 48.6 1.0 HE1 C:DHI11 4.7 65.0 1.0 CG C:IOY5 4.9 37.1 1.0 HD2 C:DHI11 4.9 52.5 1.0

Iodine binding site 4 out of 6 in the Crystal Structure of the Enantiomer 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 the Enantiomer 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:0.6 occ:1.00 I1 D:IOY5 0.0 0.6 1.0 CZ D:IOY5 2.1 47.4 1.0 CE1 D:IOY5 3.1 40.2 1.0 HE1 D:IOY5 3.1 48.2 1.0 CE2 D:IOY5 3.1 54.0 1.0 HE2 D:IOY5 3.2 64.8 1.0 O4 B:SO4101 3.7 84.5 0.3 HG22 B:MV913 3.8 46.4 1.0 HG23 B:MV913 3.9 46.4 1.0 HD2 B:IOY5 4.1 66.5 1.0 CG2 B:MV913 4.3 38.7 1.0 CD1 D:IOY5 4.3 73.2 1.0 CD2 D:IOY5 4.4 74.2 1.0 HG22 D:MV913 4.5 52.3 1.0 HG21 B:MV913 4.6 46.4 1.0 HB3 B:IOY5 4.6 38.9 1.0 CD2 B:IOY5 4.7 55.4 1.0 HG23 D:MV913 4.9 52.3 1.0 CG D:IOY5 4.9 41.5 1.0

Iodine binding site 5 out of 6 in the Crystal Structure of the Enantiomer 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 the Enantiomer 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:0.9 occ:1.00 I1 E:IOY5 0.0 0.9 1.0 CZ E:IOY5 2.1 95.5 1.0 CE1 E:IOY5 3.1 68.6 1.0 HE1 E:IOY5 3.1 82.3 1.0 CE2 E:IOY5 3.1 75.4 1.0 HE2 E:IOY5 3.2 90.5 1.0 HG21 E:DVA3 3.2 59.0 1.0 HG23 B:MV913 3.4 46.4 1.0 HG21 B:MV913 3.6 46.4 1.0 HN3 B:MV913 3.8 37.4 1.0 HG23 E:DVA3 4.0 59.0 1.0 CG2 E:DVA3 4.0 49.2 1.0 CG2 B:MV913 4.0 38.7 1.0 HG22 E:DVA3 4.3 59.0 1.0 CD1 E:IOY5 4.3 88.2 1.0 HB B:MV913 4.4 39.8 1.0 CD2 E:IOY5 4.4 65.9 1.0 HE2 D:IOY5 4.4 64.8 1.0 CN B:MV913 4.8 31.1 1.0 HG22 B:MV913 4.8 46.4 1.0 CB B:MV913 4.8 33.1 1.0 HG22 E:MV913 4.9 46.8 1.0 CG E:IOY5 4.9 44.0 1.0 HN2 B:MV913 4.9 37.4 1.0

Iodine binding site 6 out of 6 in the Crystal Structure of the Enantiomer 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 the Enantiomer 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:0.6 occ:1.00 I1 F:IOY5 0.0 0.6 1.0 CZ F:IOY5 2.1 77.8 1.0 CE1 F:IOY5 3.1 58.2 1.0 CE2 F:IOY5 3.1 72.0 1.0 HE1 F:IOY5 3.1 69.8 1.0 HE2 F:IOY5 3.1 86.4 1.0 HG22 F:DVA3 4.1 64.3 1.0 CD1 F:IOY5 4.4 73.4 1.0 CD2 F:IOY5 4.4 84.4 1.0 HE2 A:IOY5 4.5 53.4 1.0 CG F:IOY5 4.9 47.0 1.0 CG2 F:DVA3 5.0 53.6 1.0

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