Iodine in PDB 5zk7: Stapled-Peptides Tailored Against Initiation of Translation

The structure of Stapled-Peptides Tailored Against Initiation of Translation, PDB code: 5zk7 was solved by D.Lama, A.Liberator, Y.Frosi, J.Nakhle, N.Tsomia, T.Bashir, D.P.Lane, C.J.Brown, C.S.Verma, S.Auvin, F.Ciesielski, M.Uhring, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.89 / 2.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.350, 68.170, 111.010, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 27

The structure of Stapled-Peptides Tailored Against Initiation of Translation also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iodine atom in the Stapled-Peptides Tailored Against Initiation of Translation (pdb code 5zk7). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Stapled-Peptides Tailored Against Initiation of Translation, PDB code: 5zk7:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in the Stapled-Peptides Tailored Against Initiation of Translation


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Stapled-Peptides Tailored Against Initiation of Translation within 5.0Å range: probe atom residue distance (Å) B Occ A:I1002 b:89.8 occ:1.00 N A:GLY88 3.6 46.0 1.0 CB A:PRO87 3.8 49.0 1.0 N A:ALA158 4.0 48.0 1.0 CD A:ARG157 4.0 48.2 1.0 C A:PRO87 4.0 46.9 1.0 CA A:GLY88 4.0 45.4 1.0 CA A:ARG157 4.3 46.1 1.0 CA A:PRO87 4.3 47.8 1.0 CB A:ALA158 4.5 49.0 1.0 O A:PRO87 4.6 46.8 1.0 CB A:ARG157 4.6 46.9 1.0 C A:ARG157 4.7 46.5 1.0 O A:VAL156 4.8 39.8 1.0 CA A:ALA158 4.9 49.0 1.0 CG A:ARG157 4.9 47.8 1.0 NE A:ARG157 5.0 49.1 1.0

Iodine binding site 2 out of 5 in the Stapled-Peptides Tailored Against Initiation of Translation


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Stapled-Peptides Tailored Against Initiation of Translation within 5.0Å range: probe atom residue distance (Å) B Occ A:I1003 b:68.2 occ:1.00 O B:HOH1115 3.3 36.9 1.0 O D:HOH204 3.5 42.1 1.0 ND2 A:ASN77 3.6 33.6 1.0 O B:HOH1114 3.9 45.8 1.0 CA A:ALA74 4.0 25.9 1.0 CE1 A:HIS78 4.0 48.8 1.0 N B:ARG128 4.2 30.4 1.0 CB A:ALA74 4.3 26.6 1.0 CB A:ASN77 4.3 33.4 1.0 CB B:ASP127 4.3 33.1 1.0 CB B:ARG128 4.4 31.5 1.0 ND1 A:HIS78 4.4 46.9 1.0 CG A:ASN77 4.5 33.1 1.0 CA B:ARG128 4.6 30.9 1.0 O A:ALA74 4.7 26.3 1.0 O B:SER124 4.8 57.9 1.0 C B:ASP127 4.8 30.4 1.0 N A:ALA74 4.8 24.9 1.0 C A:ALA74 4.9 26.6 1.0 O A:TRP73 5.0 24.2 1.0

Iodine binding site 3 out of 5 in the Stapled-Peptides Tailored Against Initiation of Translation


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Stapled-Peptides Tailored Against Initiation of Translation within 5.0Å range: probe atom residue distance (Å) B Occ C:I101 b:39.8 occ:1.00 O C:HOH207 3.7 25.8 1.0 NH2 C:ARG4 3.8 25.7 1.0 CB1 C:MK85 4.0 23.6 1.0 CD C:ARG4 4.1 24.6 1.0 CG C:ARG4 4.3 24.8 1.0 CB1 D:MK89 4.4 22.0 1.0 CG D:MK89 4.4 23.4 1.0 N C:MK85 4.5 23.4 1.0 CB C:ARG4 4.5 24.9 1.0 CA C:MK85 4.7 24.0 1.0 CD D:MK89 4.7 23.5 1.0 CB C:MK85 4.7 23.9 1.0 CZ C:ARG4 4.8 25.4 1.0 CB D:MK89 4.8 23.0 1.0 O D:MK89 4.9 22.6 1.0 NE C:ARG4 4.9 24.0 1.0

Iodine binding site 4 out of 5 in the Stapled-Peptides Tailored Against Initiation of Translation


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Stapled-Peptides Tailored Against Initiation of Translation within 5.0Å range: probe atom residue distance (Å) B Occ D:I101 b:32.9 occ:1.00 O D:HOH205 3.8 33.0 1.0 NH2 D:ARG4 3.8 27.4 1.0 CD D:ARG4 4.2 25.8 1.0 CB1 D:MK85 4.2 22.9 1.0 CG C:MK89 4.6 24.6 1.0 CB1 C:MK89 4.6 24.9 1.0 CG D:ARG4 4.7 25.4 1.0 CZ D:ARG4 4.7 26.7 1.0 N D:MK85 4.8 22.4 1.0 CB D:ARG4 4.8 24.8 1.0 NE D:ARG4 4.9 25.9 1.0 CB C:MK89 4.9 24.8 1.0 CA D:MK85 4.9 22.2 1.0 CB D:MK85 4.9 22.9 1.0

Iodine binding site 5 out of 5 in the Stapled-Peptides Tailored Against Initiation of Translation


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Stapled-Peptides Tailored Against Initiation of Translation within 5.0Å range: probe atom residue distance (Å) B Occ D:I102 b:94.5 occ:1.00 CE C:MK85 4.4 24.1 1.0 CE D:MK85 4.4 23.9 1.0 CD D:MK85 4.8 23.5 1.0 CG D:MK85 4.9 22.9 1.0

D.Lama, A.M.Liberatore, Y.Frosi, J.Nakhle, N.Tsomaia, T.Bashir, D.P.Lane, C.J.Brown, C.S.Verma, S.Auvin. Structural Insights Reveal A Recognition Feature For Tailoring Hydrocarbon Stapled-Peptides Against the Eukaryotic Translation Initiation Factor 4E Protein. Chem Sci V. 10 2489 2019.
ISSN: ISSN 2041-6520
PubMed: 30881679
DOI: 10.1039/C8SC03759K