Iodine in PDB 4pgc: Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal

The structure of Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal, PDB code: 4pgc was solved by P.Celie, R.P.Joosten, A.Perrakis, J.Neefjes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	83.11 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.179, 90.303, 89.370, 90.00, 111.58, 90.00
R / Rfree (%)	21.2 / 24.3

The binding sites of Iodine atom in the Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal (pdb code 4pgc). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal, PDB code: 4pgc:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal within 5.0Å range: probe atom residue distance (Å) B Occ C:I6 b:62.1 occ:1.00 I1 C:TYI6 0.0 62.1 1.0 CE1 C:TYI6 2.1 59.7 1.0 CZ C:TYI6 3.0 56.6 1.0 CD1 C:TYI6 3.1 57.2 1.0 OH C:TYI6 3.1 42.0 1.0 O C:HOH101 3.3 38.4 1.0 CD C:PRO3 3.3 0.2 1.0 CG C:PRO3 3.6 0.7 1.0 CE2 A:TYR159 3.7 53.1 1.0 CD2 A:TYR159 3.7 48.0 1.0 OG A:SER99 3.8 39.2 1.0 CD1 A:LEU156 3.9 50.2 1.0 OE1 A:GLN114 4.0 42.2 1.0 CE2 C:TYI6 4.3 61.4 1.0 CZ A:TYR159 4.3 54.5 1.0 CG A:TYR159 4.4 49.3 1.0 CG C:TYI6 4.4 55.9 1.0 NE2 A:GLN114 4.6 39.4 1.0 CD A:GLN114 4.6 37.6 1.0 N C:PRO3 4.7 1.0 1.0 CD2 C:TYI6 4.9 53.4 1.0 CE1 A:TYR159 4.9 48.5 1.0 OH A:TYR159 4.9 55.2 1.0 CD1 A:TYR159 4.9 52.6 1.0

Iodine binding site 2 out of 4 in the Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal within 5.0Å range: probe atom residue distance (Å) B Occ C:I6 b:59.7 occ:1.00 I2 C:TYI6 0.0 59.7 1.0 CE2 C:TYI6 2.1 61.4 1.0 CZ C:TYI6 3.0 56.6 1.0 CD2 C:TYI6 3.0 53.4 1.0 OH C:TYI6 3.0 42.0 1.0 CG2 A:VAL9 3.7 23.2 1.0 CZ A:PHE74 4.1 30.3 1.0 CE2 A:PHE74 4.1 31.0 1.0 CE1 C:TYI6 4.3 59.7 1.0 CG C:TYI6 4.3 55.9 1.0 CB A:VAL9 4.4 23.5 1.0 O C:PRO3 4.5 0.8 1.0 ND2 A:ASN70 4.5 30.5 1.0 CG A:ASN70 4.6 28.4 1.0 CG1 A:VAL97 4.6 25.6 1.0 OH A:TYR22 4.6 29.1 1.0 CG1 A:VAL9 4.6 24.3 1.0 CB A:VAL97 4.8 23.0 1.0 OD1 A:ASN70 4.8 30.8 1.0 CD1 C:TYI6 4.9 57.2 1.0 OE2 A:GLU24 4.9 28.9 1.0 O C:ALA2 5.0 0.7 1.0

Iodine binding site 3 out of 4 in the Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal within 5.0Å range: probe atom residue distance (Å) B Occ F:I6 b:55.4 occ:1.00 I1 F:TYI6 0.0 55.4 1.0 CE1 F:TYI6 2.1 46.6 1.0 CZ F:TYI6 3.1 42.2 1.0 CD1 F:TYI6 3.1 41.1 1.0 OH F:TYI6 3.2 35.5 1.0 CD F:PRO3 3.6 0.1 1.0 CD1 D:LEU156 3.6 60.0 1.0 CG F:PRO3 3.6 0.3 1.0 CD2 D:TYR159 3.7 52.4 1.0 OG D:SER99 3.7 30.7 1.0 CE2 D:TYR159 3.7 56.4 1.0 OE1 D:GLN114 3.8 45.0 1.0 CE2 F:TYI6 4.4 45.9 1.0 CD D:GLN114 4.4 40.2 1.0 NE2 D:GLN114 4.4 44.2 1.0 CG D:TYR159 4.4 45.5 1.0 CG F:TYI6 4.4 44.6 1.0 CZ D:TYR159 4.5 56.3 1.0 CD2 F:TYI6 4.9 41.9 1.0

Iodine binding site 4 out of 4 in the Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal within 5.0Å range: probe atom residue distance (Å) B Occ F:I6 b:50.3 occ:1.00 I2 F:TYI6 0.0 50.3 1.0 CE2 F:TYI6 2.1 45.9 1.0 CZ F:TYI6 3.0 42.2 1.0 OH F:TYI6 3.0 35.5 1.0 CD2 F:TYI6 3.1 41.9 1.0 CG2 D:VAL9 3.7 23.2 1.0 CZ D:PHE74 4.0 35.7 1.0 CE2 D:PHE74 4.1 34.8 1.0 CE1 F:TYI6 4.3 46.6 1.0 CG F:TYI6 4.4 44.6 1.0 CB D:VAL9 4.4 23.6 1.0 CG1 D:VAL97 4.4 24.6 1.0 ND2 D:ASN70 4.5 29.2 1.0 O F:PRO3 4.5 78.3 1.0 CG D:ASN70 4.6 27.5 1.0 CG1 D:VAL9 4.6 25.8 1.0 CB D:VAL97 4.6 23.0 1.0 OH D:TYR22 4.7 29.1 1.0 OD1 D:ASN70 4.8 29.4 1.0 CD1 F:TYI6 4.9 41.1 1.0 CB D:SER99 5.0 27.9 1.0 CG2 D:VAL97 5.0 23.3 1.0 OE2 D:GLU24 5.0 25.5 1.0

M.A.Garstka, A.Fish, P.H.Celie, R.P.Joosten, G.M.Janssen, I.Berlin, R.Hoppes, M.Stadnik, L.Janssen, H.Ovaa, P.A.Van Veelen, A.Perrakis, J.Neefjes. The First Step of Peptide Selection in Antigen Presentation By Mhc Class I Molecules. Proc.Natl.Acad.Sci.Usa V. 112 1505 2015.
ISSN: ESSN 1091-6490
PubMed: 25605945
DOI: 10.1073/PNAS.1416543112