Iodine in PDB 7p3e: Mhc I A02 Allele Presenting Ylqlrtfll

The structure of Mhc I A02 Allele Presenting Ylqlrtfll, PDB code: 7p3e was solved by P.J.Rizkallah, A.K.Sewell, A.Wall, A.Fuller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.31 / 2.00
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	85.802, 85.802, 217.564, 90, 90, 120
R / Rfree (%)	21.4 / 24.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iodine atom in the Mhc I A02 Allele Presenting Ylqlrtfll (pdb code 7p3e). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 24 binding sites of Iodine where determined in the Mhc I A02 Allele Presenting Ylqlrtfll, PDB code: 7p3e:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 24 in the Mhc I A02 Allele Presenting Ylqlrtfll


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Mhc I A02 Allele Presenting Ylqlrtfll within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:51.1 occ:0.50 C A:ALA49 3.7 55.3 1.0 O A:ALA49 3.7 54.0 1.0 N A:ALA49 3.8 53.9 1.0 N A:PRO50 3.9 57.6 1.0 C A:ARG48 4.0 53.7 1.0 CA A:ALA49 4.1 54.0 1.0 CB A:GLU53 4.2 57.2 1.0 CG A:GLU53 4.3 60.5 1.0 CA A:PRO50 4.4 58.5 1.0 O A:PRO47 4.5 46.3 1.0 CA A:ARG48 4.5 53.1 1.0 O A:ARG48 4.5 56.9 1.0 CD A:PRO50 4.5 58.8 1.0 C A:PRO47 4.6 50.0 1.0 CB A:PRO47 4.6 53.2 1.0 N A:ARG48 4.6 49.9 1.0 CG A:PRO47 4.8 54.5 1.0

Iodine binding site 2 out of 24 in the Mhc I A02 Allele Presenting Ylqlrtfll


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Mhc I A02 Allele Presenting Ylqlrtfll within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:50.8 occ:0.50 N A:GLU232 3.6 38.8 1.0 NE2 B:GLN8 3.8 35.8 1.0 CA A:VAL231 4.0 40.9 1.0 CB A:VAL231 4.0 40.6 1.0 CG A:GLU232 4.1 55.1 1.0 CD B:GLN8 4.1 35.8 1.0 CG B:GLN8 4.2 35.2 1.0 CG1 A:VAL231 4.3 43.5 1.0 CB B:LYS6 4.3 37.9 1.0 C A:VAL231 4.3 38.3 1.0 CB A:GLU232 4.4 44.0 1.0 CD B:LYS6 4.4 49.3 1.0 CA A:GLU232 4.6 40.2 1.0 CG B:LYS6 4.8 41.5 1.0 OE1 B:GLN8 4.8 33.0 1.0

Iodine binding site 3 out of 24 in the Mhc I A02 Allele Presenting Ylqlrtfll


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Mhc I A02 Allele Presenting Ylqlrtfll within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:63.0 occ:0.50 NE A:ARG6 3.8 55.1 1.0 CE A:MET98 3.8 46.5 1.0 CE2 A:PHE8 4.0 39.4 1.0 CZ A:PHE8 4.0 38.0 1.0 CD A:ARG6 4.3 53.1 1.0 CA B:LYS58 4.5 47.5 1.0 N B:LYS58 4.5 42.0 1.0 CB B:LYS58 4.7 50.4 1.0 CZ A:ARG6 4.9 60.8 1.0 CD B:LYS58 4.9 55.7 1.0 CG A:MET98 5.0 37.9 1.0

Iodine binding site 4 out of 24 in the Mhc I A02 Allele Presenting Ylqlrtfll


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Mhc I A02 Allele Presenting Ylqlrtfll within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:64.2 occ:0.50 CG A:ARG44 3.9 56.5 1.0 CB D:PRO15 4.0 68.9 1.0 CG D:PRO15 4.1 65.2 1.0 CA D:GLY91 4.1 74.3 1.0 O A:HOH450 4.2 39.3 1.0 NE2 A:GLN43 4.2 59.7 1.0 CB A:GLN43 4.3 50.0 1.0 CD A:GLN43 4.7 57.5 1.0 CD A:ARG44 4.8 61.0 1.0 CG A:GLN43 4.8 51.9 1.0 CD D:PRO15 4.9 63.2 1.0 C D:GLY91 4.9 68.4 1.0

Iodine binding site 5 out of 24 in the Mhc I A02 Allele Presenting Ylqlrtfll


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Mhc I A02 Allele Presenting Ylqlrtfll within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:71.2 occ:0.50 OG1 A:THR178 3.5 64.0 1.0 CB A:THR178 3.9 62.3 1.0 CD1 A:TRP51 4.0 54.2 1.0 CB A:TRP51 4.1 55.8 1.0 CA A:GLY175 4.3 59.7 1.0 O A:GLY175 4.3 63.1 1.0 N A:THR178 4.4 65.7 1.0 CB A:GLU177 4.4 81.0 1.0 CG A:TRP51 4.5 54.2 1.0 C A:GLY175 4.5 63.9 1.0 N A:TRP51 4.6 55.5 1.0 CB A:PRO50 4.6 61.2 1.0 CA A:TRP51 4.8 55.3 1.0 O A:ASN174 4.8 58.6 1.0 CA A:THR178 4.8 64.1 1.0 CG2 A:THR178 4.9 61.7 1.0 CG A:PRO50 5.0 60.9 1.0

Iodine binding site 6 out of 24 in the Mhc I A02 Allele Presenting Ylqlrtfll


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Mhc I A02 Allele Presenting Ylqlrtfll within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:77.8 occ:0.50 O A:HOH402 2.9 35.7 1.0 CG A:PRO20 3.8 43.0 1.0 CB A:LEU78 4.0 32.3 1.0 CB A:SER13 4.1 35.2 1.0 CD1 A:LEU78 4.1 34.6 1.0 CD A:PRO20 4.2 42.3 1.0 CB A:PRO20 4.4 40.5 1.0 NH2 A:ARG82 4.6 56.3 1.0 NH1 A:ARG75 4.6 61.1 1.0 O A:ARG75 4.6 36.5 1.0 CG A:LEU78 4.7 33.0 1.0 CA A:SER13 4.8 34.2 1.0 O A:GLY18 5.0 48.1 1.0

Iodine binding site 7 out of 24 in the Mhc I A02 Allele Presenting Ylqlrtfll


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Mhc I A02 Allele Presenting Ylqlrtfll within 5.0Å range: probe atom residue distance (Å) B Occ A:I307 b:82.5 occ:0.50 N A:ALA139 3.7 48.9 1.0 N A:MET138 3.8 49.3 1.0 CE1 A:TYR85 3.9 36.8 1.0 CB A:MET138 3.9 60.5 1.0 CG A:ASP137 4.0 40.6 1.0 CB A:ASP137 4.0 42.9 1.0 CB A:ALA139 4.2 48.8 1.0 OD2 A:ASP137 4.2 39.9 1.0 CA A:MET138 4.3 55.2 1.0 OD1 A:ASP137 4.3 39.9 1.0 CD1 A:TYR85 4.4 37.4 1.0 C A:MET138 4.4 51.3 1.0 CA A:ALA139 4.6 47.9 1.0 C A:ASP137 4.7 44.8 1.0 CZ A:TYR85 4.9 37.8 1.0 CA A:ASP137 5.0 43.3 1.0

Iodine binding site 8 out of 24 in the Mhc I A02 Allele Presenting Ylqlrtfll


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Mhc I A02 Allele Presenting Ylqlrtfll within 5.0Å range: probe atom residue distance (Å) B Occ A:I308 b:81.6 occ:0.50 CG A:GLU173 3.5 72.5 1.0 NE2 A:GLN180 3.8 62.1 1.0 CA A:GLU173 4.0 63.3 1.0 CH2 A:TRP107 4.2 70.1 1.0 CB A:GLU173 4.3 67.2 1.0 CB A:LYS176 4.3 76.5 1.0 CD A:LYS176 4.4 82.7 1.0 O A:GLU173 4.6 62.7 1.0 CD A:GLU173 4.6 75.5 1.0 CD A:GLN180 4.7 63.8 1.0 OE1 A:GLN180 4.7 65.7 1.0 OE2 A:GLU173 4.7 76.8 1.0 NZ A:LYS176 4.8 87.2 1.0 N A:GLU173 4.8 59.8 1.0 CE A:LYS176 4.8 83.9 1.0 C A:GLU173 4.8 61.4 1.0 O A:LEU172 4.9 57.8 1.0 CZ2 A:TRP107 4.9 68.7 1.0 CG A:LYS176 5.0 79.6 1.0

Iodine binding site 9 out of 24 in the Mhc I A02 Allele Presenting Ylqlrtfll


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Mhc I A02 Allele Presenting Ylqlrtfll within 5.0Å range: probe atom residue distance (Å) B Occ B:I101 b:47.1 occ:0.75 N B:GLY43 3.3 51.7 1.0 CB B:ALA79 3.9 42.6 1.0 CA B:GLY43 3.9 52.3 1.0 N B:ASN42 4.0 48.6 1.0 O B:GLU77 4.0 47.3 1.0 C B:TYR78 4.0 42.5 1.0 N B:ALA79 4.1 39.0 1.0 C B:GLU77 4.1 49.6 1.0 N B:TYR78 4.2 45.0 1.0 C B:ASN42 4.2 53.7 1.0 CA B:ASN42 4.2 52.1 1.0 CB B:LEU40 4.3 38.0 1.0 CA B:TYR78 4.3 43.6 1.0 O B:TYR78 4.3 42.2 1.0 CB B:GLU77 4.6 57.7 1.0 CA B:ALA79 4.6 39.4 1.0 O B:LEU40 4.6 36.6 1.0 C B:LYS41 4.7 46.6 1.0 C B:LEU40 4.7 38.3 1.0 CD1 B:LEU40 4.9 38.5 1.0 CA B:GLU77 5.0 54.4 1.0

Iodine binding site 10 out of 24 in the Mhc I A02 Allele Presenting Ylqlrtfll


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Mhc I A02 Allele Presenting Ylqlrtfll within 5.0Å range: probe atom residue distance (Å) B Occ B:I102 b:63.6 occ:0.50 CE1 B:TYR67 3.8 37.0 1.0 CB B:SER52 4.0 32.6 1.0 OH B:TYR67 4.2 44.0 1.0 CD2 B:LEU65 4.2 35.3 1.0 CZ B:TYR67 4.3 40.5 1.0 CA B:SER52 4.3 35.0 1.0 CD1 B:TYR67 4.6 36.7 1.0 N B:SER52 4.7 32.5 1.0 O A:GLY237 4.8 43.7 1.0 CA A:GLY237 4.9 40.6 1.0

P.J.Rizkallah, A.K.Sewell, A.Wall, A.Fuller. Emergence of Immune Escape at Dominant Sars-Cov-2 Killer T-Cell Epitope Medrxiv 2021.
DOI: 10.1101/2021.06.21.21259010