Iodine in PDB 3rew: Crystal Structure of An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2

The structure of Crystal Structure of An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2, PDB code: 3rew was solved by A.Wood, F.Mohammed, M.Salim, A.Tranter, A.B.Rickinson, P.A.H.Moss, H.J.Stauss, N.M.Steven, B.E.Willcox, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.11 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.750, 141.440, 141.670, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 23.9

The structure of Crystal Structure of An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2 also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Iodine atom in the Crystal Structure of An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2 (pdb code 3rew). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Crystal Structure of An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2, PDB code: 3rew:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in the Crystal Structure of An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2


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 An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I276 b:16.6 occ:1.00 O A:HOH311 3.5 19.3 1.0 CA A:ALA69 4.0 12.3 1.0 CB A:ALA69 4.2 12.0 1.0 CG A:GLN72 4.2 16.3 1.0 N A:ALA69 4.3 12.1 1.0 C A:LYS68 4.6 12.3 1.0 O A:LYS68 4.7 13.7 1.0 CB A:GLN72 4.9 14.1 1.0

Iodine binding site 2 out of 8 in the Crystal Structure of An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2


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 An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I277 b:48.0 occ:1.00 OG1 A:THR178 3.2 27.5 1.0 O A:HOH432 3.7 28.6 1.0 CD1 A:TRP51 3.7 25.1 1.0 CB A:THR178 3.8 25.6 1.0 CB A:TRP51 3.9 23.3 1.0 N A:THR178 4.0 25.9 1.0 CA A:GLY175 4.0 19.6 1.0 CG A:TRP51 4.2 23.5 1.0 O A:GLY175 4.2 20.0 1.0 CB A:GLU177 4.2 28.8 1.0 C A:GLY175 4.3 20.6 1.0 N A:GLU177 4.5 25.4 1.0 N A:TRP51 4.5 24.6 1.0 O A:ASN174 4.5 19.8 1.0 CA A:THR178 4.6 25.6 1.0 CA A:TRP51 4.6 23.2 1.0 CA A:GLU177 4.7 27.6 1.0 C A:GLU177 4.7 26.8 1.0 CG A:GLU177 4.8 34.6 1.0 CB A:PRO50 4.8 25.7 1.0 NE1 A:TRP51 4.9 25.3 1.0

Iodine binding site 3 out of 8 in the Crystal Structure of An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2


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 An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I278 b:51.6 occ:1.00 NE A:ARG65 3.3 27.3 1.0 O A:HOH364 3.5 47.3 1.0 NH2 A:ARG65 3.6 29.6 1.0 NH1 A:ARG44 3.7 27.5 1.0 O A:ASP61 3.9 16.1 1.0 CZ A:ARG65 4.0 28.6 1.0 OD1 A:ASP61 4.1 17.4 1.0 CA A:ASP61 4.2 15.6 1.0 CB A:ASP61 4.2 14.8 1.0 CG A:ASP61 4.3 18.1 1.0 CG A:ARG65 4.3 17.1 1.0 CD A:ARG65 4.3 19.8 1.0 C A:ASP61 4.5 15.3 1.0 CG2 A:THR64 4.6 12.3 1.0 CB A:THR64 4.6 13.5 1.0 CZ A:ARG44 4.9 27.0 1.0

Iodine binding site 4 out of 8 in the Crystal Structure of An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2


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 An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2 within 5.0Å range: probe atom residue distance (Å) B Occ B:I100 b:32.1 occ:1.00 N B:GLY43 3.4 21.1 1.0 CB B:ALA79 3.8 18.6 1.0 N B:ASN42 4.0 20.1 1.0 CB B:GLU77 4.0 24.6 1.0 O B:GLU77 4.0 22.1 1.0 C B:TYR78 4.0 18.7 1.0 C B:GLU77 4.1 22.5 1.0 CA B:ASN42 4.1 21.3 1.0 CA B:GLY43 4.1 21.3 1.0 N B:ALA79 4.1 18.2 1.0 C B:ASN42 4.2 21.8 1.0 N B:TYR78 4.2 20.3 1.0 CA B:TYR78 4.3 19.4 1.0 O B:TYR78 4.4 16.3 1.0 CB B:LEU40 4.5 17.1 1.0 CA B:ALA79 4.6 18.4 1.0 O B:LEU40 4.6 17.5 1.0 CA B:GLU77 4.7 23.7 1.0 C B:LYS41 4.8 20.2 1.0 C B:LEU40 4.9 18.1 1.0 OE1 B:GLU77 4.9 39.0 1.0 CD1 B:LEU40 5.0 17.9 1.0

Iodine binding site 5 out of 8 in the Crystal Structure of An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2


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 An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2 within 5.0Å range: probe atom residue distance (Å) B Occ C:I10 b:19.6 occ:1.00 O C:HOH104 3.6 28.3 1.0 N C:MET8 3.8 15.6 1.0 NE1 A:TRP147 3.9 15.6 1.0 CE A:LYS146 4.0 21.5 1.0 O C:MET8 4.0 14.7 1.0 CA C:THR7 4.0 13.0 1.0 CD1 A:TRP147 4.1 14.8 1.0 C C:THR7 4.4 14.6 1.0 NZ A:LYS146 4.4 21.7 1.0 CB C:THR7 4.4 13.6 1.0 CG2 A:VAL152 4.6 10.9 1.0 O C:LEU6 4.7 11.4 1.0 CA C:MET8 4.7 16.4 1.0 CB A:ALA150 4.7 14.1 1.0 CD A:LYS146 4.7 19.3 1.0 C C:MET8 4.8 15.1 1.0 CB C:MET8 4.9 16.2 1.0 CG2 C:THR7 4.9 13.8 1.0 CG A:LYS146 4.9 16.5 1.0

Iodine binding site 6 out of 8 in the Crystal Structure of An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2


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 An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2 within 5.0Å range: probe atom residue distance (Å) B Occ D:I276 b:17.4 occ:1.00 O D:HOH360 3.5 30.9 1.0 O D:HOH335 3.6 19.9 1.0 NE D:ARG169 3.7 16.8 1.0 CZ D:ARG169 3.8 15.9 1.0 CD D:ARG169 4.0 16.5 1.0 NH1 D:ARG169 4.0 15.9 1.0 CE3 D:TRP107 4.1 18.0 1.0 NH2 D:ARG169 4.2 12.1 1.0 CB D:TRP107 4.4 18.2 1.0 CG D:ARG169 4.4 13.7 1.0 CD2 D:TRP107 4.9 17.1 1.0 CZ3 D:TRP107 4.9 19.7 1.0 CB D:ARG169 4.9 12.5 1.0

Iodine binding site 7 out of 8 in the Crystal Structure of An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2


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 An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2 within 5.0Å range: probe atom residue distance (Å) B Occ E:I100 b:26.6 occ:1.00 O E:HOH362 3.3 32.7 1.0 N E:GLY43 3.5 27.8 1.0 N E:ASN42 3.9 25.0 1.0 CB E:ALA79 3.9 19.1 1.0 C E:TYR78 4.0 20.2 1.0 O E:GLU77 4.0 22.8 1.0 C E:GLU77 4.1 25.0 1.0 CA E:ASN42 4.1 26.2 1.0 N E:ALA79 4.2 20.1 1.0 CA E:GLY43 4.2 28.4 1.0 CA E:TYR78 4.2 21.2 1.0 N E:TYR78 4.2 22.4 1.0 C E:ASN42 4.2 27.2 1.0 CB E:GLU77 4.2 28.0 1.0 O E:TYR78 4.3 18.6 1.0 CB E:LEU40 4.3 21.0 1.0 O E:LEU40 4.4 21.5 1.0 C E:LEU40 4.7 21.5 1.0 C E:LYS41 4.7 24.7 1.0 CA E:ALA79 4.7 19.5 1.0 CA E:GLU77 4.8 26.3 1.0 CD1 E:LEU40 4.9 19.9 1.0

Iodine binding site 8 out of 8 in the Crystal Structure of An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of An LMP2A-Derived Peptide Bound to Human Class I Mhc Hla-A2 within 5.0Å range: probe atom residue distance (Å) B Occ F:I10 b:18.1 occ:1.00 O F:HOH306 3.6 22.6 1.0 N F:MET8 3.7 11.0 1.0 CE D:LYS146 3.9 21.5 1.0 O F:MET8 3.9 11.7 1.0 NE1 D:TRP147 3.9 10.1 1.0 CA F:THR7 4.0 10.3 1.0 CD1 D:TRP147 4.1 11.7 1.0 NZ D:LYS146 4.3 21.9 1.0 C F:THR7 4.4 11.6 1.0 CB F:THR7 4.5 10.7 1.0 CG2 D:VAL152 4.5 13.8 1.0 CA F:MET8 4.7 12.2 1.0 O F:LEU6 4.8 10.5 1.0 C F:MET8 4.8 11.1 1.0 CD D:LYS146 4.8 19.1 1.0 CB D:ALA150 4.8 15.1 1.0 CG2 F:THR7 4.8 9.6 1.0 O D:HOH385 5.0 21.0 1.0 CB F:MET8 5.0 11.8 1.0

A.A.Simpson, F.Mohammed, M.Salim, A.Tranter, A.B.Rickinson, H.J.Stauss, P.A.Moss, N.M.Steven, B.E.Willcox. Structural and Energetic Evidence For Highly Peptide-Specific Tumor Antigen Targeting Via Allo-Mhc Restriction. Proc.Natl.Acad.Sci.Usa V. 108 21176 2011.
ISSN: ISSN 0027-8424
PubMed: 22160697
DOI: 10.1073/PNAS.1108422109