Iodine in PDB 4jrx: Crystal Structure of CA5 Tcr-Hla B*3505-Lpep Complex

The structure of Crystal Structure of CA5 Tcr-Hla B*3505-Lpep Complex, PDB code: 4jrx was solved by Y.C.Liu, J.Rossjohn, S.Gras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.80 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.100, 78.408, 105.339, 90.00, 93.06, 90.00
R / Rfree (%)	20.5 / 25.7

The structure of Crystal Structure of CA5 Tcr-Hla B*3505-Lpep Complex also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Iodine atom in the Crystal Structure of CA5 Tcr-Hla B*3505-Lpep Complex (pdb code 4jrx). 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 CA5 Tcr-Hla B*3505-Lpep Complex, PDB code: 4jrx:
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 CA5 Tcr-Hla B*3505-Lpep Complex


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 CA5 Tcr-Hla B*3505-Lpep Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:37.1 occ:1.00 NE1 A:TRP51 3.7 38.3 1.0 OG1 A:THR178 3.7 45.0 1.0 CD1 A:TRP51 3.8 38.6 1.0 CD A:ARG239 3.9 32.8 1.0 CB A:THR178 3.9 41.5 1.0 CG2 A:THR31 4.0 25.5 1.0 CG2 A:THR178 4.0 35.9 1.0 NE A:ARG239 4.2 29.0 1.0 CD A:PRO50 4.2 39.7 1.0 CZ A:ARG239 4.5 40.7 1.0 NH1 A:ARG239 4.5 29.9 1.0 CB A:ALA49 4.7 36.8 1.0 CE2 A:TRP51 5.0 40.0 1.0

Iodine binding site 2 out of 8 in the Crystal Structure of CA5 Tcr-Hla B*3505-Lpep Complex


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 CA5 Tcr-Hla B*3505-Lpep Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:44.1 occ:1.00 NH1 A:ARG62 3.6 23.5 1.0 CD A:ARG62 3.9 24.2 1.0 CA A:TYR59 4.0 36.2 1.0 CZ2 A:TRP167 4.1 32.0 1.0 CH2 A:TRP167 4.2 32.2 1.0 N A:TYR59 4.2 37.6 1.0 CB A:TYR59 4.3 36.0 1.0 O A:GLU58 4.4 42.1 1.0 C A:GLU58 4.5 43.0 1.0 CD2 A:TYR59 4.5 35.2 1.0 CZ A:ARG62 4.6 33.9 1.0 NE A:ARG62 4.7 19.1 1.0 CB A:ARG62 4.9 27.1 1.0 CG A:TYR59 4.9 34.8 1.0

Iodine binding site 3 out of 8 in the Crystal Structure of CA5 Tcr-Hla B*3505-Lpep Complex


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 CA5 Tcr-Hla B*3505-Lpep Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:56.3 occ:1.00 CG A:LYS68 3.9 40.7 1.0 CG A:PRO43 3.9 58.7 1.0 CB A:SER38 4.1 37.9 1.0 CG2 A:THR71 4.1 27.7 1.0 CB A:PRO43 4.1 54.5 1.0 CZ A:PHE36 4.1 34.2 1.0 CE A:LYS68 4.3 49.7 0.5 OG1 A:THR71 4.3 31.0 1.0 CB A:THR71 4.4 33.4 1.0 CB A:LYS68 4.4 34.5 1.0 CA A:LYS68 4.4 33.0 1.0 CA A:SER38 4.5 36.2 1.0 CD A:LYS68 4.7 44.4 0.5 CE2 A:PHE36 4.7 36.0 1.0 O A:SER38 4.9 44.2 1.0 O A:LYS68 4.9 37.7 1.0

Iodine binding site 4 out of 8 in the Crystal Structure of CA5 Tcr-Hla B*3505-Lpep Complex


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 CA5 Tcr-Hla B*3505-Lpep Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:I101 b:38.2 occ:0.50 OG1 C:THR11 3.6 45.6 1.0 N C:THR11 3.8 33.2 1.0 O C:HOH201 3.9 36.2 1.0 CG C:PRO6 3.9 35.7 1.0 O C:GLN9 4.0 30.3 1.0 CG2 A:VAL152 4.0 34.1 1.0 CG A:GLN155 4.1 36.5 1.0 CB C:THR11 4.2 43.0 1.0 CA C:LEU10 4.4 33.0 1.0 CB A:GLN155 4.4 22.7 1.0 NH1 A:ARG156 4.5 46.0 1.0 CG1 A:VAL152 4.5 34.6 1.0 CA C:THR11 4.6 33.3 1.0 CD1 C:LEU10 4.6 38.7 1.0 CB C:PRO6 4.6 31.4 1.0 C C:LEU10 4.6 36.3 1.0 CB A:VAL152 4.6 35.1 1.0 CA A:VAL152 4.7 32.5 1.0 CD C:PRO6 4.9 31.7 1.0 C C:GLN9 5.0 32.5 1.0

Iodine binding site 5 out of 8 in the Crystal Structure of CA5 Tcr-Hla B*3505-Lpep Complex


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 CA5 Tcr-Hla B*3505-Lpep Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:I302 b:67.1 occ:0.50 CD1 D:ILE120 3.3 37.9 0.5 N E:GLU70 3.7 37.8 1.0 CB E:GLU70 3.8 39.7 1.0 CG2 D:ILE120 3.9 31.5 0.5 CG1 D:ILE120 4.0 30.5 0.5 CA E:GLU70 4.0 38.0 1.0 CD D:LYS118 4.1 43.1 1.0 CG E:GLU70 4.2 51.1 1.0 C E:GLY69 4.3 40.8 1.0 CE D:LYS118 4.3 54.9 1.0 CB E:LEU52 4.3 24.9 1.0 CD2 E:LEU52 4.4 30.9 1.0 OE1 E:GLU70 4.6 63.3 1.0 CA E:GLY69 4.6 37.8 1.0 NZ D:LYS118 4.7 61.5 1.0 CD E:GLU70 4.8 70.7 1.0 CG E:LEU52 5.0 28.6 1.0

Iodine binding site 6 out of 8 in the Crystal Structure of CA5 Tcr-Hla B*3505-Lpep Complex


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 CA5 Tcr-Hla B*3505-Lpep Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:I303 b:0.3 occ:1.00 OD1 D:ASP160 3.5 56.4 1.0 CB D:SER161 3.6 38.8 1.0 N D:ILE133 3.7 43.0 1.0 O D:PRO131 3.8 42.6 1.0 NE2 D:GLN162 3.8 52.6 1.0 N D:SER161 3.9 37.2 1.0 OG D:SER161 4.0 40.3 1.0 OD1 D:ASN132 4.1 54.1 1.0 CA D:ASN132 4.2 42.8 1.0 CA D:SER161 4.2 37.7 1.0 CG D:GLN162 4.3 52.5 1.0 CG D:ASP160 4.3 54.7 1.0 O D:ILE133 4.4 46.8 1.0 C D:ASN132 4.4 47.0 1.0 N D:GLN162 4.5 41.7 1.0 CD D:GLN162 4.6 67.8 1.0 CA D:ILE133 4.6 42.2 1.0 CG2 D:VAL14 4.7 42.2 1.0 C D:SER161 4.7 44.5 1.0 C D:ILE133 4.7 47.6 1.0 OD2 D:ASP160 4.8 64.1 1.0 C D:PRO131 4.8 43.2 1.0 CG1 D:ILE133 4.9 44.6 0.5 CB D:ILE133 4.9 44.8 1.0 CG D:ASN132 4.9 65.8 1.0 C D:ASP160 5.0 39.4 1.0 N D:ASN132 5.0 41.9 1.0

Iodine binding site 7 out of 8 in the Crystal Structure of CA5 Tcr-Hla B*3505-Lpep Complex


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 CA5 Tcr-Hla B*3505-Lpep Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:I304 b:64.7 occ:0.50 CA D:ALA101 4.0 24.9 1.0 C D:ALA101 4.2 25.2 1.0 NE D:ARG126 4.3 57.1 1.0 CG2 D:VAL102 4.3 26.2 1.0 CG D:PRO46 4.3 44.4 1.0 CG D:ARG126 4.3 42.5 1.0 CD D:ARG126 4.4 49.0 1.0 N D:ALA101 4.4 26.1 1.0 N D:VAL102 4.4 22.3 1.0 N D:PRO46 4.5 37.9 1.0 CD D:PRO46 4.6 40.1 1.0 O D:ALA101 4.6 22.6 1.0 CA D:PRO46 4.6 37.9 1.0 CZ D:ARG126 4.7 70.0 1.0 C D:SER100 4.7 31.1 1.0 CB E:PRO183 4.8 39.1 1.0 O D:GLN44 4.8 29.8 1.0 O D:SER100 4.8 31.7 1.0 CB D:PRO46 4.9 39.5 1.0

Iodine binding site 8 out of 8 in the Crystal Structure of CA5 Tcr-Hla B*3505-Lpep Complex


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 CA5 Tcr-Hla B*3505-Lpep Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:I302 b:0.7 occ:0.50 O E:ASP162 3.4 42.5 1.0 CG2 E:VAL164 3.5 37.1 1.0 CG E:PRO185 3.7 42.1 1.0 CD E:PRO185 3.8 38.2 1.0 CB E:PRO185 4.0 37.6 1.0 O E:VAL164 4.1 36.4 1.0 C E:ASP162 4.4 41.7 1.0 CD2 E:LEU199 4.4 26.7 1.0 N E:VAL164 4.5 35.6 1.0 CE1 E:PHE159 4.5 27.1 1.0 CZ E:PHE159 4.6 24.3 1.0 CD1 E:LEU199 4.6 23.2 1.0 N E:PRO185 4.7 36.9 1.0 CB E:ASP162 4.7 39.8 1.0 CB E:VAL164 4.8 37.5 1.0 C E:VAL164 4.9 36.2 1.0 CA E:VAL164 4.9 34.2 1.0 CA E:ASP162 4.9 36.7 1.0

Y.C.Liu, J.J.Miles, M.A.Neller, E.Gostick, D.A.Price, A.W.Purcell, J.Mccluskey, S.R.Burrows, J.Rossjohn, S.Gras. Highly Divergent T-Cell Receptor Binding Modes Underlie Specific Recognition of A Bulged Viral Peptide Bound to A Human Leukocyte Antigen Class I Molecule. J.Biol.Chem. V. 288 15442 2013.
ISSN: ISSN 0021-9258
PubMed: 23569211
DOI: 10.1074/JBC.M112.447185