Iodine in PDB 2ak4: Crystal Structure of SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide

The structure of Crystal Structure of SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide, PDB code: 2ak4 was solved by F.E.Tynan, S.R.Burrows, A.M.Buckle, C.S.Clements, N.A.Borg, J.J.Miles, T.Beddoe, J.C.Whisstock, M.C.Wilce, S.L.Silins, J.M.Burrows, L.Kjer-Nielsen, L.Konstenko, A.W.Purcell, J.Mccluskey, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.154, 213.282, 122.303, 90.00, 89.94, 90.00
R / Rfree (%)	24.6 / 27.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide (pdb code 2ak4). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 22 binding sites of Iodine where determined in the Crystal Structure of SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide, PDB code: 2ak4:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 22 in the Crystal Structure of SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide


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 SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I1002 b:3.1 occ:1.00 O K:HOH1021 3.4 2.0 1.0 OG1 A:THR178 3.5 3.5 1.0 NE1 A:TRP51 3.6 2.6 1.0 CD1 A:TRP51 3.8 2.0 1.0 CD A:ARG239 3.9 3.1 1.0 N K:ARG17 3.9 7.3 1.0 CB A:THR178 3.9 4.3 1.0 CD A:PRO50 4.2 4.0 1.0 CG2 A:THR31 4.2 2.0 1.0 CA K:GLY16 4.2 9.2 1.0 CG2 A:THR178 4.2 3.3 1.0 NE A:ARG239 4.2 4.5 1.0 CB K:ARG17 4.5 7.2 1.0 C K:GLY16 4.6 8.1 1.0 CB A:ALA49 4.6 2.0 1.0 O A:HOH1028 4.7 12.8 1.0 CZ A:ARG239 4.7 3.1 1.0 CE2 A:TRP51 4.8 2.1 1.0 CA K:ARG17 4.9 6.6 1.0 NH1 A:ARG239 4.9 4.5 1.0

Iodine binding site 2 out of 22 in the Crystal Structure of SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide


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 SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I1006 b:3.0 occ:1.00 NH1 A:ARG62 3.6 2.0 1.0 CD A:ARG62 3.9 3.2 1.0 CA A:TYR59 3.9 3.2 1.0 CH2 A:TRP167 4.2 4.9 1.0 N A:TYR59 4.2 3.8 1.0 CZ2 A:TRP167 4.2 4.2 1.0 CB A:TYR59 4.2 2.7 1.0 CD1 A:TYR59 4.3 2.8 1.0 C A:GLU58 4.5 5.1 1.0 O A:GLU58 4.6 5.1 1.0 CZ A:ARG62 4.6 3.5 1.0 NE A:ARG62 4.7 5.5 1.0 CG A:TYR59 4.8 2.2 1.0 CB A:ARG62 4.9 2.9 1.0

Iodine binding site 3 out of 22 in the Crystal Structure of SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide


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 SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I1010 b:12.1 occ:1.00 CG A:PRO43 3.4 13.8 1.0 CG A:LYS68 3.9 8.2 1.0 OG1 A:THR71 4.1 6.3 1.0 CG2 A:THR71 4.1 4.3 1.0 CB A:THR71 4.2 4.8 1.0 CB A:SER38 4.2 5.6 1.0 CZ A:PHE36 4.3 3.0 1.0 CB A:PRO43 4.3 13.0 1.0 CA A:LYS68 4.3 4.5 1.0 CB A:LYS68 4.4 4.5 1.0 CD A:LYS68 4.5 13.6 1.0 CE A:LYS68 4.5 17.6 1.0 CD A:PRO43 4.6 14.8 1.0 CA A:SER38 4.6 7.0 1.0 O A:LYS68 4.8 4.7 1.0 CE1 A:PHE36 4.8 2.0 1.0 O A:SER38 4.9 9.2 1.0

Iodine binding site 4 out of 22 in the Crystal Structure of SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide


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 SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:I1016 b:52.1 occ:1.00 N B:GLY43 3.4 9.6 1.0 O B:GLU77 3.6 12.9 1.0 CB B:ALA79 3.7 7.6 1.0 C B:TYR78 4.0 8.4 1.0 N B:ASN42 4.0 7.8 1.0 N B:ALA79 4.0 8.8 1.0 C B:GLU77 4.1 13.1 1.0 CA B:GLY43 4.1 10.6 1.0 CA B:ASN42 4.2 8.4 1.0 CA B:TYR78 4.3 8.7 1.0 C B:ASN42 4.3 8.8 1.0 O B:TYR78 4.3 8.3 1.0 N B:TYR78 4.3 10.7 1.0 CB B:LEU40 4.4 7.9 1.0 O B:LEU40 4.4 8.1 1.0 CA B:ALA79 4.5 9.7 1.0 C B:LEU40 4.7 7.5 1.0 C B:LYS41 4.7 7.2 1.0 CB B:GLU77 4.7 15.3 1.0 CD1 B:LEU40 5.0 10.2 1.0 N B:LYS41 5.0 7.3 1.0

Iodine binding site 5 out of 22 in the Crystal Structure of SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide


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 SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:I1013 b:9.8 occ:1.00 OG1 C:THR11 3.8 4.1 1.0 N C:THR11 4.0 3.3 1.0 O C:GLN9 4.0 4.2 1.0 CD1 C:LEU10 4.1 5.4 1.0 CG C:PRO6 4.1 2.2 1.0 CG2 A:VAL152 4.2 3.6 1.0 CG A:GLN155 4.3 6.6 1.0 CG1 A:VAL152 4.4 2.8 1.0 CA C:LEU10 4.5 4.8 1.0 CB C:THR11 4.5 2.5 1.0 CB A:GLN155 4.5 4.4 1.0 CB C:PRO6 4.7 2.2 1.0 CD C:PRO6 4.8 2.2 1.0 C C:LEU10 4.8 4.2 1.0 CB A:VAL152 4.8 4.3 1.0 CA C:THR11 4.9 2.6 1.0 CA A:VAL152 5.0 3.7 1.0

Iodine binding site 6 out of 22 in the Crystal Structure of SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide


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 SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:I1019 b:52.4 occ:1.00 N D:ILE118 3.4 12.0 1.0 OD1 D:ASN117 3.7 14.5 1.0 NE2 D:GLN147 3.8 19.9 1.0 CA D:ASN117 3.9 10.0 1.0 O D:PRO116 4.0 6.8 1.0 N D:SER146 4.1 20.1 1.0 C D:ASN117 4.2 10.8 1.0 CB D:SER146 4.2 20.6 1.0 O D:ILE118 4.3 15.2 1.0 OG D:SER146 4.3 19.9 1.0 CA D:ILE118 4.4 13.6 1.0 CB D:ILE118 4.5 13.7 1.0 CG D:ASN117 4.6 11.3 1.0 CG1 D:VAL13 4.6 6.7 1.0 CG1 D:ILE118 4.7 12.1 1.0 CA D:SER146 4.7 20.6 1.0 CG2 D:VAL13 4.7 6.8 1.0 C D:ILE118 4.7 15.0 1.0 CB D:ASP145 4.8 19.1 1.0 CB D:ASN117 4.8 10.3 1.0 N D:ASN117 4.8 8.7 1.0 CD D:GLN147 4.8 19.9 1.0 C D:PRO116 4.8 7.5 1.0 CG D:GLN147 4.9 21.6 1.0 CA D:ASP145 5.0 19.1 1.0

Iodine binding site 7 out of 22 in the Crystal Structure of SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide


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 SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide within 5.0Å range: probe atom residue distance (Å) B Occ E:I1021 b:58.8 occ:1.00 NH1 E:ARG230 3.5 5.3 1.0 CD E:ARG230 3.7 13.7 1.0 CB E:LYS121 3.9 12.9 1.0 CG E:GLN228 4.0 16.2 1.0 CG E:ARG230 4.0 17.1 1.0 CD E:LYS121 4.2 15.8 1.0 OE1 E:GLN228 4.2 20.6 1.0 CD E:GLN228 4.4 15.8 1.0 O E:LYS121 4.4 11.8 1.0 CZ E:ARG230 4.5 9.4 1.0 CB E:GLN228 4.5 15.7 1.0 NE E:ARG230 4.5 13.3 1.0 CG E:LYS121 4.5 16.2 1.0 CA E:LYS121 4.9 13.1 1.0

Iodine binding site 8 out of 22 in the Crystal Structure of SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide


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 SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide within 5.0Å range: probe atom residue distance (Å) B Occ F:I1003 b:2.5 occ:1.00 OG1 F:THR178 3.5 3.3 1.0 NE1 F:TRP51 3.6 2.5 1.0 CD1 F:TRP51 3.8 2.0 1.0 CD F:ARG239 3.9 3.2 1.0 CB F:THR178 3.9 4.1 1.0 CD F:PRO50 4.2 4.0 1.0 CG2 F:THR31 4.2 2.0 1.0 CG2 F:THR178 4.2 3.5 1.0 NE F:ARG239 4.2 4.6 1.0 CB F:ALA49 4.6 2.0 1.0 CZ F:ARG239 4.7 2.9 1.0 CE2 F:TRP51 4.8 2.2 1.0 NH1 F:ARG239 4.9 4.4 1.0

Iodine binding site 9 out of 22 in the Crystal Structure of SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide within 5.0Å range: probe atom residue distance (Å) B Occ F:I1004 b:5.3 occ:1.00 N F:ARG17 3.5 7.4 1.0 NE1 Q:TRP51 3.5 2.7 1.0 OG1 Q:THR178 3.6 3.5 1.0 CD1 Q:TRP51 3.7 2.0 1.0 CD Q:ARG239 3.9 3.3 1.0 CD Q:PRO50 3.9 3.8 1.0 CA F:GLY16 4.0 9.2 1.0 CB Q:THR178 4.0 4.3 1.0 CB F:ARG17 4.1 7.3 1.0 NE Q:ARG239 4.2 4.4 1.0 C F:GLY16 4.2 8.1 1.0 CG2 Q:THR178 4.3 3.2 1.0 CG2 Q:THR31 4.3 2.0 1.0 CA F:ARG17 4.4 6.6 1.0 CB Q:ALA49 4.5 2.0 1.0 CZ Q:ARG239 4.6 3.0 1.0 NH1 Q:ARG239 4.8 4.6 1.0 CE2 Q:TRP51 4.8 2.2 1.0 CG Q:PRO50 4.8 5.3 1.0

Iodine binding site 10 out of 22 in the Crystal Structure of SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of SB27 Tcr in Complex with Hla-B*3508- 13MER Peptide within 5.0Å range: probe atom residue distance (Å) B Occ F:I1008 b:4.6 occ:1.00 NH1 F:ARG62 3.5 2.0 1.0 CD F:ARG62 3.9 3.2 1.0 CA F:TYR59 4.0 3.1 1.0 CZ2 F:TRP167 4.2 4.1 1.0 CH2 F:TRP167 4.2 4.9 1.0 N F:TYR59 4.2 3.8 1.0 CB F:TYR59 4.3 2.6 1.0 CD1 F:TYR59 4.4 2.7 1.0 C F:GLU58 4.6 5.1 1.0 CZ F:ARG62 4.6 3.5 1.0 O F:GLU58 4.6 5.0 1.0 NE F:ARG62 4.7 5.5 1.0 CG F:GLU58 4.7 9.2 1.0 CG F:TYR59 4.8 2.2 1.0 CB F:ARG62 4.9 2.9 1.0

F.E.Tynan, S.R.Burrows, A.M.Buckle, C.S.Clements, N.A.Borg, J.J.Miles, T.Beddoe, J.C.Whisstock, M.C.Wilce, S.L.Silins, J.M.Burrows, L.Kjer-Nielsen, L.Kostenko, A.W.Purcell, J.Mccluskey, J.Rossjohn. T Cell Receptor Recognition of A 'Super-Bulged' Major Histocompatibility Complex Class I-Bound Peptide Nat.Immunol. V. 6 1114 2005.
ISSN: ISSN 1529-2908
PubMed: 16186824
DOI: 10.1038/NI1257