Iodine in PDB 4qrp: Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr

The structure of Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr, PDB code: 4qrp was solved by S.Gras, R.Berry, I.S.Lucet, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.85 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.160, 252.190, 79.450, 90.00, 101.97, 90.00
R / Rfree (%)	20.6 / 24.8

The structure of Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr (pdb code 4qrp). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr, PDB code: 4qrp:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in the Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr


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 Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ D:I301 b:81.5 occ:1.00 OG1 D:THR24 3.6 65.8 1.0 O D:THR5 3.7 61.4 1.0 O D:ASN22 4.3 57.0 1.0 CG2 D:THR5 4.3 66.1 1.0 CB D:ASN22 4.3 53.4 1.0 C D:THR5 4.3 62.5 1.0 N D:THR24 4.3 59.0 1.0 C D:ASN22 4.3 57.4 1.0 CG2 D:THR24 4.4 65.6 1.0 N D:CYS23 4.4 55.0 1.0 CB D:THR24 4.5 67.1 1.0 CA D:CYS23 4.5 55.5 1.0 N D:MET7 4.6 59.3 1.0 C D:GLN6 4.6 63.0 1.0 CB D:THR5 4.7 67.9 1.0 C D:CYS23 4.7 61.0 1.0 N D:GLN6 4.8 59.3 1.0 CA D:GLN6 4.9 59.1 1.0 CA D:ASN22 5.0 51.7 1.0

Iodine binding site 2 out of 12 in the Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr


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 Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ E:I301 b:57.9 occ:1.00 N E:GLY176 3.5 27.5 1.0 NE E:ARG222 3.7 44.6 1.0 ND1 E:HIS220 3.9 29.2 1.0 CA E:GLY176 4.0 27.6 1.0 CB E:ARG222 4.0 28.0 1.0 CE1 E:HIS220 4.1 28.6 1.0 NE2 G:GLN2 4.2 48.7 1.0 N E:ASN175 4.2 25.3 1.0 CB E:TRP173 4.3 22.4 1.0 CG2 G:VAL85 4.3 31.2 1.0 O E:TRP173 4.3 24.4 1.0 CG E:HIS220 4.3 27.6 1.0 CD E:ARG222 4.4 39.9 1.0 NH1 E:ARG222 4.5 40.4 1.0 C E:ASN175 4.5 30.5 1.0 C E:TRP173 4.5 25.7 1.0 CZ E:ARG222 4.5 55.5 1.0 CA E:ASN175 4.6 25.1 1.0 O E:HIS220 4.6 27.0 1.0 NE2 E:HIS220 4.6 29.0 1.0 C E:VAL174 4.7 28.2 1.0 CD2 E:HIS220 4.8 29.3 1.0 OE1 G:GLN2 4.8 47.2 1.0 CB E:HIS220 4.8 24.6 1.0 N E:VAL174 4.8 22.2 1.0 CG E:ARG222 4.8 33.5 1.0 C E:GLY176 4.9 32.5 1.0 CD G:GLN2 5.0 55.6 1.0 N E:ARG222 5.0 28.0 1.0

Iodine binding site 3 out of 12 in the Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr


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 Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ E:I302 b:67.6 occ:0.88 N E:GLU178 3.7 26.4 1.0 NA E:NA303 3.8 39.8 1.0 CZ3 E:TRP173 4.0 26.2 1.0 CG E:LYS177 4.0 52.0 1.0 CG F:GLN87 4.1 33.0 1.0 CA E:LYS177 4.2 28.3 1.0 CE1 F:HIS93 4.2 33.2 1.0 NE2 F:GLN87 4.3 33.1 1.0 CB E:GLU178 4.3 27.8 1.0 C E:LYS177 4.5 30.9 1.0 CH2 E:TRP173 4.5 26.9 1.0 CD F:GLN87 4.6 45.2 1.0 O E:GLY176 4.6 32.8 1.0 NE2 F:HIS93 4.6 33.5 1.0 CA E:GLU178 4.6 26.6 1.0 CB E:LYS177 4.7 30.9 1.0 CB F:GLN87 4.8 29.1 1.0 CB G:MET0 4.8 62.1 1.0 CE3 E:TRP173 4.9 24.7 1.0

Iodine binding site 4 out of 12 in the Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr


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 Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ G:I101 b:90.6 occ:0.58 CG F:PRO235 3.9 43.0 1.0 CE1 G:TYR63 3.9 39.1 1.0 CB G:LEU65 4.1 35.1 1.0 CD1 G:TYR63 4.2 37.7 1.0 OG G:SER52 4.2 57.3 1.0 CB G:SER52 4.3 49.6 1.0 CB F:PRO235 4.3 38.6 1.0 O G:HOH203 4.5 48.6 1.0 CD2 G:LEU65 4.7 40.2 1.0 N G:LEU65 4.8 35.5 1.0 CE1 G:TYR26 4.9 34.6 1.0

Iodine binding site 5 out of 12 in the Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr


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 Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ I:I301 b:76.5 occ:0.79 N I:GLU178 3.6 60.8 1.0 CZ3 I:TRP173 3.8 62.5 1.0 CD I:LYS177 3.8 85.7 1.0 NZ I:LYS177 4.0 0.8 1.0 CE1 A:HIS93 4.0 59.3 1.0 CA I:LYS177 4.0 60.3 1.0 CE I:LYS177 4.0 94.1 1.0 CB I:GLU178 4.1 62.0 1.0 CG A:GLN87 4.2 71.6 1.0 NE2 A:GLN87 4.3 77.7 1.0 CH2 I:TRP173 4.3 63.2 1.0 C I:LYS177 4.4 64.1 1.0 O I:GLY176 4.4 63.2 1.0 CG I:LYS177 4.4 76.2 1.0 CA I:GLU178 4.5 60.6 1.0 CB I:LYS177 4.7 62.6 1.0 NE2 A:HIS93 4.7 59.6 1.0 CE3 I:TRP173 4.7 61.1 1.0 CD A:GLN87 4.7 86.5 1.0 CB A:GLN87 4.9 60.8 1.0 ND1 A:HIS93 5.0 60.0 1.0

Iodine binding site 6 out of 12 in the Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr


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 Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ I:I302 b:0.4 occ:1.00 N I:GLY176 3.4 59.7 1.0 ND1 I:HIS220 3.9 65.6 1.0 NE I:ARG222 4.0 79.4 1.0 CA I:GLY176 4.0 59.8 1.0 N I:ASN175 4.2 58.3 1.0 CB I:ARG222 4.3 58.0 1.0 CB I:TRP173 4.3 58.9 1.0 CG2 B:VAL85 4.3 70.7 1.0 O I:TRP173 4.3 61.6 1.0 NE2 B:GLN2 4.4 75.3 1.0 CE1 I:HIS220 4.4 65.0 1.0 C I:ASN175 4.4 62.7 1.0 CG I:HIS220 4.5 63.9 1.0 CA I:ASN175 4.5 58.2 1.0 C I:TRP173 4.6 62.3 1.0 CD I:ARG222 4.7 72.4 1.0 O I:HIS220 4.7 63.0 1.0 CB I:HIS220 4.8 60.5 1.0 NH1 I:ARG222 4.8 71.2 1.0 CZ I:ARG222 4.9 89.1 1.0 C I:VAL174 4.9 61.5 1.0 N I:VAL174 5.0 58.0 1.0

Iodine binding site 7 out of 12 in the Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr


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 Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ J:I301 b:70.0 occ:0.86 OG1 J:THR24 3.7 50.6 1.0 O J:THR5 3.8 45.2 1.0 CG2 J:THR5 4.1 47.7 1.0 C J:THR5 4.2 45.9 1.0 CB J:ASN22 4.2 41.4 1.0 CG2 J:THR24 4.2 48.3 1.0 N J:THR24 4.3 43.4 1.0 C J:GLN6 4.3 44.9 1.0 O J:ASN22 4.3 45.2 1.0 C J:ASN22 4.3 46.3 1.0 N J:MET7 4.4 41.5 1.0 N J:CYS23 4.4 43.5 1.0 CB J:THR24 4.5 50.6 1.0 O J:GLN6 4.5 44.1 1.0 N J:GLN6 4.5 42.0 1.0 CA J:GLN6 4.6 41.5 1.0 CA J:CYS23 4.6 43.6 1.0 CB J:THR5 4.6 49.4 1.0 C J:CYS23 4.7 47.2 1.0 CA J:MET7 4.9 41.2 1.0 CA J:ASN22 4.9 42.8 1.0 CA J:THR5 5.0 43.1 1.0

Iodine binding site 8 out of 12 in the Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr


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 Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ K:I301 b:51.9 occ:0.52 OE1 K:GLN155 3.4 89.5 1.0 N K:SER154 3.5 45.0 1.0 N K:ILE126 3.7 41.3 1.0 CB K:ASP153 3.7 43.1 1.0 CB K:SER154 3.8 48.4 1.0 O K:PRO124 3.9 40.9 1.0 OG K:SER154 3.9 54.4 1.0 CA K:SER154 4.2 45.6 1.0 CB K:ILE126 4.2 44.1 1.0 CA K:ASP153 4.3 40.6 1.0 CG1 K:ILE126 4.3 44.4 1.0 C K:ASP153 4.3 46.5 1.0 O K:ILE126 4.3 46.5 1.0 CA K:ASN125 4.4 39.4 1.0 CA K:ILE126 4.4 41.3 1.0 OD1 K:ASN125 4.5 57.3 1.0 CD K:GLN155 4.5 92.2 1.0 C K:ASN125 4.5 44.3 1.0 N K:GLN155 4.6 49.6 1.0 CG K:ASP153 4.8 59.2 1.0 C K:ILE126 4.9 46.7 1.0 C K:SER154 4.9 51.8 1.0 C K:PRO124 4.9 41.6 1.0

Iodine binding site 9 out of 12 in the Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr


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 Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ K:I302 b:80.3 occ:0.48 N K:LYS54 3.6 35.4 1.0 O K:LYS54 3.8 38.7 1.0 CA K:GLY62 3.8 42.2 1.0 CB K:LEU53 4.0 35.9 1.0 CA K:LEU53 4.0 36.1 1.0 C K:GLY62 4.0 45.8 1.0 C K:LEU53 4.3 39.2 1.0 O K:GLY62 4.4 44.7 1.0 CG K:LYS54 4.4 51.2 1.0 N K:SER66 4.5 42.8 1.0 O K:SER66 4.6 45.0 1.0 CA K:LYS54 4.6 35.1 1.0 C K:LYS54 4.6 39.2 1.0

Iodine binding site 10 out of 12 in the Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr


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 Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ L:I301 b:89.3 occ:0.55 O K:LEU49 3.6 49.1 1.0 N L:PHE118 3.6 52.2 1.0 N K:LEU51 3.8 42.1 1.0 CA K:GLN50 3.9 43.5 1.0 CA L:HIS117 3.9 51.5 1.0 C L:HIS117 4.3 55.6 1.0 C K:GLN50 4.3 47.0 1.0 ND1 L:HIS117 4.3 57.8 1.0 O L:PHE118 4.3 56.2 1.0 O L:GLN116 4.4 54.9 1.0 CB L:HIS117 4.5 52.4 1.0 C K:LEU49 4.5 49.2 1.0 CA L:PHE118 4.6 51.9 1.0 N K:GLN50 4.6 44.4 1.0 CB K:LEU51 4.6 41.2 1.0 CG L:HIS117 4.6 55.9 1.0 CB L:PHE118 4.8 53.4 1.0 CA K:LEU51 4.8 41.1 1.0 CB K:GLN50 4.9 44.6 1.0 CE1 K:TYR41 4.9 48.2 1.0 C L:PHE118 5.0 56.8 1.0 N L:HIS117 5.0 51.6 1.0 CG K:GLN50 5.0 61.6 1.0

U.K.Nivarthi, S.Gras, L.Kjer-Nielsen, R.Berry, I.S.Lucet, J.J.Miles, S.L.Tracy, A.W.Purcell, D.S.Bowden, M.Hellard, J.Rossjohn, J.Mccluskey, M.Bharadwaj. An Extensive Antigenic Footprint Underpins Immunodominant Tcr Adaptability Against A Hypervariable Viral Determinant. J.Immunol. 2014.
ISSN: ISSN 0022-1767
PubMed: 25355921
DOI: 10.4049/JIMMUNOL.1401357