Iodine in PDB 4ll9: Crystal Structure of D3D4 Domain of the LILRB1 Molecule

The structure of Crystal Structure of D3D4 Domain of the LILRB1 Molecule, PDB code: 4ll9 was solved by G.Nam, Y.Shi, M.Ryu, Q.Wang, H.Song, J.Liu, J.Yan, J.Qi, G.F.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.81 / 2.69
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	121.257, 71.976, 75.036, 90.00, 95.20, 90.00
R / Rfree (%)	24.5 / 27.5

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of D3D4 Domain of the LILRB1 Molecule (pdb code 4ll9). 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 D3D4 Domain of the LILRB1 Molecule, PDB code: 4ll9:
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 D3D4 Domain of the LILRB1 Molecule


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 D3D4 Domain of the LILRB1 Molecule within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:58.2 occ:1.00 N A:ARG150 3.6 76.8 1.0 CB A:ARG150 3.7 81.9 1.0 CA A:ARG150 4.2 77.6 1.0 CG A:LEU149 4.5 59.0 1.0 CD1 A:LEU149 4.5 61.5 1.0 C A:LEU149 4.5 59.3 1.0 CA A:LEU149 4.6 59.3 1.0 CG A:ARG150 5.0 84.5 1.0

Iodine binding site 2 out of 12 in the Crystal Structure of D3D4 Domain of the LILRB1 Molecule


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 D3D4 Domain of the LILRB1 Molecule within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:59.5 occ:1.00 CD A:PRO185 3.6 53.3 1.0 CA A:LYS184 3.7 62.1 1.0 N A:PRO185 3.9 51.9 1.0 N A:TYR186 3.9 47.5 1.0 C A:LYS184 3.9 61.0 1.0 CD1 A:LEU187 4.1 39.1 1.0 CB A:LYS184 4.1 61.0 1.0 CD2 A:TYR186 4.2 49.2 1.0 CD2 A:LEU187 4.4 38.4 1.0 CB A:TYR186 4.4 48.7 1.0 CA A:TYR186 4.6 46.5 1.0 CG A:LYS184 4.6 62.6 1.0 O A:LYS184 4.6 59.7 1.0 N A:LEU187 4.6 39.8 1.0 CG A:LEU187 4.7 37.1 1.0 CG A:PRO185 4.7 52.6 1.0 C A:TYR186 4.8 45.0 1.0 CG A:TYR186 4.8 50.3 1.0 CA A:PRO185 4.8 50.2 1.0 C A:PRO185 4.8 49.7 1.0 O A:SER183 4.8 61.0 1.0 CB A:LEU187 4.9 36.9 1.0 CB A:PRO185 5.0 51.8 1.0

Iodine binding site 3 out of 12 in the Crystal Structure of D3D4 Domain of the LILRB1 Molecule


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 D3D4 Domain of the LILRB1 Molecule within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:50.5 occ:1.00 CB B:ARG150 3.6 44.9 1.0 N A:ARG69 3.6 37.8 1.0 NE2 A:GLN101 3.7 32.6 1.0 N B:ARG150 3.8 41.7 1.0 CA A:SER68 3.9 41.3 1.0 CB A:PRO18 3.9 38.7 1.0 CB A:SER68 4.0 43.5 1.0 CG A:PRO18 4.1 38.1 1.0 CD1 B:LEU149 4.1 54.2 1.0 C A:SER68 4.2 40.3 1.0 OE1 A:GLN101 4.3 31.1 1.0 CG B:LEU149 4.3 54.8 1.0 CA B:ARG150 4.4 41.5 1.0 CD A:GLN101 4.4 32.1 1.0 CB A:ARG69 4.6 40.8 1.0 CA A:ARG69 4.6 39.9 1.0 CA B:LEU149 4.7 52.6 1.0 CD B:ARG150 4.8 50.2 1.0 C B:LEU149 4.8 54.0 1.0 CG B:ARG150 4.8 46.6 1.0 O A:VAL67 4.9 36.6 1.0

Iodine binding site 4 out of 12 in the Crystal Structure of D3D4 Domain of the LILRB1 Molecule


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 D3D4 Domain of the LILRB1 Molecule within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:61.6 occ:1.00 CE1 A:HIS190 3.4 71.4 1.0 CD A:PRO191 3.5 57.1 1.0 ND1 A:HIS190 3.6 66.4 1.0 CD A:PRO18 3.9 40.3 1.0 CA A:GLY100 4.0 37.0 1.0 NE2 A:HIS190 4.0 67.2 1.0 CB A:ALA17 4.1 37.8 1.0 N A:GLY100 4.1 36.9 1.0 CG A:PRO191 4.2 57.9 1.0 O A:HOH325 4.2 37.4 1.0 CG A:HIS190 4.3 65.2 1.0 C A:ALA99 4.4 37.1 1.0 CB A:ALA99 4.4 35.7 1.0 CD2 A:HIS190 4.6 64.3 1.0 O A:ALA99 4.6 36.0 1.0 CA A:ALA17 4.7 36.7 1.0 CG A:PRO18 4.8 38.1 1.0 N A:PRO191 4.8 56.0 1.0 N A:PRO18 4.9 38.6 1.0 CA A:HIS190 4.9 60.8 1.0

Iodine binding site 5 out of 12 in the Crystal Structure of D3D4 Domain of the LILRB1 Molecule


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 D3D4 Domain of the LILRB1 Molecule within 5.0Å range: probe atom residue distance (Å) B Occ A:I205 b:0.4 occ:1.00 CE A:LYS4 3.6 67.1 1.0 NZ A:LYS4 3.8 71.4 1.0 N A:ASP29 3.9 74.3 1.0 CA A:SER28 3.9 70.0 1.0 OD2 A:ASP29 4.1 82.8 1.0 CG A:ASP29 4.1 81.6 1.0 OD1 A:ASP29 4.2 79.1 1.0 OG A:SER28 4.2 71.8 1.0 O A:LYS5 4.2 62.9 1.0 CD A:LYS4 4.3 68.7 1.0 C A:SER28 4.3 75.6 1.0 CB A:SER28 4.5 67.5 1.0 O A:GLY27 4.6 59.6 1.0 CB A:ASP29 4.9 82.8 1.0 N A:SER28 4.9 69.0 1.0 CG A:LYS4 4.9 67.1 1.0 OG A:SER7 4.9 60.4 1.0 CA A:ASP29 5.0 78.7 1.0 N A:SER7 5.0 54.9 1.0 CB A:SER7 5.0 57.9 1.0

Iodine binding site 6 out of 12 in the Crystal Structure of D3D4 Domain of the LILRB1 Molecule


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 D3D4 Domain of the LILRB1 Molecule within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:52.9 occ:1.00 N B:ARG69 3.6 46.6 1.0 N C:ARG150 3.7 56.7 1.0 NE2 B:GLN101 3.8 47.2 1.0 CA B:SER68 3.9 56.0 1.0 CB B:PRO18 3.9 47.6 1.0 CB C:ARG150 3.9 63.7 1.0 CD C:ARG150 4.0 69.3 1.0 CB B:SER68 4.1 59.1 1.0 CG B:PRO18 4.1 48.7 1.0 C B:SER68 4.2 54.2 1.0 CG C:ARG150 4.3 65.0 1.0 CD1 C:LEU149 4.3 51.1 1.0 CG C:LEU149 4.3 53.7 1.0 CA C:ARG150 4.5 60.0 1.0 OE1 B:GLN101 4.5 48.6 1.0 CB B:ARG69 4.6 47.0 1.0 CA B:ARG69 4.6 47.2 1.0 CD B:GLN101 4.6 45.8 1.0 CA C:LEU149 4.6 48.0 1.0 C C:LEU149 4.6 52.6 1.0 NE C:ARG150 4.7 76.5 1.0 O B:VAL67 5.0 45.6 1.0

Iodine binding site 7 out of 12 in the Crystal Structure of D3D4 Domain of the LILRB1 Molecule


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 D3D4 Domain of the LILRB1 Molecule within 5.0Å range: probe atom residue distance (Å) B Occ B:I202 b:72.0 occ:1.00 N B:TYR186 3.6 52.5 1.0 CD B:PRO185 3.7 57.3 1.0 N B:PRO185 3.8 52.5 1.0 CD1 B:LEU187 3.9 47.6 1.0 C B:LYS184 3.9 59.7 1.0 CA B:LYS184 3.9 57.5 1.0 CD2 B:TYR186 3.9 56.5 1.0 CB B:TYR186 4.1 50.9 1.0 CA B:TYR186 4.2 48.6 1.0 CB B:LYS184 4.3 56.0 1.0 CD2 B:LEU187 4.4 38.7 1.0 N B:LEU187 4.4 45.2 1.0 C B:TYR186 4.5 43.1 1.0 CG B:TYR186 4.5 54.4 1.0 O B:LYS184 4.5 58.6 1.0 CG B:LEU187 4.6 43.4 1.0 C B:PRO185 4.6 52.0 1.0 CA B:PRO185 4.6 50.3 1.0 CG B:PRO185 4.7 56.9 1.0 CB B:LEU187 4.9 42.7 1.0 CB B:PRO185 4.9 53.3 1.0 CG B:LYS184 4.9 56.0 1.0 CE2 B:TYR186 4.9 59.5 1.0

Iodine binding site 8 out of 12 in the Crystal Structure of D3D4 Domain of the LILRB1 Molecule


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 D3D4 Domain of the LILRB1 Molecule within 5.0Å range: probe atom residue distance (Å) B Occ B:I203 b:71.0 occ:1.00 ND1 B:HIS190 3.4 53.0 1.0 CD B:PRO191 3.5 38.5 1.0 CE1 B:HIS190 3.6 50.8 1.0 CB B:ALA17 3.9 40.7 1.0 CA B:GLY100 4.1 40.2 1.0 CD B:PRO18 4.1 48.4 1.0 N B:GLY100 4.1 38.2 1.0 CG B:PRO191 4.2 38.5 1.0 CG B:HIS190 4.3 51.0 1.0 C B:ALA99 4.3 30.5 1.0 CB B:ALA99 4.4 27.9 1.0 NE2 B:HIS190 4.5 46.4 1.0 O B:ALA99 4.5 30.2 1.0 CA B:ALA17 4.7 39.2 1.0 CA B:HIS190 4.7 46.3 1.0 N B:PRO191 4.9 38.3 1.0 CD2 B:HIS190 4.9 50.7 1.0 CB B:HIS190 5.0 49.2 1.0

Iodine binding site 9 out of 12 in the Crystal Structure of D3D4 Domain of the LILRB1 Molecule


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 D3D4 Domain of the LILRB1 Molecule within 5.0Å range: probe atom residue distance (Å) B Occ B:I204 b:0.6 occ:0.50 CG B:GLN111 3.6 82.0 1.0 CD B:PRO112 3.7 77.0 1.0 N B:PRO112 3.8 71.0 1.0 C B:GLN111 3.9 78.9 1.0 CB B:GLN111 4.0 77.6 1.0 O B:GLN111 4.0 77.9 1.0 O B:ASN121 4.3 86.5 1.0 CB B:PRO112 4.4 72.0 1.0 CA B:GLN111 4.5 75.7 1.0 CA B:PRO112 4.5 68.8 1.0 CG B:PRO112 4.5 77.1 1.0 CD B:GLN111 4.9 82.1 1.0

Iodine binding site 10 out of 12 in the Crystal Structure of D3D4 Domain of the LILRB1 Molecule


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 D3D4 Domain of the LILRB1 Molecule within 5.0Å range: probe atom residue distance (Å) B Occ C:I201 b:81.3 occ:1.00 CD1 C:LEU187 3.8 50.5 1.0 CD C:PRO185 4.0 59.0 1.0 CD2 C:TYR186 4.0 70.0 1.0 N C:TYR186 4.0 66.4 1.0 CA C:LYS184 4.1 73.3 1.0 CB C:LYS184 4.2 71.4 1.0 C C:LYS184 4.2 65.8 1.0 N C:PRO185 4.2 55.4 1.0 CD2 C:LEU187 4.3 54.1 1.0 CG C:PRO185 4.3 58.5 1.0 CB C:TYR186 4.4 64.1 1.0 CG C:LEU187 4.6 51.3 1.0 CA C:TYR186 4.6 62.7 1.0 CG C:LYS184 4.6 76.3 1.0 CG C:TYR186 4.7 67.6 1.0 N C:LEU187 4.7 43.9 1.0 C C:TYR186 4.7 62.4 1.0 O C:LYS184 4.9 61.5 1.0 CB C:LEU187 4.9 51.0 1.0 CE2 C:TYR186 5.0 73.0 1.0

G.Nam, Y.Shi, M.Ryu, Q.Wang, H.Song, J.Liu, J.Yan, J.Qi, G.F.Gao. Crystal Structures of the Two Membrane-Proximal Ig-Like Domains (D3D4) of LILRB1/B2: Alternative Models For Their Involvement in Peptide-Hla Binding Protein Cell V. 4 761 2013.
ISSN: ISSN 1674-800X
PubMed: 23955630
DOI: 10.1007/S13238-013-3908-X