Iodine in PDB 5ud7: Crystal Structure of Wild-Type Ig-Like Domain

The structure of Crystal Structure of Wild-Type Ig-Like Domain, PDB code: 5ud7 was solved by A.Sudom, X.Min, Z.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.49 / 2.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	160.664, 160.664, 86.574, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 27.7

The binding sites of Iodine atom in the Crystal Structure of Wild-Type Ig-Like Domain (pdb code 5ud7). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Crystal Structure of Wild-Type Ig-Like Domain, PDB code: 5ud7:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in the Crystal Structure of Wild-Type Ig-Like Domain


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 Wild-Type Ig-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:39.7 occ:1.00 N B:LEU71 3.7 35.5 1.0 N B:TRP70 3.8 36.9 1.0 CB B:LEU69 3.8 38.7 1.0 CB B:LEU71 3.9 39.1 1.0 CG B:LEU71 3.9 38.8 1.0 CA B:LEU69 4.0 36.7 1.0 C B:LEU69 4.0 40.9 1.0 CD1 B:LEU71 4.2 32.8 1.0 CD2 B:LEU69 4.4 39.1 1.0 CA B:LEU71 4.4 35.7 1.0 CA B:TRP70 4.6 37.5 1.0 C B:TRP70 4.6 35.9 1.0 CG B:LEU69 4.7 38.5 1.0 O B:LEU69 4.8 36.0 1.0 CB B:TRP70 4.8 36.6 1.0

Iodine binding site 2 out of 5 in the Crystal Structure of Wild-Type Ig-Like Domain


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 Wild-Type Ig-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:I201 b:34.3 occ:1.00 N C:LEU71 3.6 34.4 1.0 N C:TRP70 3.6 32.5 1.0 CB C:LEU69 3.9 31.6 1.0 CG C:LEU71 4.0 34.4 1.0 C C:LEU69 4.0 38.5 1.0 CB C:LEU71 4.0 33.6 1.0 CA C:LEU69 4.0 38.2 1.0 CD1 C:LEU71 4.2 36.4 1.0 O C:HOH302 4.3 41.1 1.0 CA C:LEU71 4.4 36.8 1.0 CD2 C:LEU69 4.4 34.0 1.0 CA C:TRP70 4.5 37.9 1.0 C C:TRP70 4.5 37.3 1.0 CG C:LEU69 4.7 32.8 1.0 O C:LEU69 4.7 36.8 1.0 CB C:TRP70 4.8 34.8 1.0

Iodine binding site 3 out of 5 in the Crystal Structure of Wild-Type Ig-Like Domain


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 Wild-Type Ig-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:I201 b:36.4 occ:1.00 N E:LEU71 3.6 33.8 1.0 N E:TRP70 3.8 36.2 1.0 CB E:LEU71 3.9 32.5 1.0 CB E:LEU69 3.9 30.8 1.0 CA E:LEU69 4.0 36.7 1.0 CG E:LEU71 4.0 35.9 1.0 C E:LEU69 4.0 36.6 1.0 CD1 E:LEU71 4.1 33.8 1.0 O E:HOH312 4.2 41.2 1.0 CA E:LEU71 4.4 33.2 1.0 CD2 E:LEU69 4.6 31.4 1.0 C E:TRP70 4.6 35.2 1.0 CA E:TRP70 4.6 32.5 1.0 CG E:LEU69 4.8 39.2 1.0 O E:LEU69 4.8 34.4 1.0

Iodine binding site 4 out of 5 in the Crystal Structure of Wild-Type Ig-Like Domain


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 Wild-Type Ig-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:I202 b:0.2 occ:1.00 CD E:ARG46 3.8 55.5 1.0 NE E:ARG46 4.0 62.6 1.0 CG E:ARG46 4.1 51.9 1.0 CB E:HIS114 4.3 72.0 1.0 CZ E:ARG46 4.8 66.9 1.0

Iodine binding site 5 out of 5 in the Crystal Structure of Wild-Type Ig-Like Domain


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 Wild-Type Ig-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:I203 b:0.2 occ:1.00 O E:HOH322 3.2 52.1 1.0 OG E:SER65 3.4 47.5 1.0 NH1 E:ARG62 3.8 51.6 1.0 CG E:ARG62 4.1 57.1 1.0 N E:SER65 4.1 44.9 1.0 CB E:SER65 4.1 42.2 1.0 CD E:ARG62 4.3 54.2 1.0 CA E:VAL64 4.6 48.1 1.0 C E:VAL64 4.6 50.7 1.0 O6 E:NAG204 4.7 85.8 1.0 CA E:SER65 4.8 45.0 1.0 CZ E:ARG62 4.9 48.7 1.0 O E:VAL63 5.0 56.4 1.0

A.Sudom, S.Talreja, J.Danao, E.Bragg, R.Kegel, X.Min, J.Richardson, Z.Zhang, N.Sharkov, E.Marcora, S.Thibault, J.Bradley, S.Wood, A.C.Lim, H.Chen, S.Wang, I.N.Foltz, S.Sambashivan, Z.Wang. Molecular Basis For the Loss-of-Function Effects of the Alzheimer'S Disease-Associated R47H Variant of the Immune Receptor TREM2. J. Biol. Chem. V. 293 12634 2018.
ISSN: ESSN 1083-351X
PubMed: 29794134
DOI: 10.1074/JBC.RA118.002352