Iodine in PDB 5k6u: Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1

The structure of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1, PDB code: 5k6u was solved by X.Jin, K.M.Goodman, S.Mannepalli, B.Honig, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.19 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	163.072, 49.260, 60.728, 90.00, 110.50, 90.00
R / Rfree (%)	19.1 / 22.8

The structure of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1 also contains other interesting chemical elements:

Caesium

(Cs)

1 atom

The binding sites of Iodine atom in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1 (pdb code 5k6u). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1, PDB code: 5k6u:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I405 b:40.7 occ:0.55 NZ A:LYS84 3.2 66.9 1.0 O A:PHE68 3.3 47.8 1.0 N A:ASP44 3.5 51.4 1.0 N A:ASN43 3.6 46.8 1.0 CD A:ARG70 3.7 42.2 1.0 OD1 A:ASP44 3.8 87.3 1.0 C A:PHE68 4.0 42.9 1.0 CG A:LYS84 4.0 51.8 1.0 CA A:ASN43 4.0 51.4 1.0 CB A:PHE68 4.1 45.8 1.0 CG2 A:ILE41 4.2 42.8 1.0 CG A:ARG70 4.2 40.8 1.0 CD A:LYS84 4.2 59.8 1.0 C A:ASN43 4.3 51.1 1.0 CE A:LYS84 4.3 67.2 1.0 O A:ILE41 4.4 33.4 1.0 CA A:ASP44 4.4 56.9 1.0 C A:ARG42 4.4 48.1 1.0 N A:TYR69 4.6 33.8 1.0 C A:ILE41 4.6 35.1 1.0 C A:TYR69 4.6 29.8 1.0 CA A:ARG42 4.7 35.9 1.0 CB A:ARG70 4.7 34.3 1.0 N A:ARG70 4.7 31.4 1.0 NH1 A:ARG70 4.7 52.1 1.0 CA A:PHE68 4.7 46.4 1.0 CG A:ASP44 4.7 81.8 1.0 NE A:ARG70 4.7 42.3 1.0 CA A:TYR69 4.7 31.3 1.0 CB A:ILE41 4.8 40.1 1.0 N A:ARG42 4.8 29.4 1.0 O A:TYR69 5.0 30.9 1.0

Iodine binding site 2 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I406 b:91.7 occ:0.39 N A:GLU274 3.4 33.8 1.0 I A:IOD409 3.5 56.6 0.3 CB A:GLU274 3.8 39.2 1.0 CD1 A:PHE273 4.0 44.7 1.0 CA A:GLU274 4.2 36.4 1.0 CA A:PHE273 4.2 27.3 1.0 C A:PHE273 4.3 34.5 1.0 CB A:PHE273 4.5 28.8 1.0 CB A:ALA194 4.7 26.7 1.0 O A:HOH516 4.7 26.4 1.0 O A:GLU274 4.7 38.3 1.0 CG A:PHE273 4.8 36.8 1.0 CE1 A:PHE273 4.9 42.8 1.0 C A:GLU274 5.0 40.8 1.0

Iodine binding site 3 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I407 b:55.7 occ:0.45 N A:TRP322 3.5 41.8 1.0 CG2 A:VAL339 4.0 54.5 1.0 CB A:TRP322 4.1 33.5 1.0 CA A:GLN321 4.3 40.2 1.0 CA A:TRP322 4.3 30.6 1.0 CB A:LEU329 4.4 26.5 1.0 C A:GLN321 4.4 43.0 1.0 O A:TRP322 4.4 29.4 1.0 CD1 A:TRP322 4.5 38.7 1.0 O A:LEU320 4.6 55.8 1.0 CG A:GLN321 4.6 61.4 1.0 CG A:TRP322 4.7 34.6 1.0 C A:TRP322 4.9 24.3 1.0 CG A:LEU329 4.9 37.3 1.0 CG1 A:VAL339 4.9 50.2 1.0 CB A:VAL339 4.9 51.7 1.0 CD1 A:LEU329 5.0 34.1 1.0

Iodine binding site 4 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I408 b:82.8 occ:0.34 N A:ALA194 3.1 24.2 1.0 I A:IOD409 3.6 56.6 0.3 CB A:ALA194 3.7 26.7 1.0 CA A:MET193 3.8 28.2 1.0 C A:MET193 3.9 29.6 1.0 CE1 A:PHE273 4.0 42.8 1.0 CA A:ALA194 4.0 28.5 1.0 O A:ALA192 4.2 36.9 1.0 CZ A:PHE273 4.3 38.2 1.0 CB A:MET193 4.6 28.6 1.0 N A:MET193 4.7 32.6 1.0 CD1 A:PHE273 4.8 44.7 1.0 C A:ALA192 4.8 35.9 1.0

Iodine binding site 5 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I409 b:56.6 occ:0.27 I A:IOD406 3.5 91.7 0.4 I A:IOD408 3.6 82.8 0.3 CE1 A:PHE273 3.7 42.8 1.0 CD1 A:PHE273 3.9 44.7 1.0 CB A:ALA194 4.3 26.7 1.0 CZ A:PHE273 4.9 38.2 1.0

Iodine binding site 6 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I410 b:84.9 occ:0.52 ND1 A:HIS372 3.2 33.8 1.0 OE1 A:GLN370 3.4 81.3 1.0 CG A:GLN370 3.5 60.7 1.0 CD A:GLN370 3.5 73.6 1.0 NE2 A:GLN359 3.5 27.3 1.0 CB A:GLN370 3.6 46.4 1.0 O A:HOH503 3.7 58.8 1.0 C A:GLN370 3.8 35.2 1.0 N A:THR371 3.8 31.4 1.0 CA A:THR371 3.8 31.1 1.0 C A:THR371 3.9 31.1 1.0 O A:GLN370 3.9 33.3 1.0 CG A:HIS372 4.1 33.8 1.0 CB A:HIS372 4.1 30.4 1.0 N A:HIS372 4.1 35.6 1.0 CE1 A:HIS372 4.2 41.0 1.0 CG A:GLN359 4.2 33.5 1.0 O A:THR371 4.3 34.3 1.0 CD A:GLN359 4.3 30.2 1.0 CA A:GLN370 4.4 38.0 1.0 O A:HOH636 4.4 52.5 1.0 NE2 A:GLN370 4.4 75.1 1.0 CD1 A:LEU80 4.7 26.9 1.0 NH2 A:ARG83 4.7 55.5 1.0 CA A:HIS372 4.7 34.5 1.0

K.M.Goodman, M.Yamagata, X.Jin, S.Mannepalli, P.S.Katsamba, G.Ahlsen, A.P.Sergeeva, B.Honig, J.R.Sanes, L.Shapiro. Molecular Basis of Sidekick-Mediated Cell-Cell Adhesion and Specificity. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27644106
DOI: 10.7554/ELIFE.19058