Iodine in PDB 4s22: Crystal Structure of K29 Linked Di-Ubiquitin

The structure of Crystal Structure of K29 Linked Di-Ubiquitin, PDB code: 4s22 was solved by Y.A.Kristariyanto, S.A.Abdul Rehman, D.G.Campbell, N.A.Morrice, C.Johnson, R.Toth, Y.Kulathu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.05 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.450, 69.245, 60.055, 90.00, 90.22, 90.00
R / Rfree (%)	19.8 / 24.6

The binding sites of Iodine atom in the Crystal Structure of K29 Linked Di-Ubiquitin (pdb code 4s22). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of K29 Linked Di-Ubiquitin, PDB code: 4s22:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Crystal Structure of K29 Linked Di-Ubiquitin


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 K29 Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:I101 b:24.8 occ:0.80 OG A:SER65 3.5 18.7 1.0 CZ A:PHE45 3.8 18.1 1.0 CE1 A:PHE45 3.9 16.8 1.0 CB A:SER65 4.1 17.8 1.0 CA A:SER65 4.3 20.3 1.0

Iodine binding site 2 out of 6 in the Crystal Structure of K29 Linked Di-Ubiquitin


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 K29 Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:I102 b:93.6 occ:1.00 N A:LEU73 3.5 37.9 1.0 O A:HOH206 3.6 22.7 1.0 CA A:ARG72 3.8 28.5 1.0 CD A:ARG42 4.1 33.5 1.0 C A:ARG72 4.1 30.1 1.0 CD1 A:LEU73 4.2 53.4 1.0 CB A:ARG72 4.3 30.8 1.0 CB A:LEU73 4.3 47.1 1.0 NH1 A:ARG42 4.3 46.4 1.0 CG A:LEU73 4.3 51.7 1.0 NE A:ARG42 4.4 31.8 1.0 CA A:LEU73 4.5 44.5 1.0 CZ A:ARG42 4.5 42.9 1.0 CG A:ARG72 4.8 34.8 1.0 O A:LEU71 4.8 20.6 1.0

Iodine binding site 3 out of 6 in the Crystal Structure of K29 Linked Di-Ubiquitin


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 K29 Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:I103 b:28.5 occ:1.00 O A:HOH201 3.2 13.4 1.0 N A:LEU71 3.7 18.3 1.0 CG A:LEU71 4.3 26.0 1.0 CA A:VAL70 4.3 25.5 1.0 CB A:LEU71 4.4 25.1 1.0 C A:VAL70 4.5 21.2 1.0 CA A:LEU71 4.7 22.0 1.0 CD1 A:LEU71 4.7 27.5 1.0 CG1 A:VAL70 4.8 33.4 1.0 O A:LEU69 4.9 21.5 1.0

Iodine binding site 4 out of 6 in the Crystal Structure of K29 Linked Di-Ubiquitin


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 K29 Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:I101 b:31.9 occ:1.00 O B:HOH202 3.4 13.7 1.0 N B:LEU71 3.4 21.9 1.0 CD1 B:LEU8 3.9 23.3 1.0 CA B:VAL70 3.9 22.2 1.0 CB B:LEU71 4.1 26.9 1.0 C B:VAL70 4.1 22.4 1.0 CD2 B:LEU8 4.2 21.4 1.0 CG1 B:VAL70 4.2 22.9 1.0 CA B:LEU71 4.2 26.1 1.0 CG B:LEU71 4.3 30.5 1.0 CG B:LEU8 4.3 22.7 1.0 CB B:LEU8 4.3 22.0 1.0 O B:LEU71 4.4 29.6 1.0 CB B:VAL70 4.6 22.5 1.0 CD1 B:LEU71 4.6 29.9 1.0 O B:LEU69 4.7 29.2 1.0 C B:LEU71 4.8 28.1 1.0

Iodine binding site 5 out of 6 in the Crystal Structure of K29 Linked Di-Ubiquitin


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 K29 Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:I102 b:37.5 occ:1.00 N B:GLY47 3.7 17.3 1.0 CG2 B:ILE44 3.8 22.4 1.0 CA B:GLY47 4.0 21.2 1.0 CD2 B:HIS68 4.1 27.9 1.0 N B:ALA46 4.6 20.8 1.0 NE2 B:HIS68 4.7 26.1 1.0 C B:ALA46 4.7 20.1 1.0 CB B:ILE44 4.9 24.1 1.0 CG B:HIS68 4.9 21.6 1.0 C B:PHE45 5.0 21.2 1.0

Iodine binding site 6 out of 6 in the Crystal Structure of K29 Linked Di-Ubiquitin


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 K29 Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ D:I101 b:73.3 occ:1.00 N D:GLU16 3.6 25.6 1.0 O D:GLU16 3.9 29.2 1.0 CA D:LEU15 4.0 26.6 1.0 CD2 D:LEU15 4.1 29.2 1.0 NZ D:LYS29 4.1 53.4 1.0 CB D:LEU15 4.3 28.3 1.0 CG D:LYS29 4.3 26.1 1.0 C D:LEU15 4.3 25.2 1.0 CA D:GLU16 4.4 31.4 1.0 CB D:LYS29 4.4 25.1 1.0 CB D:GLU16 4.4 32.5 1.0 CD D:LYS29 4.5 31.8 1.0 C D:GLU16 4.6 34.1 1.0 CD D:LYS33 4.7 45.6 1.0 CG D:LEU15 4.8 30.5 1.0 O D:THR14 4.8 36.3 1.0 CE D:LYS29 4.9 42.5 1.0 NZ D:LYS33 5.0 64.8 1.0

Y.A.Kristariyanto, S.A.Abdul Rehman, D.G.Campbell, N.A.Morrice, C.Johnson, R.Toth, Y.Kulathu. K29-Selective Ubiquitin Binding Domain Reveals Structural Basis of Specificity and Heterotypic Nature of K29 Polyubiquitin. Mol.Cell 2015.
ISSN: ISSN 1097-2765
PubMed: 25752573
DOI: 10.1016/J.MOLCEL.2015.01.041