Arsenic in PDB 4ci1: Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Thalidomide

The structure of Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Thalidomide, PDB code: 4ci1 was solved by E.S.Fischer, K.Boehm, N.H.Thoma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.82 / 2.98
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	172.180, 172.180, 140.090, 90.00, 90.00, 120.00
R / Rfree (%)	19.69 / 23.32

The structure of Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Thalidomide also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Arsenic atom in the Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Thalidomide (pdb code 4ci1). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Thalidomide, PDB code: 4ci1:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in the Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Thalidomide


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Thalidomide within 5.0Å range: probe atom residue distance (Å) B Occ A:As87 b:86.5 occ:0.51 AS A:CAF87 0.0 86.5 0.5 O1 A:CAF87 1.6 86.1 0.5 CE2 A:CAF87 1.9 86.1 0.5 CE1 A:CAF87 1.9 87.3 0.5 SG A:CAF87 2.3 84.4 1.0 CB A:CAF87 3.4 83.4 1.0 CA A:GLY1066 3.7 78.1 1.0 CD1 A:ILE1068 3.9 81.8 1.0 CE A:MET57 4.0 84.4 1.0 O A:VAL1065 4.3 81.9 1.0 N A:CAF87 4.3 81.2 1.0 O A:GLY1066 4.3 82.4 1.0 CA A:CAF87 4.4 81.6 1.0 CG1 A:ILE1068 4.4 76.4 1.0 C A:GLY1066 4.4 81.8 1.0 O A:ILE79 4.5 80.2 1.0 O A:ASN85 4.5 79.9 1.0 C A:ALA86 4.5 84.7 1.0 CB A:ILE79 4.6 80.2 1.0 N A:GLY1066 4.7 78.5 1.0 O A:ALA86 4.7 85.3 1.0 CG2 A:THR81 4.8 67.8 1.0 C A:ASN85 4.8 80.6 1.0 CB A:ASN85 4.8 74.6 1.0 C A:VAL1065 4.8 82.3 1.0 CG2 A:ILE79 4.9 80.0 1.0

Arsenic binding site 2 out of 4 in the Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Thalidomide


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Thalidomide within 5.0Å range: probe atom residue distance (Å) B Occ A:As977 b:86.3 occ:0.69 AS A:CAF977 0.0 86.3 0.7 O1 A:CAF977 1.6 88.7 0.7 CE2 A:CAF977 1.9 84.0 0.7 CE1 A:CAF977 1.9 87.0 0.7 SG A:CAF977 2.2 84.6 1.0 CB A:CAF977 3.3 81.0 1.0 OD2 A:ASP948 3.8 0.4 1.0 CG A:ASP948 4.0 92.5 1.0 NH2 A:ARG928 4.1 85.7 1.0 CB A:ASP948 4.2 80.2 1.0 CZ A:PHE965 4.3 91.0 1.0 NH1 A:ARG928 4.4 87.8 1.0 CZ A:ARG928 4.4 98.2 1.0 CE2 A:PHE965 4.4 91.2 1.0 CB A:LEU992 4.5 0.3 1.0 OD1 A:ASP948 4.5 93.0 1.0 CA A:CAF977 4.7 76.4 1.0 CE2 A:PHE975 4.8 71.0 1.0 CD1 A:LEU992 5.0 0.2 1.0

Arsenic binding site 3 out of 4 in the Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Thalidomide


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Thalidomide within 5.0Å range: probe atom residue distance (Å) B Occ B:As312 b:67.1 occ:0.62 AS B:CAF312 0.0 67.1 0.6 O1 B:CAF312 1.6 68.7 0.6 CE2 B:CAF312 1.9 64.8 0.6 CE1 B:CAF312 1.9 65.1 0.6 SG B:CAF312 2.3 66.0 1.0 CB B:CAF312 3.3 62.5 1.0 ND2 A:ASN908 3.6 0.3 1.0 OD1 A:ASN908 3.7 0.7 1.0 CA B:CAF312 4.0 56.9 1.0 CG A:ASN908 4.1 0.1 1.0 C B:CAF312 4.6 56.0 1.0 O B:CAF312 4.7 55.2 1.0 CD1 B:ILE316 4.8 58.2 1.0 CD1 B:ILE303 4.9 66.6 1.0 CD1 B:LEU296 4.9 62.1 1.0

Arsenic binding site 4 out of 4 in the Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Thalidomide


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Thalidomide within 5.0Å range: probe atom residue distance (Å) B Occ B:As320 b:67.2 occ:0.71 AS B:CAF320 0.0 67.2 0.7 O1 B:CAF320 1.6 69.0 0.7 CE2 B:CAF320 1.9 65.6 0.7 CE1 B:CAF320 1.9 65.6 0.7 SG B:CAF320 2.3 69.5 1.0 CB B:CAF320 3.2 66.9 1.0 CG B:PRO291 4.1 62.6 1.0 CD B:PRO291 4.2 58.3 1.0 CD1 B:ILE339 4.5 57.3 1.0 O B:PRO291 4.6 61.4 1.0 CA B:CAF320 4.6 65.8 1.0 CD1 B:LEU323 4.8 49.1 1.0 CD2 B:LEU323 4.8 52.4 1.0 O B:ILE316 4.9 64.2 1.0

E.S.Fischer, K.Bohm, J.R.Lydeard, H.Yang, M.B.Stadler, S.Cavadini, J.Nagel, F.Serluca, V.Acker, G.M.Lingaraju, R.B.Tichkule, M.Schebesta, W.C.Forrester, M.Schirle, U.Hassiepen, J.Ottl, M.Hild, R.E.J.Beckwith, J.W.Harper, J.L.Jenkins, N.H.Thoma. Structure of the DDB1-Crbn E3 Ubiquitin Ligase in Complex with Thalidomide. Nature V. 512 49 2014.
ISSN: ISSN 0028-0836
PubMed: 25043012
DOI: 10.1038/NATURE13527