Zinc in PDB 2hye: Crystal Structure of the DDB1-CUL4A-RBX1-SV5V Complex

The structure of Crystal Structure of the DDB1-CUL4A-RBX1-SV5V Complex, PDB code: 2hye was solved by S.Angers, T.Li, X.Yi, M.J.Maccoss, R.T.Moon, N.Zheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	83.452, 203.165, 424.875, 90.00, 90.00, 90.00
R / Rfree (%)	25 / 31.6

The binding sites of Zinc atom in the Crystal Structure of the DDB1-CUL4A-RBX1-SV5V Complex (pdb code 2hye). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the DDB1-CUL4A-RBX1-SV5V Complex, PDB code: 2hye:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of the DDB1-CUL4A-RBX1-SV5V Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the DDB1-CUL4A-RBX1-SV5V Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3001 b:0.9 occ:1.00 SG B:CYS194 2.4 0.8 1.0 SG B:CYS208 2.4 0.0 1.0 SG B:CYS211 2.7 0.9 1.0 O B:CYS208 2.9 0.6 1.0 SG B:CYS206 2.9 96.9 1.0 CB B:CYS211 3.3 0.9 1.0 N B:CYS208 3.3 0.6 1.0 C B:CYS208 3.4 0.6 1.0 CB B:CYS208 3.6 0.0 1.0 CA B:CYS206 3.6 0.3 1.0 CA B:CYS208 3.6 0.6 1.0 C B:CYS206 3.9 0.3 1.0 CB B:CYS206 3.9 96.9 1.0 N B:THR207 3.9 94.2 1.0 N B:CYS211 4.2 0.7 1.0 CB B:PRO192 4.2 77.3 1.0 CB B:CYS194 4.2 0.8 1.0 CA B:CYS211 4.3 0.7 1.0 C B:THR207 4.4 94.2 1.0 N B:CYS194 4.5 0.6 1.0 N B:HIS209 4.5 0.1 1.0 O B:CYS206 4.5 0.3 1.0 CA B:THR207 4.8 94.2 1.0 CA B:CYS194 4.9 0.6 1.0 N B:CYS206 4.9 0.3 1.0 N B:GLN210 5.0 0.2 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of the DDB1-CUL4A-RBX1-SV5V Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the DDB1-CUL4A-RBX1-SV5V Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3002 b:91.3 occ:1.00 SG B:CYS190 2.4 79.7 1.0 SG B:CYS218 2.4 48.5 1.0 CB B:HIS171 2.5 0.7 1.0 CB B:CYS215 2.8 76.5 1.0 ND1 B:HIS171 2.9 0.7 1.0 SG B:CYS215 2.9 76.5 1.0 CG B:HIS171 3.1 0.7 1.0 CB B:CYS190 3.5 79.7 1.0 CA B:HIS171 3.8 66.6 1.0 C B:HIS171 4.1 66.6 1.0 CA B:CYS215 4.1 0.9 1.0 N B:ARG172 4.1 92.8 1.0 CE1 B:HIS171 4.2 0.7 1.0 CB B:CYS218 4.2 48.5 1.0 O B:ARG172 4.4 92.8 1.0 CD2 B:HIS171 4.4 0.7 1.0 N B:CYS218 4.4 0.1 1.0 N B:CYS215 4.4 0.9 1.0 CG B:GLU217 4.5 1.0 1.0 C B:CYS215 4.5 0.9 1.0 CB B:GLU217 4.5 1.0 1.0 O B:CYS215 4.6 0.9 1.0 O B:HIS171 4.7 66.6 1.0 N B:HIS171 4.8 66.6 1.0 CA B:CYS190 4.8 70.0 1.0 C B:ARG172 4.9 92.8 1.0 CA B:CYS218 4.9 0.1 1.0 NE2 B:HIS171 4.9 0.7 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of the DDB1-CUL4A-RBX1-SV5V Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the DDB1-CUL4A-RBX1-SV5V Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn4001 b:77.7 occ:1.00 SG D:CYS45 2.1 69.9 1.0 SG D:CYS42 2.2 86.1 1.0 SG D:CYS83 2.4 1.0 1.0 CB D:CYS83 2.4 1.0 1.0 ND1 D:HIS80 2.9 46.6 1.0 CG D:HIS80 3.0 46.6 1.0 CB D:HIS80 3.2 46.6 1.0 CB D:CYS42 3.3 86.1 1.0 CE1 D:HIS80 3.6 46.6 1.0 CA D:CYS83 3.7 80.2 1.0 N D:HIS80 3.8 41.9 1.0 CB D:CYS45 3.8 69.9 1.0 CD2 D:HIS80 3.8 46.6 1.0 O D:CYS83 3.8 80.2 1.0 N D:CYS83 4.0 80.2 1.0 CA D:HIS80 4.1 41.9 1.0 NE2 D:HIS80 4.1 46.6 1.0 N D:CYS45 4.2 48.1 1.0 C D:CYS83 4.3 80.2 1.0 CA D:CYS42 4.4 88.3 1.0 CB D:CYS53 4.4 54.8 1.0 CA D:CYS45 4.6 48.1 1.0 O D:HIS80 4.7 41.9 1.0 CB D:ILE44 4.7 53.5 1.0 C D:HIS80 4.8 41.9 1.0 ND2 D:ASN47 4.9 93.1 1.0 N D:ILE44 4.9 60.1 1.0 C D:PHE79 4.9 58.4 1.0 C D:ILE44 5.0 60.1 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of the DDB1-CUL4A-RBX1-SV5V Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the DDB1-CUL4A-RBX1-SV5V Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn4003 b:84.4 occ:1.00 SG D:CYS56 2.2 53.0 1.0 ND1 D:HIS82 2.3 82.0 1.0 SG D:CYS68 2.5 69.5 1.0 SG D:CYS53 2.7 54.8 1.0 CB D:CYS68 2.9 69.5 1.0 CG D:HIS82 3.0 82.0 1.0 CE1 D:HIS82 3.0 82.0 1.0 CB D:HIS82 3.4 82.0 1.0 CB D:CYS56 3.5 53.0 1.0 CA D:CYS68 3.7 56.4 1.0 CD2 D:HIS82 3.9 82.0 1.0 NE2 D:HIS82 3.9 82.0 1.0 CB D:CYS53 4.2 54.8 1.0 N D:CYS68 4.4 56.4 1.0 O D:GLU67 4.5 0.1 1.0 CA D:CYS56 4.7 89.4 1.0 N D:CYS53 4.7 56.5 1.0 C D:GLU67 4.8 0.1 1.0 N D:CYS56 4.8 89.4 1.0 CA D:HIS82 4.8 57.5 1.0 C D:LEU52 4.8 75.1 1.0 C D:CYS68 4.8 56.4 1.0 CA D:SER65 4.9 86.8 1.0 O D:LEU52 4.9 75.1 1.0 O D:THR64 4.9 62.9 1.0 N D:HIS82 5.0 57.5 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of the DDB1-CUL4A-RBX1-SV5V Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the DDB1-CUL4A-RBX1-SV5V Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn4002 b:99.3 occ:1.00 ND1 D:HIS77 2.0 87.7 1.0 OD2 D:ASP97 2.2 20.0 1.0 SG D:CYS94 2.3 48.6 1.0 SG D:CYS75 2.4 40.6 1.0 CG D:HIS77 2.4 87.7 1.0 CB D:HIS77 2.6 87.7 1.0 CG D:ASP97 2.7 20.0 1.0 CE1 D:HIS77 3.1 87.7 1.0 OD1 D:ASP97 3.2 20.0 1.0 N D:HIS77 3.5 72.2 1.0 CD2 D:HIS77 3.5 87.7 1.0 CA D:HIS77 3.6 72.2 1.0 CB D:ASP97 3.7 58.8 1.0 NE2 D:HIS77 3.8 87.7 1.0 CB D:CYS75 3.8 40.6 1.0 CB D:CYS94 4.0 48.6 1.0 CB D:LEU96 4.1 57.9 1.0 N D:ASP97 4.1 88.4 1.0 O D:CYS75 4.3 53.8 1.0 C D:CYS75 4.4 53.8 1.0 CZ D:PHE79 4.4 61.9 1.0 C D:HIS77 4.5 72.2 1.0 O D:HIS77 4.5 72.2 1.0 CA D:ASP97 4.5 88.4 1.0 CE1 D:PHE79 4.6 61.9 1.0 C D:LEU96 4.6 54.6 1.0 C D:ASN76 4.7 48.1 1.0 CA D:CYS75 4.7 53.8 1.0 NE1 D:TRP35 4.8 53.0 1.0 N D:ASN76 4.8 48.1 1.0 CD1 D:LEU96 4.8 57.9 1.0 CA D:LEU96 4.9 54.6 1.0 CD1 D:TRP35 4.9 53.0 1.0

S.Angers, T.Li, X.Yi, M.J.Maccoss, R.T.Moon, N.Zheng. Molecular Architecture and Assembly of the DDB1-CUL4A Ubiquitin Ligase Machinery. Nature V. 443 590 2006.
ISSN: ISSN 0028-0836
PubMed: 16964240
DOI: 10.1038/NATURE05175