Zinc in PDB 4p5o: Structure of An RBX1-UBC12~NEDD8-CUL1-DCN1 Complex: A Ring-E3- E2~Ubiquitin-Like Protein-Substrate Intermediate Trapped in Action

The structure of Structure of An RBX1-UBC12~NEDD8-CUL1-DCN1 Complex: A Ring-E3- E2~Ubiquitin-Like Protein-Substrate Intermediate Trapped in Action, PDB code: 4p5o was solved by D.C.Scott, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.13 / 3.11
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.105, 129.606, 119.940, 90.00, 111.79, 90.00
R / Rfree (%)	22.7 / 28.4

The binding sites of Zinc atom in the Structure of An RBX1-UBC12~NEDD8-CUL1-DCN1 Complex: A Ring-E3- E2~Ubiquitin-Like Protein-Substrate Intermediate Trapped in Action (pdb code 4p5o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of An RBX1-UBC12~NEDD8-CUL1-DCN1 Complex: A Ring-E3- E2~Ubiquitin-Like Protein-Substrate Intermediate Trapped in Action, PDB code: 4p5o:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of An RBX1-UBC12~NEDD8-CUL1-DCN1 Complex: A Ring-E3- E2~Ubiquitin-Like Protein-Substrate Intermediate Trapped in Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of An RBX1-UBC12~NEDD8-CUL1-DCN1 Complex: A Ring-E3- E2~Ubiquitin-Like Protein-Substrate Intermediate Trapped in Action within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:93.1 occ:1.00 ND1 B:HIS80 2.0 84.2 1.0 SG B:CYS83 2.3 0.7 1.0 SG B:CYS45 2.3 0.7 1.0 SG B:CYS42 2.3 84.5 1.0 CE1 B:HIS80 2.8 81.2 1.0 CG B:HIS80 3.2 88.8 1.0 CB B:CYS45 3.3 65.7 1.0 CB B:CYS42 3.5 86.2 1.0 N B:CYS45 3.6 74.1 1.0 CB B:CYS83 3.7 98.5 1.0 CB B:HIS80 3.7 93.4 1.0 NE2 B:HIS80 4.0 80.0 1.0 CA B:CYS45 4.0 71.4 1.0 CB B:CYS53 4.0 98.9 1.0 N B:HIS80 4.1 88.7 1.0 CD2 B:HIS80 4.2 84.3 1.0 CA B:HIS80 4.5 92.2 1.0 CB B:ILE44 4.5 67.7 1.0 CA B:CYS53 4.5 0.8 1.0 C B:ILE44 4.7 72.7 1.0 CA B:CYS83 4.9 93.7 1.0 CA B:CYS42 4.9 92.2 1.0 CA B:ILE44 5.0 68.3 1.0 CG2 B:ILE44 5.0 69.1 1.0

Zinc binding site 2 out of 6 in the Structure of An RBX1-UBC12~NEDD8-CUL1-DCN1 Complex: A Ring-E3- E2~Ubiquitin-Like Protein-Substrate Intermediate Trapped in Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of An RBX1-UBC12~NEDD8-CUL1-DCN1 Complex: A Ring-E3- E2~Ubiquitin-Like Protein-Substrate Intermediate Trapped in Action within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:82.1 occ:1.00 OD2 B:ASP97 2.0 73.3 1.0 ND1 B:HIS77 2.0 72.8 1.0 SG B:CYS75 2.3 0.6 1.0 SG B:CYS94 2.3 80.7 1.0 CG B:ASP97 2.6 74.4 1.0 CE1 B:HIS77 2.8 74.9 1.0 OD1 B:ASP97 2.8 78.8 1.0 CB B:CYS75 3.1 95.5 1.0 CG B:HIS77 3.1 76.6 1.0 CB B:CYS94 3.3 91.2 1.0 CB B:HIS77 3.6 75.9 1.0 CB B:ASP97 3.9 75.3 1.0 NE2 B:HIS77 4.0 80.8 1.0 N B:ASP97 4.1 86.9 1.0 CD2 B:HIS77 4.2 82.6 1.0 CB B:LEU96 4.4 67.0 1.0 CA B:CYS75 4.5 0.2 1.0 CA B:ASP97 4.6 83.8 1.0 CA B:CYS94 4.7 87.2 1.0 O B:ASP97 4.7 0.4 1.0 N B:HIS77 4.8 89.3 1.0 CA B:HIS77 4.8 84.8 1.0 C B:CYS75 4.9 99.4 1.0

Zinc binding site 3 out of 6 in the Structure of An RBX1-UBC12~NEDD8-CUL1-DCN1 Complex: A Ring-E3- E2~Ubiquitin-Like Protein-Substrate Intermediate Trapped in Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of An RBX1-UBC12~NEDD8-CUL1-DCN1 Complex: A Ring-E3- E2~Ubiquitin-Like Protein-Substrate Intermediate Trapped in Action within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:0.7 occ:1.00 ND1 B:HIS82 2.0 0.8 1.0 SG B:CYS53 2.3 0.9 1.0 SG B:CYS68 2.3 82.7 1.0 SG B:CYS56 2.3 0.7 1.0 CE1 B:HIS82 2.8 0.2 1.0 CB B:CYS68 3.1 0.2 1.0 CG B:HIS82 3.2 0.6 1.0 CB B:CYS56 3.2 0.5 1.0 CB B:CYS53 3.3 98.9 1.0 CB B:HIS82 3.7 0.9 1.0 N B:CYS53 3.9 0.6 1.0 NE2 B:HIS82 4.0 0.8 1.0 CA B:CYS68 4.0 0.9 1.0 CA B:CYS53 4.1 0.8 1.0 N B:CYS56 4.1 98.6 1.0 CD2 B:HIS82 4.2 0.6 1.0 CA B:CYS56 4.2 0.6 1.0 O B:CYS53 4.4 0.6 1.0 C B:CYS53 4.5 1.0 1.0 N B:CYS68 5.0 0.8 1.0

Zinc binding site 4 out of 6 in the Structure of An RBX1-UBC12~NEDD8-CUL1-DCN1 Complex: A Ring-E3- E2~Ubiquitin-Like Protein-Substrate Intermediate Trapped in Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of An RBX1-UBC12~NEDD8-CUL1-DCN1 Complex: A Ring-E3- E2~Ubiquitin-Like Protein-Substrate Intermediate Trapped in Action within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:0.7 occ:1.00 ND1 D:HIS80 2.0 84.7 1.0 SG D:CYS83 2.3 72.5 1.0 SG D:CYS42 2.3 75.1 1.0 SG D:CYS45 2.3 0.5 1.0 CE1 D:HIS80 2.7 85.0 1.0 CB D:CYS42 3.1 92.9 1.0 CG D:HIS80 3.2 95.5 1.0 CB D:CYS45 3.3 90.6 1.0 CB D:CYS83 3.6 87.6 1.0 N D:CYS45 3.7 88.8 1.0 CB D:HIS80 3.8 0.8 1.0 NE2 D:HIS80 3.9 89.3 1.0 CA D:CYS45 4.0 90.7 1.0 N D:HIS80 4.2 95.6 1.0 CD2 D:HIS80 4.2 95.4 1.0 CB D:CYS53 4.2 0.3 1.0 CA D:CYS42 4.6 94.8 1.0 CA D:CYS53 4.6 0.4 1.0 CA D:HIS80 4.6 99.8 1.0 CB D:ILE44 4.7 74.8 1.0 C D:CYS45 4.8 93.3 1.0 C D:ILE44 4.8 83.9 1.0 N D:ARG46 4.9 90.0 1.0 N D:ILE44 4.9 80.7 1.0 C D:CYS42 4.9 87.5 1.0 CA D:CYS83 5.0 84.4 1.0

Zinc binding site 5 out of 6 in the Structure of An RBX1-UBC12~NEDD8-CUL1-DCN1 Complex: A Ring-E3- E2~Ubiquitin-Like Protein-Substrate Intermediate Trapped in Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of An RBX1-UBC12~NEDD8-CUL1-DCN1 Complex: A Ring-E3- E2~Ubiquitin-Like Protein-Substrate Intermediate Trapped in Action within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:78.7 occ:1.00 OD2 D:ASP97 2.0 59.0 1.0 ND1 D:HIS77 2.0 76.3 1.0 SG D:CYS94 2.3 71.9 1.0 SG D:CYS75 2.3 0.8 1.0 CG D:ASP97 2.6 59.2 1.0 CE1 D:HIS77 2.7 74.0 1.0 OD1 D:ASP97 2.8 62.8 1.0 CB D:CYS75 3.1 0.3 1.0 CB D:CYS94 3.2 74.3 1.0 CG D:HIS77 3.2 79.7 1.0 CB D:HIS77 3.8 81.4 1.0 NE2 D:HIS77 3.9 77.3 1.0 CB D:ASP97 4.0 59.5 1.0 N D:ASP97 4.1 75.2 1.0 CD2 D:HIS77 4.2 80.4 1.0 CB D:LEU96 4.4 58.6 1.0 CA D:CYS75 4.5 0.6 1.0 CA D:ASP97 4.6 72.0 1.0 CA D:CYS94 4.6 71.7 1.0 N D:HIS77 4.7 98.4 1.0 C D:CYS75 4.7 0.6 1.0 O D:ASP97 4.8 87.9 1.0 CA D:HIS77 4.9 90.6 1.0 O D:CYS75 4.9 0.5 1.0

Zinc binding site 6 out of 6 in the Structure of An RBX1-UBC12~NEDD8-CUL1-DCN1 Complex: A Ring-E3- E2~Ubiquitin-Like Protein-Substrate Intermediate Trapped in Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of An RBX1-UBC12~NEDD8-CUL1-DCN1 Complex: A Ring-E3- E2~Ubiquitin-Like Protein-Substrate Intermediate Trapped in Action within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn203 b:0.8 occ:1.00 ND1 D:HIS82 2.0 0.7 1.0 SG D:CYS53 2.3 0.0 1.0 SG D:CYS68 2.3 87.6 1.0 SG D:CYS56 2.3 0.6 1.0 CE1 D:HIS82 2.8 0.8 1.0 CB D:CYS68 3.1 0.5 1.0 CB D:CYS56 3.1 0.6 1.0 CG D:HIS82 3.2 0.4 1.0 CB D:CYS53 3.3 0.3 1.0 CB D:HIS82 3.7 93.8 1.0 NE2 D:HIS82 4.0 0.5 1.0 N D:CYS56 4.0 0.5 1.0 N D:CYS53 4.0 0.5 1.0 CA D:CYS68 4.0 0.3 1.0 CA D:CYS56 4.2 0.1 1.0 CA D:CYS53 4.2 0.4 1.0 CD2 D:HIS82 4.2 0.8 1.0 O D:CYS53 4.5 0.5 1.0 C D:CYS53 4.6 0.3 1.0

D.C.Scott, V.O.Sviderskiy, J.K.Monda, J.R.Lydeard, S.E.Cho, J.W.Harper, B.A.Schulman. Structure of A Ring E3 Trapped in Action Reveals Ligation Mechanism For the Ubiquitin-Like Protein NEDD8. Cell V. 157 1671 2014.
ISSN: ISSN 1097-4172
PubMed: 24949976
DOI: 10.1016/J.CELL.2014.04.037