Zinc in PDB 3dbr: Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190GLN-NEDD8ALA72ARG)

The structure of Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190GLN-NEDD8ALA72ARG), PDB code: 3dbr was solved by J.Souphron, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	134.322, 198.531, 208.795, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 28

The binding sites of Zinc atom in the Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190GLN-NEDD8ALA72ARG) (pdb code 3dbr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190GLN-NEDD8ALA72ARG), PDB code: 3dbr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190GLN-NEDD8ALA72ARG)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190GLN-NEDD8ALA72ARG) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:70.9 occ:1.00 SG B:CYS202 2.3 64.8 1.0 SG B:CYS343 2.3 75.3 1.0 SG B:CYS346 2.4 69.9 1.0 SG B:CYS199 2.5 54.5 1.0 CB B:CYS343 3.0 76.8 1.0 N B:CYS346 3.5 72.8 1.0 CB B:CYS346 3.6 72.9 1.0 N B:CYS202 3.6 65.7 1.0 CB B:CYS202 3.7 65.3 1.0 CA B:CYS202 3.9 65.0 1.0 CB B:CYS199 4.0 55.9 1.0 CB B:ALA345 4.1 73.5 1.0 CA B:CYS346 4.1 75.1 1.0 N B:CYS199 4.2 58.0 1.0 CB B:GLU201 4.4 63.0 1.0 CA B:CYS343 4.5 78.3 1.0 C B:GLU201 4.5 64.7 1.0 C B:ALA345 4.5 72.7 1.0 CA B:CYS199 4.6 58.9 1.0 CA B:ALA345 4.7 73.2 1.0 C B:CYS346 4.8 78.8 1.0 N B:ALA345 4.8 73.6 1.0 O B:LYS340 4.8 82.9 1.0 CA B:GLU201 4.9 64.1 1.0 CG B:ARG339 4.9 77.5 1.0 C B:CYS343 5.0 77.5 1.0 C B:CYS199 5.0 61.4 1.0

Zinc binding site 2 out of 4 in the Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190GLN-NEDD8ALA72ARG)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190GLN-NEDD8ALA72ARG) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn2 b:84.9 occ:1.00 SG H:CYS346 2.5 87.4 1.0 SG H:CYS202 2.5 68.6 1.0 SG H:CYS343 2.6 92.0 1.0 SG H:CYS199 2.7 69.1 1.0 CB H:CYS346 2.8 90.1 1.0 CB H:CYS343 3.0 95.5 1.0 N H:CYS346 3.1 89.9 1.0 CA H:CYS346 3.5 90.6 1.0 N H:CYS202 3.8 74.7 1.0 CB H:ALA345 3.9 89.4 1.0 CB H:CYS202 3.9 71.8 1.0 CB H:CYS199 3.9 68.9 1.0 C H:ALA345 4.1 90.2 1.0 CA H:CYS202 4.2 74.1 1.0 N H:CYS199 4.3 69.0 1.0 CA H:CYS343 4.4 96.6 1.0 CB H:GLU201 4.4 79.0 1.0 CA H:ALA345 4.5 90.8 1.0 C H:GLU201 4.7 76.4 1.0 CA H:CYS199 4.7 69.2 1.0 N H:ALA345 4.7 93.1 1.0 C H:CYS343 4.7 96.4 1.0 C H:CYS346 4.7 92.0 1.0 O H:LYS340 4.7 97.0 1.0 O H:CYS343 4.8 96.2 1.0 N H:SER347 4.9 93.8 1.0 CA H:GLU201 5.0 77.7 1.0

Zinc binding site 3 out of 4 in the Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190GLN-NEDD8ALA72ARG)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190GLN-NEDD8ALA72ARG) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn3 b:67.8 occ:1.00 SG D:CYS343 2.4 85.9 1.0 SG D:CYS202 2.5 70.2 1.0 SG D:CYS346 2.5 82.6 1.0 SG D:CYS199 2.6 69.8 1.0 CB D:CYS343 3.1 89.1 1.0 CB D:CYS346 3.5 86.8 1.0 CB D:CYS202 3.6 71.6 1.0 CB D:CYS199 3.6 68.2 1.0 N D:CYS202 3.6 71.0 1.0 N D:CYS346 3.8 87.4 1.0 CA D:CYS202 3.9 71.6 1.0 N D:CYS199 4.0 67.0 1.0 CA D:CYS346 4.2 87.5 1.0 CA D:CYS199 4.3 68.1 1.0 C D:GLU201 4.6 69.5 1.0 CB D:GLU201 4.6 68.8 1.0 CA D:CYS343 4.6 90.3 1.0 O D:CYS199 4.6 70.2 1.0 C D:CYS199 4.7 69.7 1.0 CB D:ALA345 4.8 88.6 1.0 C D:CYS346 4.8 89.3 1.0 C D:ALA345 4.9 87.3 1.0 O D:LYS340 4.9 89.3 1.0 N D:GLU201 4.9 68.8 1.0 CA D:GLU201 5.0 68.7 1.0

Zinc binding site 4 out of 4 in the Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190GLN-NEDD8ALA72ARG)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190GLN-NEDD8ALA72ARG) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn4 b:67.9 occ:1.00 SG F:CYS202 2.3 60.7 1.0 SG F:CYS199 2.4 59.2 1.0 SG F:CYS343 2.5 80.7 1.0 SG F:CYS346 2.5 80.2 1.0 CB F:CYS346 2.7 80.4 1.0 CB F:CYS343 3.2 83.5 1.0 N F:CYS346 3.4 79.4 1.0 CB F:CYS199 3.5 58.5 1.0 CB F:CYS202 3.6 62.0 1.0 CA F:CYS346 3.6 80.5 1.0 N F:CYS202 3.7 64.5 1.0 N F:CYS199 3.9 57.8 1.0 CA F:CYS202 4.0 64.1 1.0 CA F:CYS199 4.3 58.4 1.0 CB F:GLU201 4.3 66.2 1.0 CB F:ALA345 4.4 75.8 1.0 C F:ALA345 4.6 78.0 1.0 CA F:CYS343 4.7 83.9 1.0 C F:GLU201 4.7 65.2 1.0 CG F:ARG339 4.7 67.4 1.0 O F:LYS340 4.8 80.1 1.0 C F:CYS199 4.8 59.9 1.0 C F:CYS346 4.9 82.5 1.0 CA F:ALA345 4.9 77.3 1.0 CA F:GLU201 5.0 64.4 1.0

J.Souphron, M.B.Waddell, A.Paydar, Z.Tokgoz-Gromley, M.F.Roussel, B.A.Schulman. Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1. Biochemistry V. 47 8961 2008.
ISSN: ISSN 0006-2960
PubMed: 18652489
DOI: 10.1021/BI800604C