Zinc in PDB 3dbh: Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190ALA-NEDD8ALA72ARG)

The structure of Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190ALA-NEDD8ALA72ARG), PDB code: 3dbh 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 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	135.647, 198.100, 210.961, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 27.4

The binding sites of Zinc atom in the Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190ALA-NEDD8ALA72ARG) (pdb code 3dbh). 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- UBA3ARG190ALA-NEDD8ALA72ARG), PDB code: 3dbh:
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- UBA3ARG190ALA-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- UBA3ARG190ALA-NEDD8ALA72ARG) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:79.2 occ:1.00 SG B:CYS346 2.2 79.5 1.0 SG B:CYS202 2.3 71.7 1.0 SG B:CYS199 2.4 66.9 1.0 SG B:CYS343 2.5 75.3 1.0 CB B:CYS343 3.3 84.1 1.0 CB B:CYS346 3.5 84.2 1.0 CB B:CYS202 3.5 70.1 1.0 CB B:CYS199 3.5 68.2 1.0 N B:CYS202 3.6 71.7 1.0 N B:CYS346 3.7 84.8 1.0 N B:CYS199 3.8 67.8 1.0 CA B:CYS202 3.8 71.3 1.0 CA B:CYS199 4.2 69.8 1.0 CA B:CYS346 4.2 86.8 1.0 CB B:ALA345 4.3 83.5 1.0 CB B:GLU201 4.5 73.5 1.0 C B:GLU201 4.5 72.0 1.0 C B:CYS199 4.6 72.0 1.0 O B:CYS199 4.7 72.8 1.0 C B:ALA345 4.8 84.3 1.0 CA B:CYS343 4.8 86.0 1.0 O B:LYS340 4.9 0.2 1.0 CA B:ALA345 4.9 83.5 1.0 CA B:GLU201 4.9 72.2 1.0 N B:ALA345 4.9 83.4 1.0 C B:ALA198 4.9 65.9 1.0 C B:CYS346 5.0 89.9 1.0 N B:GLU201 5.0 71.1 1.0 CG B:ARG339 5.0 90.7 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- UBA3ARG190ALA-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- UBA3ARG190ALA-NEDD8ALA72ARG) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn2 b:84.5 occ:1.00 SG H:CYS346 2.4 76.6 1.0 SG H:CYS202 2.5 78.9 1.0 SG H:CYS343 2.6 0.6 1.0 SG H:CYS199 2.6 80.4 1.0 CB H:CYS343 3.1 0.8 1.0 N H:CYS346 3.4 93.5 1.0 CB H:CYS346 3.4 88.4 1.0 N H:CYS202 3.4 80.6 1.0 CB H:CYS202 3.7 78.0 1.0 CA H:CYS202 3.8 79.9 1.0 CB H:GLU201 3.9 84.8 1.0 CB H:CYS199 3.9 76.5 1.0 CA H:CYS346 3.9 93.0 1.0 N H:CYS199 4.2 78.2 1.0 C H:GLU201 4.3 82.5 1.0 CB H:ALA345 4.3 95.3 1.0 C H:ALA345 4.5 94.9 1.0 CA H:GLU201 4.5 83.1 1.0 CA H:CYS343 4.6 0.9 1.0 CA H:CYS199 4.6 77.8 1.0 C H:CYS346 4.7 95.7 1.0 O H:CYS199 4.7 76.1 1.0 CA H:ALA345 4.7 95.7 1.0 O H:LYS340 4.7 0.7 1.0 N H:GLU201 4.8 81.8 1.0 C H:CYS199 4.9 77.2 1.0 N H:ALA345 4.9 98.7 1.0 N H:SER347 4.9 98.6 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- UBA3ARG190ALA-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- UBA3ARG190ALA-NEDD8ALA72ARG) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn3 b:93.8 occ:1.00 SG D:CYS346 2.3 88.6 1.0 SG D:CYS199 2.3 75.3 1.0 SG D:CYS202 2.3 74.0 1.0 SG D:CYS343 2.4 86.5 1.0 CB D:CYS343 3.3 93.6 1.0 CB D:CYS346 3.3 94.2 1.0 N D:CYS202 3.4 82.6 1.0 CB D:CYS202 3.4 79.9 1.0 CB D:CYS199 3.6 75.2 1.0 CA D:CYS202 3.7 81.8 1.0 N D:CYS346 3.8 93.9 1.0 N D:CYS199 3.9 76.4 1.0 CA D:CYS346 4.1 95.4 1.0 CB D:GLU201 4.3 80.2 1.0 C D:GLU201 4.3 81.0 1.0 CA D:CYS199 4.3 76.3 1.0 O D:CYS199 4.5 76.3 1.0 C D:CYS199 4.6 76.2 1.0 CA D:GLU201 4.7 79.5 1.0 CA D:CYS343 4.7 94.7 1.0 N D:SER347 4.8 0.3 1.0 C D:CYS346 4.8 98.2 1.0 O D:LYS340 4.8 0.3 1.0 N D:GLU201 4.8 78.2 1.0 C D:ALA345 4.9 93.5 1.0 CB D:ALA345 4.9 93.3 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- UBA3ARG190ALA-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- UBA3ARG190ALA-NEDD8ALA72ARG) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn4 b:74.8 occ:1.00 SG F:CYS202 2.4 66.8 1.0 SG F:CYS346 2.4 83.5 1.0 SG F:CYS199 2.4 67.5 1.0 SG F:CYS343 2.5 81.6 1.0 CB F:CYS346 3.1 84.9 1.0 CB F:CYS343 3.2 87.1 1.0 CB F:CYS199 3.2 64.3 1.0 N F:CYS346 3.6 84.4 1.0 N F:CYS202 3.8 72.7 1.0 CB F:CYS202 3.8 68.3 1.0 N F:CYS199 3.9 64.3 1.0 CA F:CYS346 3.9 86.5 1.0 CA F:CYS199 4.1 64.7 1.0 CA F:CYS202 4.2 72.0 1.0 CB F:GLU201 4.4 73.1 1.0 CB F:ALA345 4.6 83.5 1.0 C F:GLU201 4.7 73.9 1.0 C F:CYS199 4.7 65.8 1.0 CA F:CYS343 4.7 88.2 1.0 C F:ALA345 4.7 84.3 1.0 C F:CYS346 4.7 89.3 1.0 N F:GLU201 4.9 70.6 1.0 CA F:GLU201 4.9 72.6 1.0 N F:SER347 4.9 93.4 1.0 O F:CYS199 4.9 66.5 1.0 O F:LYS340 5.0 93.9 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