Zinc in PDB 3dbl: Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190WT-NEDD8ALA72GLN)

The structure of Structural Dissection of A Gating Mechanism Preventing Misactivation of Ubiquitin By NEDD8'S E1 (APPBP1- UBA3ARG190WT-NEDD8ALA72GLN), PDB code: 3dbl 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 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	136.118, 198.947, 210.021, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 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- UBA3ARG190WT-NEDD8ALA72GLN) (pdb code 3dbl). 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- UBA3ARG190WT-NEDD8ALA72GLN), PDB code: 3dbl:
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- UBA3ARG190WT-NEDD8ALA72GLN)


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- UBA3ARG190WT-NEDD8ALA72GLN) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:65.0 occ:1.00 SG B:CYS343 2.3 71.3 1.0 SG B:CYS346 2.5 63.6 1.0 SG B:CYS202 2.5 58.0 1.0 SG B:CYS199 2.5 56.3 1.0 CB B:CYS343 3.0 72.1 1.0 CB B:CYS346 3.5 64.1 1.0 CB B:CYS202 3.5 58.0 1.0 N B:CYS202 3.6 60.7 1.0 N B:CYS346 3.6 62.9 1.0 CA B:CYS202 3.8 59.4 1.0 CB B:CYS199 3.8 54.4 1.0 N B:CYS199 4.0 53.4 1.0 CA B:CYS346 4.1 64.7 1.0 CB B:ALA345 4.3 63.5 1.0 CA B:CYS199 4.4 54.7 1.0 CA B:CYS343 4.5 73.0 1.0 C B:GLU201 4.5 60.0 1.0 CB B:GLU201 4.6 60.5 1.0 C B:ALA345 4.7 63.3 1.0 O B:CYS199 4.8 55.6 1.0 C B:CYS199 4.8 56.2 1.0 O B:LYS340 4.8 76.4 1.0 CA B:ALA345 4.9 64.3 1.0 C B:CYS346 4.9 67.5 1.0 N B:ALA345 4.9 66.4 1.0 CA B:GLU201 5.0 59.2 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- UBA3ARG190WT-NEDD8ALA72GLN)


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- UBA3ARG190WT-NEDD8ALA72GLN) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn2 b:80.8 occ:1.00 SG H:CYS346 2.3 63.2 1.0 SG H:CYS202 2.3 64.9 1.0 SG H:CYS343 2.5 85.3 1.0 SG H:CYS199 2.6 56.0 1.0 CB H:CYS343 2.7 88.8 1.0 CB H:CYS346 3.3 74.4 1.0 N H:CYS346 3.3 77.5 1.0 CB H:CYS199 3.7 58.7 1.0 CB H:CYS202 3.7 66.1 1.0 N H:CYS202 3.8 67.3 1.0 CA H:CYS346 3.8 77.8 1.0 CA H:CYS202 4.1 67.5 1.0 CA H:CYS343 4.2 89.1 1.0 N H:CYS199 4.3 61.3 1.0 CB H:ALA345 4.4 77.9 1.0 C H:ALA345 4.4 77.8 1.0 C H:CYS346 4.5 81.2 1.0 O H:LYS340 4.5 91.5 1.0 CB H:GLU201 4.5 68.2 1.0 CA H:CYS199 4.6 59.8 1.0 C H:GLU201 4.6 66.8 1.0 N H:SER347 4.7 84.3 1.0 C H:CYS343 4.7 88.0 1.0 CA H:ALA345 4.7 78.6 1.0 N H:ALA345 4.8 81.6 1.0 O H:CYS343 4.9 88.4 1.0 N H:CYS343 5.0 91.2 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- UBA3ARG190WT-NEDD8ALA72GLN)


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- UBA3ARG190WT-NEDD8ALA72GLN) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn3 b:74.6 occ:1.00 SG D:CYS343 2.4 68.3 1.0 SG D:CYS202 2.4 59.0 1.0 SG D:CYS346 2.5 67.9 1.0 SG D:CYS199 2.6 56.9 1.0 CB D:CYS343 3.0 72.4 1.0 CB D:CYS346 3.4 72.2 1.0 CB D:CYS202 3.5 62.1 1.0 N D:CYS202 3.6 62.3 1.0 CB D:CYS199 3.7 54.9 1.0 CA D:CYS202 3.8 62.1 1.0 N D:CYS346 3.8 72.1 1.0 N D:CYS199 4.2 56.0 1.0 CA D:CYS346 4.2 72.5 1.0 C D:GLU201 4.3 60.6 1.0 CB D:GLU201 4.4 62.3 1.0 CA D:CYS199 4.4 55.7 1.0 CA D:CYS343 4.4 73.9 1.0 O D:CYS199 4.5 54.3 1.0 C D:CYS199 4.7 55.9 1.0 CA D:GLU201 4.8 60.4 1.0 N D:GLU201 4.8 59.3 1.0 O D:LYS340 4.8 79.4 1.0 C D:CYS346 4.9 74.6 1.0 C D:ALA345 5.0 71.2 1.0 CG D:ARG339 5.0 74.4 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- UBA3ARG190WT-NEDD8ALA72GLN)


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- UBA3ARG190WT-NEDD8ALA72GLN) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn4 b:62.0 occ:1.00 SG F:CYS202 2.4 49.5 1.0 SG F:CYS199 2.4 49.9 1.0 SG F:CYS343 2.5 68.5 1.0 SG F:CYS346 2.5 76.6 1.0 CB F:CYS346 2.6 74.5 1.0 CB F:CYS343 2.9 73.9 1.0 N F:CYS346 3.3 73.6 1.0 CB F:CYS199 3.5 50.8 1.0 CA F:CYS346 3.5 75.0 1.0 CB F:CYS202 3.9 52.1 1.0 N F:CYS202 4.0 57.0 1.0 N F:CYS199 4.1 52.7 1.0 CA F:CYS202 4.3 56.1 1.0 CA F:CYS199 4.3 50.5 1.0 CA F:CYS343 4.4 75.2 1.0 C F:ALA345 4.4 73.0 1.0 CB F:ALA345 4.4 72.2 1.0 CB F:GLU201 4.6 60.0 1.0 O F:LYS340 4.7 76.6 1.0 CA F:ALA345 4.8 73.2 1.0 C F:CYS346 4.8 77.3 1.0 N F:ALA345 4.8 74.8 1.0 C F:CYS343 4.8 74.8 1.0 C F:GLU201 4.8 57.8 1.0 C F:CYS199 4.9 51.1 1.0 O F:CYS343 5.0 74.0 1.0 N F:SER347 5.0 80.0 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