Zinc in PDB 1r4m: APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex

The structure of APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex, PDB code: 1r4m was solved by H.Walden, M.S.Podgorski, J.M.Holton, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	135.400, 198.900, 209.800, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 28

The binding sites of Zinc atom in the APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex (pdb code 1r4m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex, PDB code: 1r4m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn1 b:68.3 occ:1.00 SG H:CYS346 2.0 54.1 1.0 SG H:CYS199 2.2 70.4 1.0 SG H:CYS343 2.2 66.0 1.0 SG H:CYS202 2.4 48.1 1.0 CB H:CYS346 2.9 54.1 1.0 CB H:CYS343 2.9 66.0 1.0 N H:CYS346 3.3 65.5 1.0 CB H:CYS199 3.3 70.4 1.0 CA H:CYS346 3.6 65.5 1.0 N H:CYS202 3.8 64.6 1.0 CB H:CYS202 3.8 48.1 1.0 N H:CYS199 3.9 64.8 1.0 CA H:CYS202 4.2 64.6 1.0 CA H:CYS199 4.2 64.8 1.0 CA H:CYS343 4.4 94.2 1.0 CB H:GLU201 4.4 76.4 1.0 C H:CYS346 4.4 65.5 1.0 C H:ALA345 4.4 88.9 1.0 CB H:ALA345 4.5 34.5 1.0 C H:GLU201 4.8 77.9 1.0 C H:CYS199 4.8 64.8 1.0 CA H:ALA345 4.9 88.9 1.0 N H:SER347 4.9 98.8 1.0 C H:CYS343 4.9 94.2 1.0 O H:LYS340 4.9 70.8 1.0 CG H:ARG339 5.0 73.8 1.0

Zinc binding site 2 out of 4 in the APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn2 b:68.3 occ:1.00 CB D:GLU338 3.1 0.9 1.0 NZ J:LYS148 3.1 82.5 1.0 CD J:LYS148 3.4 82.5 1.0 CG D:GLU338 3.7 0.9 1.0 CE J:LYS148 3.7 82.5 1.0 OE1 D:GLU338 4.0 0.9 1.0 CD D:GLU338 4.4 0.9 1.0 CA D:GLU338 4.4 63.0 1.0 C D:GLU338 4.5 63.0 1.0 O D:GLU338 4.7 63.0 1.0 CG J:LYS148 4.7 82.5 1.0 O D:ARG339 4.7 57.7 1.0 C D:ARG339 4.9 57.7 1.0 N D:ARG339 4.9 57.7 1.0 CA D:LYS340 4.9 74.2 1.0 N D:LYS340 4.9 74.2 1.0

Zinc binding site 3 out of 4 in the APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn3 b:68.3 occ:1.00 SG F:CYS346 2.0 49.3 1.0 SG F:CYS343 2.1 68.9 1.0 SG F:CYS199 2.2 54.6 1.0 SG F:CYS202 2.2 32.8 1.0 CB F:CYS343 2.8 68.9 1.0 CB F:CYS346 3.1 49.3 1.0 CB F:CYS199 3.3 54.6 1.0 N F:CYS346 3.4 53.0 1.0 CB F:CYS202 3.6 32.8 1.0 N F:CYS202 3.6 50.5 1.0 CA F:CYS346 3.8 53.0 1.0 N F:CYS199 3.9 56.6 1.0 CA F:CYS202 4.0 50.5 1.0 CA F:CYS199 4.2 56.6 1.0 CA F:CYS343 4.3 69.0 1.0 CB F:GLU201 4.3 65.0 1.0 CB F:ALA345 4.6 57.5 1.0 C F:CYS346 4.6 53.0 1.0 C F:ALA345 4.6 76.9 1.0 C F:GLU201 4.6 56.5 1.0 C F:CYS199 4.7 56.6 1.0 O F:LYS340 4.8 66.5 1.0 C F:CYS343 4.9 69.0 1.0 CA F:GLU201 4.9 56.5 1.0 CG F:ARG339 4.9 54.7 1.0 CA F:ALA345 4.9 76.9 1.0 O F:CYS199 5.0 56.6 1.0 N F:SER347 5.0 69.5 1.0

Zinc binding site 4 out of 4 in the APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn4 b:68.3 occ:1.00 CD H:LYS340 2.9 66.3 1.0 NZ H:LYS340 3.2 66.3 1.0 CB H:SER373 3.3 74.6 1.0 CE H:LYS340 3.5 66.3 1.0 O H:SER373 3.6 74.5 1.0 CA H:SER373 4.0 74.5 1.0 OG H:SER373 4.2 74.6 1.0 CG H:LYS340 4.2 66.3 1.0 C H:SER373 4.3 74.5 1.0 CD H:PRO344 4.3 98.9 1.0 O H:GLU201 4.5 77.9 1.0 CB H:LYS340 4.6 66.3 1.0 O H:CYS202 4.6 64.6 1.0 OE2 H:GLU205 4.9 90.9 1.0 CA H:CYS343 5.0 94.2 1.0

H.Walden, M.S.Podgorski, D.T.Huang, D.W.Miller, R.J.Howard, D.L.Minor, J.M.Holton, B.A.Schulman. The Structure of the APPBP1-UBA3-NEDD8-Atp Complex Reveals the Basis For Selective Ubiquitin-Like Protein Activation By An E1. Mol.Cell V. 12 1427 2003.
ISSN: ISSN 1097-2765
PubMed: 14690597
DOI: 10.1016/S1097-2765(03)00452-0