Zinc in PDB 1r4n: APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex with Atp

The structure of APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex with Atp, PDB code: 1r4n 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 / 3.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	135.000, 197.900, 211.000, 90.00, 90.00, 90.00
R / Rfree (%)	25.1 / 29

The binding sites of Zinc atom in the APPBP1-UBA3-NEDD8, An E1-Ubiquitin-Like Protein Complex with Atp (pdb code 1r4n). 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 with Atp, PDB code: 1r4n:
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 with Atp


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 with Atp within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn1 b:71.9 occ:1.00 SG H:CYS346 2.0 63.0 1.0 SG H:CYS343 2.2 65.1 1.0 SG H:CYS199 2.2 0.0 1.0 SG H:CYS202 2.5 52.5 1.0 CB H:CYS346 2.7 63.0 1.0 CB H:CYS343 2.8 65.1 1.0 N H:CYS346 2.9 80.7 1.0 CB H:CYS199 3.3 0.0 1.0 CA H:CYS346 3.3 80.7 1.0 N H:CYS199 4.0 56.7 1.0 N H:CYS202 4.0 63.9 1.0 CB H:CYS202 4.0 52.5 1.0 C H:ALA345 4.1 72.4 1.0 CA H:CYS199 4.2 56.7 1.0 C H:CYS346 4.3 80.7 1.0 CA H:CYS343 4.3 92.6 1.0 CA H:CYS202 4.3 63.9 1.0 CB H:ALA345 4.4 83.8 1.0 CB H:GLU201 4.5 83.0 1.0 CA H:ALA345 4.6 72.4 1.0 C H:GLU201 4.7 0.5 1.0 N H:ALA345 4.7 72.4 1.0 C H:CYS343 4.8 92.6 1.0 O H:CYS346 4.8 80.7 1.0 C H:CYS199 4.8 56.7 1.0 N H:SER347 4.9 88.6 1.0 O H:CYS343 4.9 92.6 1.0

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


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 with Atp within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn2 b:71.9 occ:1.00 CB D:GLU338 2.9 0.2 1.0 NZ J:LYS148 3.2 99.1 1.0 CD J:LYS148 3.3 99.1 1.0 CG D:GLU338 3.5 0.2 1.0 CE J:LYS148 3.5 99.1 1.0 OE1 D:GLU338 3.6 0.2 1.0 CD D:GLU338 4.0 0.2 1.0 CA D:GLU338 4.3 83.5 1.0 CG J:LYS148 4.4 99.1 1.0 C D:GLU338 4.5 83.5 1.0 O D:GLU338 4.8 83.5 1.0 O D:ARG339 4.8 68.0 1.0 N D:ARG339 4.9 68.0 1.0 CA J:LYS148 5.0 88.9 1.0 C D:ARG339 5.0 68.0 1.0

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


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 with Atp within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn3 b:71.9 occ:1.00 SG F:CYS199 2.0 67.8 1.0 SG F:CYS343 2.0 71.3 1.0 SG F:CYS346 2.1 48.4 1.0 SG F:CYS202 2.3 31.7 1.0 CB F:CYS343 2.9 71.3 1.0 CB F:CYS346 3.0 48.4 1.0 CB F:CYS199 3.1 67.8 1.0 N F:CYS346 3.3 82.2 1.0 N F:CYS202 3.6 91.0 1.0 CB F:CYS202 3.7 31.7 1.0 CA F:CYS346 3.7 82.2 1.0 N F:CYS199 3.8 51.9 1.0 CA F:CYS202 4.0 91.0 1.0 CA F:CYS199 4.0 51.9 1.0 CB F:GLU201 4.3 89.9 1.0 CA F:CYS343 4.3 80.0 1.0 C F:GLU201 4.3 89.9 1.0 C F:ALA345 4.4 60.6 1.0 CB F:ALA345 4.5 51.9 1.0 C F:CYS199 4.6 51.9 1.0 C F:CYS346 4.6 82.2 1.0 N F:GLU201 4.7 89.9 1.0 CA F:GLU201 4.7 89.9 1.0 CA F:ALA345 4.8 60.6 1.0 N F:ALA345 4.9 60.6 1.0 C F:CYS343 4.9 80.0 1.0

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


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 with Atp within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn4 b:71.9 occ:1.00 CB H:SER373 2.7 0.2 1.0 O H:SER373 2.8 58.8 1.0 CA H:SER373 3.0 58.8 1.0 NZ H:LYS340 3.3 85.7 1.0 C H:SER373 3.3 58.8 1.0 CD H:LYS340 4.0 85.7 1.0 OG H:SER373 4.0 0.2 1.0 CE H:LYS340 4.1 85.7 1.0 O H:GLU201 4.2 0.5 1.0 N H:SER373 4.4 58.8 1.0 CD H:PRO344 4.4 1.0 1.0 OE2 H:GLU205 4.6 1.0 1.0 O H:CYS202 4.6 63.9 1.0 N H:LEU374 4.6 86.9 1.0 CG H:PRO344 4.7 1.0 1.0 O H:ALA372 4.7 0.5 1.0 C H:ALA372 5.0 0.5 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