Zinc in PDB 1yov: Insights Into the Ubiquitin Transfer Cascade From the Refined Structure of the Activating Enzyme For NEDD8

The structure of Insights Into the Ubiquitin Transfer Cascade From the Refined Structure of the Activating Enzyme For NEDD8, PDB code: 1yov was solved by H.Walden, M.S.Podgorski, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.400, 123.600, 198.200, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 28

The binding sites of Zinc atom in the Insights Into the Ubiquitin Transfer Cascade From the Refined Structure of the Activating Enzyme For NEDD8 (pdb code 1yov). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Insights Into the Ubiquitin Transfer Cascade From the Refined Structure of the Activating Enzyme For NEDD8, PDB code: 1yov:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Insights Into the Ubiquitin Transfer Cascade From the Refined Structure of the Activating Enzyme For NEDD8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Insights Into the Ubiquitin Transfer Cascade From the Refined Structure of the Activating Enzyme For NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn443 b:43.1 occ:1.00 SG B:CYS346 2.3 48.7 1.0 SG B:CYS343 2.4 54.2 1.0 SG B:CYS202 2.4 49.6 1.0 SG B:CYS199 2.5 43.9 1.0 CB B:CYS343 3.1 66.6 1.0 CB B:CYS346 3.2 57.4 1.0 CB B:CYS202 3.4 56.8 1.0 N B:CYS202 3.6 59.0 1.0 CB B:CYS199 3.7 42.8 1.0 CA B:CYS202 3.7 61.3 1.0 N B:CYS346 3.7 58.1 1.0 N B:CYS199 4.0 42.9 1.0 CA B:CYS346 4.0 62.5 1.0 CA B:CYS199 4.3 46.9 1.0 C B:GLU201 4.3 59.2 1.0 CA B:CYS343 4.6 72.0 1.0 CB B:GLU201 4.6 62.1 1.0 O B:CYS199 4.7 45.1 1.0 O B:HOH470 4.7 52.3 1.0 C B:CYS199 4.7 43.2 1.0 C B:CYS346 4.8 61.5 1.0 C B:ALA345 4.8 57.0 1.0 CB B:ALA345 4.8 56.2 1.0 CA B:GLU201 4.9 57.1 1.0 N B:GLU201 4.9 52.7 1.0

Zinc binding site 2 out of 2 in the Insights Into the Ubiquitin Transfer Cascade From the Refined Structure of the Activating Enzyme For NEDD8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Insights Into the Ubiquitin Transfer Cascade From the Refined Structure of the Activating Enzyme For NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn443 b:0.0 occ:1.00 SG D:CYS346 2.3 91.5 1.0 SG D:CYS199 2.5 67.3 1.0 SG D:CYS343 2.5 96.3 1.0 SG D:CYS202 2.5 89.0 1.0 CB D:CYS202 2.8 89.3 1.0 CB D:CYS343 3.2 99.9 1.0 CB D:CYS346 3.3 96.5 1.0 CB D:CYS199 3.4 60.3 1.0 N D:CYS202 3.5 85.4 1.0 N D:CYS199 3.7 55.3 1.0 CA D:CYS202 3.8 87.8 1.0 N D:CYS346 3.9 96.8 1.0 CA D:CYS199 4.0 58.5 1.0 CA D:CYS346 4.1 98.5 1.0 C D:CYS199 4.5 60.4 1.0 O D:CYS199 4.6 60.4 1.0 C D:GLU201 4.6 82.7 1.0 CA D:CYS343 4.7 0.7 1.0 CB D:GLU201 4.7 83.2 1.0 C D:ALA198 4.8 55.8 1.0 N D:GLU201 4.9 75.0 1.0 C D:CYS346 4.9 0.8 1.0 CB D:ALA345 4.9 93.6 1.0 C D:CYS202 4.9 89.1 1.0 O D:LYS340 4.9 0.3 1.0 CA D:GLU201 5.0 80.6 1.0

H.Walden, M.S.Podgorski, B.A.Schulman. Insights Into the Ubiquitin Transfer Cascade From the Refined Structure of the Activating Enzyme For NEDD8 Nature V. 422 330 2003.
ISSN: ISSN 0028-0836
PubMed: 12646924
DOI: 10.1038/NATURE01456