Zinc in PDB 1y8r: Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex

The structure of Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex, PDB code: 1y8r was solved by L.M.Lois, C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 2.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	117.197, 215.151, 100.870, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 27.6

The structure of Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex (pdb code 1y8r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex, PDB code: 1y8r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn642 b:37.7 occ:1.00 SG B:CYS444 2.0 32.1 1.0 SG B:CYS441 2.1 32.2 1.0 SG B:CYS161 2.2 28.9 1.0 SG B:CYS158 2.2 34.3 1.0 CB B:CYS441 2.9 31.8 1.0 CB B:CYS444 3.2 34.2 1.0 CB B:CYS158 3.4 33.2 1.0 CB B:CYS161 3.5 29.9 1.0 N B:CYS444 3.6 33.4 1.0 CA B:CYS161 3.7 32.6 1.0 N B:CYS158 3.7 32.4 1.0 N B:CYS161 3.8 32.6 1.0 CA B:CYS444 3.9 34.6 1.0 CA B:CYS158 4.1 34.0 1.0 C B:GLU160 4.4 31.7 1.0 CA B:CYS441 4.4 32.5 1.0 C B:CYS444 4.7 36.3 1.0 C B:CYS158 4.7 34.6 1.0 C B:VAL443 4.7 29.7 1.0 N B:ALA445 4.8 37.8 1.0 O B:GLU160 4.8 30.8 1.0 O B:CYS158 4.8 34.6 1.0 CB B:VAL443 4.9 28.6 1.0 C B:GLU157 4.9 32.6 1.0 O B:ASN438 4.9 39.2 1.0 N B:VAL443 4.9 30.6 1.0 N B:ASN438 5.0 37.1 1.0

Zinc binding site 2 out of 2 in the Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn642 b:31.9 occ:1.00 SG E:CYS161 2.0 45.5 1.0 SG E:CYS158 2.1 17.6 1.0 SG E:CYS441 2.2 32.8 1.0 SG E:CYS444 2.3 30.2 1.0 CB E:CYS441 2.7 35.6 1.0 CB E:CYS161 3.0 48.3 1.0 CA E:CYS161 3.1 49.4 1.0 CB E:CYS444 3.4 31.9 1.0 N E:CYS161 3.5 46.0 1.0 CB E:CYS158 3.6 23.1 1.0 N E:CYS158 3.7 25.9 1.0 N E:CYS444 3.9 34.0 1.0 CA E:CYS158 4.1 25.4 1.0 CA E:CYS441 4.1 36.0 1.0 CA E:CYS444 4.2 34.0 1.0 C E:GLU160 4.3 41.7 1.0 O E:CYS158 4.4 28.4 1.0 C E:CYS161 4.5 52.6 1.0 C E:CYS158 4.5 27.2 1.0 O E:GLU160 4.7 41.5 1.0 O E:ASN438 4.7 39.1 1.0 C E:GLU157 4.8 25.9 1.0 O E:CYS161 4.9 52.9 1.0 C E:CYS444 4.9 35.8 1.0 C E:CYS441 4.9 36.0 1.0 CB E:ASN438 4.9 37.0 1.0 N E:ASN438 5.0 32.9 1.0

L.M.Lois, C.D.Lima. Structures of the Sumo E1 Provide Mechanistic Insights Into Sumo Activation and E2 Recruitment to E1 Embo J. V. 24 439 2005.
ISSN: ISSN 0261-4189
PubMed: 15660128
DOI: 10.1038/SJ.EMBOJ.7600552