Zinc in PDB 3gzn: Structure of NEDD8-Activating Enzyme in Complex with NEDD8 and MLN4924

The structure of Structure of NEDD8-Activating Enzyme in Complex with NEDD8 and MLN4924, PDB code: 3gzn was solved by M.D.Sintchak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.36 / 3.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	135.030, 228.715, 229.307, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 28.7

The binding sites of Zinc atom in the Structure of NEDD8-Activating Enzyme in Complex with NEDD8 and MLN4924 (pdb code 3gzn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of NEDD8-Activating Enzyme in Complex with NEDD8 and MLN4924, PDB code: 3gzn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of NEDD8-Activating Enzyme in Complex with NEDD8 and MLN4924


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of NEDD8-Activating Enzyme in Complex with NEDD8 and MLN4924 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn465 b:56.7 occ:1.00 SG B:CYS367 2.0 61.4 1.0 SG B:CYS223 2.1 53.5 1.0 SG B:CYS364 2.3 63.8 1.0 SG B:CYS220 2.5 50.8 1.0 CB B:CYS364 3.1 65.6 1.0 CB B:CYS367 3.2 63.8 1.0 CB B:CYS223 3.5 56.0 1.0 N B:CYS223 3.6 57.1 1.0 CB B:CYS220 3.7 54.3 1.0 N B:CYS367 3.8 64.0 1.0 CA B:CYS223 3.9 56.2 1.0 N B:CYS220 4.0 56.2 1.0 CA B:CYS367 4.0 64.1 1.0 CA B:CYS220 4.3 54.9 1.0 C B:GLU222 4.5 57.4 1.0 CA B:CYS364 4.6 65.5 1.0 CB B:GLU222 4.7 57.9 1.0 CB B:ALA366 4.7 64.3 1.0 C B:CYS220 4.7 55.0 1.0 O B:CYS220 4.8 54.6 1.0 C B:CYS367 4.8 65.2 1.0 C B:ALA366 4.9 64.4 1.0 O B:LYS361 4.9 69.0 1.0 N B:SER368 4.9 66.3 1.0 CA B:GLU222 5.0 57.2 1.0

Zinc binding site 2 out of 2 in the Structure of NEDD8-Activating Enzyme in Complex with NEDD8 and MLN4924


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of NEDD8-Activating Enzyme in Complex with NEDD8 and MLN4924 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn465 b:56.6 occ:1.00 SG D:CYS367 2.0 59.6 1.0 SG D:CYS223 2.2 53.6 1.0 SG D:CYS364 2.3 60.6 1.0 SG D:CYS220 2.4 53.5 1.0 CB D:CYS367 3.2 62.2 1.0 CB D:CYS364 3.2 62.1 1.0 N D:CYS223 3.5 58.5 1.0 CB D:CYS223 3.5 57.4 1.0 CB D:CYS220 3.6 54.5 1.0 N D:CYS367 3.8 62.0 1.0 CA D:CYS223 3.9 57.7 1.0 N D:CYS220 4.0 55.6 1.0 CA D:CYS367 4.1 62.6 1.0 CA D:CYS220 4.3 55.1 1.0 CB D:GLU222 4.4 59.5 1.0 C D:GLU222 4.4 58.9 1.0 C D:CYS220 4.6 55.4 1.0 O D:CYS220 4.7 54.7 1.0 CA D:CYS364 4.7 61.8 1.0 CA D:GLU222 4.8 58.9 1.0 N D:GLU222 4.8 58.3 1.0 C D:CYS367 4.8 64.0 1.0 CB D:ALA366 4.9 61.6 1.0 C D:ALA366 4.9 61.8 1.0 CG D:ARG360 5.0 65.3 1.0

J.E.Brownell, M.D.Sintchak, J.M.Gavin, H.Liao, F.J.Bruzzese, N.J.Bump, T.A.Soucy, M.A.Milhollen, X.Yang, A.L.Burkhardt, J.Ma, H.K.Loke, T.Lingaraj, D.Wu, K.B.Hamman, J.J.Spelman, C.A.Cullis, S.P.Langston, S.Vyskocil, T.B.Sells, W.D.Mallender, I.Visiers, P.Li, C.F.Claiborne, M.Rolfe, J.B.Bolen, L.R.Dick. Substrate-Assisted Inhibition of Ubiquitin-Like Protein-Activating Enzymes: the NEDD8 E1 Inhibitor MLN4924 Forms A NEDD8-Amp Mimetic in Situ. Mol.Cell V. 37 102 2010.
ISSN: ISSN 1097-2765
PubMed: 20129059
DOI: 10.1016/J.MOLCEL.2009.12.024