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

Protein crystallography data

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

Zinc Binding Sites:

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 3gzn

Go back to Zinc Binding Sites List in 3gzn
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 3gzn

Go back to Zinc Binding Sites List in 3gzn
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

Reference:

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
Page generated: Wed Dec 16 04:22:16 2020

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