Atomistry » Zinc » PDB 1yjo-1z3i » 1yov
Atomistry »
  Zinc »
    PDB 1yjo-1z3i »
      1yov »

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

Protein crystallography data

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

Zinc Binding Sites:

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 1yov

Go back to Zinc Binding Sites List in 1yov
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 1yov

Go back to Zinc Binding Sites List in 1yov
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

Reference:

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
Page generated: Wed Dec 16 03:14:54 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy