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Zinc in PDB 2y6e: Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain

Enzymatic activity of Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain

All present enzymatic activity of Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain:
3.1.2.15;

Protein crystallography data

The structure of Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain, PDB code: 2y6e was solved by M.P.A.Luna-Vargas, A.C.Faesen, W.J.Van Dijk, M.Rape, A.Fish, T.K.Sixma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.59 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.500, 151.030, 178.670, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.04

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain (pdb code 2y6e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain, PDB code: 2y6e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2y6e

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Zinc binding site 1 out of 6 in the Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1000

b:0.7
occ:1.00
 SG A:CYS799 2.2 0.7 1.0
SG A:CYS464 2.2 0.2 1.0
SG A:CYS461 2.5 0.5 1.0
SG A:CYS802 2.5 0.9 1.0
CB A:CYS461 3.3 98.4 1.0
CB A:CYS464 3.4 0.2 1.0
CB A:CYS802 3.6 0.7 1.0
CB A:CYS799 3.6 0.8 1.0
N A:CYS464 3.8 0.2 1.0
N A:CYS802 3.8 0.4 1.0
CA A:CYS464 4.2 0.9 1.0
CB A:ASN801 4.2 0.3 1.0
CA A:CYS802 4.3 0.2 1.0
C A:ASN801 4.6 0.8 1.0
NE2 A:GLN806 4.7 0.8 1.0
CB A:GLU463 4.7 0.7 1.0
CA A:CYS461 4.8 95.7 1.0
CA A:ASN801 4.8 0.1 1.0
N A:ASN801 4.8 0.2 1.0
CB A:LYS466 4.9 99.3 1.0
C A:CYS464 4.9 1.0 1.0
CA A:CYS799 4.9 0.8 1.0
C A:GLU463 4.9 0.7 1.0
CG A:GLN806 5.0 0.6 1.0

Zinc binding site 2 out of 6 in 2y6e

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Zinc binding site 2 out of 6 in the Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1000

b:88.8
occ:1.00
 SG B:CYS799 2.2 0.1 1.0
SG B:CYS464 2.2 80.6 1.0
SG B:CYS461 2.5 81.0 1.0
SG B:CYS802 2.6 0.3 1.0
CB B:CYS461 3.2 74.7 1.0
CB B:CYS464 3.4 79.2 1.0
CB B:CYS799 3.5 0.4 1.0
CB B:CYS802 3.5 0.6 1.0
N B:CYS802 3.8 0.5 1.0
N B:CYS464 3.9 79.2 1.0
CB B:ASN801 4.1 98.3 1.0
CA B:CYS802 4.2 0.6 1.0
CA B:CYS464 4.2 78.7 1.0
C B:ASN801 4.6 0.8 1.0
CA B:CYS461 4.7 73.0 1.0
CB B:LYS466 4.7 71.1 1.0
CA B:ASN801 4.8 99.7 1.0
CA B:CYS799 4.8 0.6 1.0
N B:ASN801 4.9 0.4 1.0
CG B:GLN806 4.9 0.4 1.0
C B:CYS464 4.9 77.8 1.0
CB B:GLU463 4.9 84.4 1.0

Zinc binding site 3 out of 6 in 2y6e

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Zinc binding site 3 out of 6 in the Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1000

b:0.2
occ:1.00
 SG C:CYS799 2.2 1.0 1.0
SG C:CYS464 2.2 83.0 1.0
SG C:CYS461 2.5 82.4 1.0
SG C:CYS802 2.5 0.6 1.0
CB C:CYS799 3.3 0.7 1.0
CB C:CYS461 3.3 76.0 1.0
CB C:CYS464 3.4 81.5 1.0
CB C:CYS802 3.6 0.2 1.0
N C:CYS802 3.8 0.4 1.0
N C:CYS464 3.8 81.6 1.0
CA C:CYS464 4.2 81.3 1.0
CA C:CYS802 4.3 0.0 1.0
CB C:ASN801 4.4 0.0 1.0
C C:ASN801 4.6 0.3 1.0
CA C:CYS799 4.7 0.4 1.0
CB C:GLU463 4.7 86.5 1.0
CA C:CYS461 4.8 74.2 1.0
CA C:ASN801 4.9 0.4 1.0
N C:ASN801 4.9 0.2 1.0
C C:GLU463 4.9 87.5 1.0
OE1 C:GLN806 4.9 0.3 1.0
C C:CYS464 5.0 82.3 1.0
CD C:GLN806 5.0 0.6 1.0
NE2 C:GLN806 5.0 0.5 1.0

Zinc binding site 4 out of 6 in 2y6e

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Zinc binding site 4 out of 6 in the Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1000

b:0.0
occ:1.00
 CB D:CYS802 2.8 0.7 1.0
SG D:CYS799 3.1 0.2 1.0
CB D:CYS461 3.2 0.2 1.0
SG D:CYS802 3.4 0.9 1.0
SG D:CYS464 3.6 0.3 1.0
CB D:CYS799 3.9 0.2 1.0
N D:CYS464 3.9 0.9 1.0
CB D:GLU463 4.1 0.8 1.0
CA D:CYS802 4.1 0.5 1.0
N D:GLU463 4.2 0.1 1.0
CA D:CYS461 4.2 0.8 1.0
O D:LYS804 4.3 0.4 1.0
SG D:CYS461 4.4 0.8 1.0
N D:CYS802 4.4 0.3 1.0
CB D:CYS464 4.5 0.8 1.0
CD D:PRO462 4.5 0.7 1.0
CA D:GLU463 4.5 0.8 1.0
C D:CYS461 4.6 0.2 1.0
N D:PRO462 4.6 0.4 1.0
C D:GLU463 4.7 1.0 1.0
CA D:CYS464 4.8 0.4 1.0
C D:CYS802 4.9 0.4 1.0

Zinc binding site 5 out of 6 in 2y6e

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Zinc binding site 5 out of 6 in the Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1000

b:0.2
occ:1.00
 SG E:CYS461 2.3 0.1 1.0
CB E:CYS464 2.6 0.8 1.0
SG E:CYS464 3.1 0.2 1.0
CB E:CYS461 3.5 0.5 1.0
CA E:CYS464 4.0 0.1 1.0
N E:CYS464 4.4 0.5 1.0
O E:PRO462 4.5 0.9 1.0
CB E:LYS466 4.9 99.5 1.0
C E:CYS464 4.9 0.7 1.0
CA E:CYS461 4.9 99.7 1.0

Zinc binding site 6 out of 6 in 2y6e

Go back to Zinc Binding Sites List in 2y6e
Zinc binding site 6 out of 6 in the Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the D1D2 Domain of USP4, the Conserved Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1000

b:99.1
occ:1.00
 SG F:CYS464 2.2 96.9 1.0
SG F:CYS461 2.5 97.3 1.0
CB F:CYS461 3.3 89.6 1.0
CB F:CYS464 3.4 95.0 1.0
N F:CYS464 3.9 95.3 1.0
CA F:CYS464 4.2 94.3 1.0
CB F:GLU463 4.6 0.4 1.0
CA F:CYS461 4.7 88.0 1.0
CB F:LYS466 4.8 82.2 1.0
C F:GLU463 5.0 0.8 1.0
C F:CYS464 5.0 95.5 1.0

Reference:

M.Clerici, M.P.A.Luna-Vargas, A.C.Faesen, T.K.Sixma. The Dusp-Ubl Domain of USP4 Enhances Its Catalytic Efficiency By Promoting Ubiquitin Exchange. Nat.Commun. V. 5 5399 2014.
ISSN: ISSN 2041-1723
PubMed: 25404403
DOI: 10.1038/NCOMMS6399
Page generated: Thu Oct 17 05:45:01 2024

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