Zinc in PDB 7ms5: Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid

Enzymatic activity of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid

All present enzymatic activity of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid:
3.4.19.12;

Protein crystallography data

The structure of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid, PDB code: 7ms5 was solved by M.K.Mann, C.A.Zepeda-Velazquez, H.G.Alvarez, A.Dong, T.Kiyota, A.Aman, C.H.Arrowsmith, R.Al-Awar, R.J.Harding, M.Schapira, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.53 / 1.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 61.697, 84.494, 59.642, 90, 98.27, 90
R / Rfree (%) 18.2 / 21.6

Other elements in 7ms5:

The structure of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Fluorine (F) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid (pdb code 7ms5). 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 USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid, PDB code: 7ms5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7ms5

Go back to Zinc Binding Sites List in 7ms5
Zinc binding site 1 out of 2 in the Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:18.1
occ:1.00
 ND1 A:HIS232 2.1 16.5 1.0
SG A:CYS202 2.3 17.9 1.0
SG A:CYS219 2.3 15.0 1.0
SG A:CYS199 2.3 17.6 1.0
CE1 A:HIS232 3.1 18.4 1.0
CG A:HIS232 3.1 16.1 1.0
CB A:CYS199 3.3 19.5 1.0
CB A:HIS232 3.4 15.8 1.0
CB A:CYS219 3.4 14.8 1.0
CB A:CYS202 3.5 20.8 1.0
N A:CYS202 3.9 22.5 1.0
N A:CYS219 3.9 15.2 1.0
NE2 A:HIS232 4.2 17.4 1.0
CA A:CYS202 4.2 23.0 1.0
CD2 A:HIS232 4.2 17.6 1.0
CB A:ASN230 4.3 19.9 1.0
CA A:CYS219 4.3 15.0 1.0
C A:LYS201 4.4 23.5 1.0
CB A:LYS201 4.4 24.0 1.0
ND2 A:ASN230 4.5 19.0 1.0
CA A:HIS232 4.7 15.4 1.0
CA A:CYS199 4.7 19.9 1.0
CA A:LYS201 4.8 23.1 1.0
N A:HIS232 4.8 15.3 1.0
C A:CYS202 4.8 23.4 1.0
N A:LYS201 4.8 23.4 1.0
CG A:ASN230 4.9 21.0 1.0
CB A:MET204 5.0 25.5 1.0
O A:LYS201 5.0 25.4 1.0

Zinc binding site 2 out of 2 in 7ms5

Go back to Zinc Binding Sites List in 7ms5
Zinc binding site 2 out of 2 in the Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 4-(4-(4-(3,4-Difluoro-Phenyl)-Piperidin-1-Ylsulfonyl)-Phenyl)-4- Oxo-Butanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:16.8
occ:1.00
 ND1 B:HIS232 2.0 16.0 1.0
SG B:CYS202 2.3 15.6 1.0
SG B:CYS199 2.3 16.1 1.0
SG B:CYS219 2.3 14.7 1.0
CE1 B:HIS232 2.9 17.1 1.0
CG B:HIS232 3.0 15.9 1.0
CB B:CYS199 3.2 17.6 1.0
CB B:CYS219 3.3 14.4 1.0
CB B:HIS232 3.4 15.1 1.0
CB B:CYS202 3.5 19.2 1.0
N B:CYS202 3.9 21.4 1.0
N B:CYS219 3.9 14.2 1.0
NE2 B:HIS232 4.1 16.7 1.0
CB B:ASN230 4.1 17.7 1.0
CD2 B:HIS232 4.1 17.4 1.0
CA B:CYS202 4.2 20.3 1.0
CA B:CYS219 4.2 13.8 1.0
CB B:LYS201 4.3 23.1 1.0
C B:LYS201 4.4 21.3 1.0
ND2 B:ASN230 4.6 17.6 1.0
CA B:CYS199 4.6 17.3 1.0
CA B:HIS232 4.6 15.2 1.0
N B:HIS232 4.7 14.8 1.0
CA B:LYS201 4.7 22.8 1.0
N B:LYS201 4.7 19.6 1.0
C B:CYS202 4.8 22.9 1.0
CA B:ASN230 4.9 17.5 1.0
CG B:ASN230 4.9 18.5 1.0
CB B:MET204 4.9 22.0 1.0
C B:ASN230 5.0 16.4 1.0

Reference:

M.K.Mann, C.A.Zepeda-Velazquez, H.G.Alvarez, A.Dong, T.Kiyota, A.Aman, C.H.Arrowsmith, R.Al-Awar, R.J.Harding, M.Schapira. Structure Activity Relationship of Allosteric Inhibitors of USP5 To Be Published.
Page generated: Mon Jul 12 17:25:46 2021

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