Atomistry » Zinc » PDB 7mmh-7n5t » 7ms5
Atomistry »
  Zinc »
    PDB 7mmh-7n5t »
      7ms5 »

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: Wed Oct 30 07:35:55 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy