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

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