Calcium 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:

Zinc (Zn) 2 atoms
Fluorine (F) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was 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:

Calcium binding site 1 out of 1 in 7ms5

Go back to Calcium Binding Sites List in 7ms5
Calcium binding site 1 out of 1 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 Calcium with other atoms in the Ca 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
B:Ca304

b:50.3
occ:1.00
 O B:GLU263 2.8 19.3 1.0
OD2 B:ASP265 3.1 40.8 1.0
OD1 B:ASP265 3.3 40.0 1.0
CG B:ASP265 3.4 33.5 1.0
O B:ASP264 3.5 21.4 1.0
O B:HOH426 3.7 40.4 0.5
C B:GLU263 3.9 19.4 1.0
CB B:ASP264 3.9 24.5 1.0
C B:ASP264 3.9 22.8 1.0
OD2 B:ASP264 4.2 26.8 1.0
CA B:ASP264 4.4 21.6 1.0
CG B:ASP264 4.5 25.3 1.0
CB B:ASP265 4.6 26.7 1.0
N B:ASP264 4.6 20.1 1.0
N B:ASP265 4.7 20.9 1.0
CA B:ASP265 5.0 22.3 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: Sat Jul 10 11:39:29 2021

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