Zinc in PDB 7ms7: Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with (5-((4-(4-Chlorophenyl)Piperidin-1-Yl)Sulfonyl)Picolinoyl) Glycine

Enzymatic activity of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with (5-((4-(4-Chlorophenyl)Piperidin-1-Yl)Sulfonyl)Picolinoyl) Glycine

All present enzymatic activity of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with (5-((4-(4-Chlorophenyl)Piperidin-1-Yl)Sulfonyl)Picolinoyl) Glycine:
3.4.19.12;

Protein crystallography data

The structure of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with (5-((4-(4-Chlorophenyl)Piperidin-1-Yl)Sulfonyl)Picolinoyl) Glycine, PDB code: 7ms7 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, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.42 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 61.556, 84.87, 59.542, 90, 98.86, 90
R / Rfree (%) 16.9 / 18.1

Other elements in 7ms7:

The structure of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with (5-((4-(4-Chlorophenyl)Piperidin-1-Yl)Sulfonyl)Picolinoyl) Glycine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with (5-((4-(4-Chlorophenyl)Piperidin-1-Yl)Sulfonyl)Picolinoyl) Glycine (pdb code 7ms7). 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 (5-((4-(4-Chlorophenyl)Piperidin-1-Yl)Sulfonyl)Picolinoyl) Glycine, PDB code: 7ms7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7ms7

Go back to Zinc Binding Sites List in 7ms7
Zinc binding site 1 out of 2 in the Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with (5-((4-(4-Chlorophenyl)Piperidin-1-Yl)Sulfonyl)Picolinoyl) Glycine


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 (5-((4-(4-Chlorophenyl)Piperidin-1-Yl)Sulfonyl)Picolinoyl) Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:16.6
occ:1.00
ND1 A:HIS232 2.0 16.4 1.0
SG A:CYS202 2.3 19.5 1.0
SG A:CYS199 2.3 15.6 1.0
SG A:CYS219 2.3 16.6 1.0
CE1 A:HIS232 3.1 17.6 1.0
CG A:HIS232 3.1 16.9 1.0
CB A:CYS199 3.2 16.3 1.0
CB A:CYS219 3.3 15.5 1.0
CB A:CYS202 3.4 20.7 1.0
CB A:HIS232 3.5 16.9 1.0
N A:CYS202 3.8 20.4 1.0
N A:CYS219 3.9 13.9 1.0
CA A:CYS202 4.1 21.1 1.0
NE2 A:HIS232 4.2 19.6 1.0
CD2 A:HIS232 4.2 18.5 1.0
CA A:CYS219 4.3 15.2 1.0
CB A:ASN230 4.3 20.2 1.0
C A:LYS201 4.3 22.3 1.0
CB A:LYS201 4.5 23.5 1.0
ND2 A:ASN230 4.5 22.7 1.0
CA A:CYS199 4.7 17.7 1.0
CA A:HIS232 4.7 15.9 1.0
C A:CYS202 4.8 23.4 1.0
CA A:LYS201 4.8 22.1 1.0
N A:HIS232 4.8 16.3 1.0
N A:LYS201 4.8 21.2 1.0
CB A:MET204 4.9 24.0 1.0
O A:LYS201 4.9 27.2 1.0
CG A:ASN230 5.0 21.9 1.0
CG A:MET204 5.0 24.9 1.0
O A:CYS202 5.0 24.5 1.0

Zinc binding site 2 out of 2 in 7ms7

Go back to Zinc Binding Sites List in 7ms7
Zinc binding site 2 out of 2 in the Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with (5-((4-(4-Chlorophenyl)Piperidin-1-Yl)Sulfonyl)Picolinoyl) Glycine


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 (5-((4-(4-Chlorophenyl)Piperidin-1-Yl)Sulfonyl)Picolinoyl) Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:14.5
occ:1.00
ND1 B:HIS232 2.0 16.1 1.0
SG B:CYS202 2.3 17.0 1.0
SG B:CYS199 2.3 13.4 1.0
SG B:CYS219 2.3 14.1 1.0
CE1 B:HIS232 3.0 16.5 1.0
CG B:HIS232 3.1 13.1 1.0
CB B:CYS199 3.2 15.2 1.0
CB B:CYS219 3.3 15.6 1.0
CB B:CYS202 3.4 16.8 1.0
CB B:HIS232 3.5 14.2 1.0
N B:CYS202 3.8 17.7 1.0
N B:CYS219 3.9 12.7 1.0
CB B:ASN230 4.1 17.8 1.0
CA B:CYS202 4.2 16.6 1.0
NE2 B:HIS232 4.2 16.4 1.0
CD2 B:HIS232 4.2 16.8 1.0
CA B:CYS219 4.3 12.8 1.0
C B:LYS201 4.3 17.8 1.0
CB B:LYS201 4.6 18.8 1.0
CA B:CYS199 4.6 14.0 1.0
ND2 B:ASN230 4.7 21.9 1.0
N B:HIS232 4.7 15.2 1.0
CA B:HIS232 4.8 13.4 1.0
CA B:LYS201 4.8 16.4 1.0
C B:CYS202 4.8 19.4 1.0
N B:LYS201 4.8 15.0 1.0
CG B:MET204 4.9 16.8 0.5
CB B:MET204 4.9 16.2 0.5
CA B:ASN230 4.9 16.8 1.0
O B:LYS201 4.9 22.1 1.0
CG B:ASN230 5.0 19.5 1.0
N B:ASN230 5.0 15.3 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: Mon Jul 12 17:25:46 2021

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