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Zinc in PDB 3ihp: Covalent Ubiquitin-USP5 Complex

Enzymatic activity of Covalent Ubiquitin-USP5 Complex

All present enzymatic activity of Covalent Ubiquitin-USP5 Complex:
3.1.2.15;

Protein crystallography data

The structure of Covalent Ubiquitin-USP5 Complex, PDB code: 3ihp was solved by J.R.Walker, G.V.Avvakumov, S.Xue, C.Butler-Cole, J.Weigelt, C.Bountra, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.90 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.295, 188.845, 207.860, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 27.6

Other elements in 3ihp:

The structure of Covalent Ubiquitin-USP5 Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Covalent Ubiquitin-USP5 Complex (pdb code 3ihp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Covalent Ubiquitin-USP5 Complex, PDB code: 3ihp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3ihp

Go back to Zinc Binding Sites List in 3ihp
Zinc binding site 1 out of 2 in the Covalent Ubiquitin-USP5 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Covalent Ubiquitin-USP5 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn836

b:85.6
occ:1.00
ND1 A:HIS232 2.0 92.3 1.0
SG A:CYS219 2.2 81.5 1.0
SG A:CYS199 2.2 81.0 1.0
SG A:CYS202 2.8 93.6 1.0
CE1 A:HIS232 2.9 95.4 1.0
CB A:CYS199 3.0 83.3 1.0
CB A:CYS219 3.1 83.5 1.0
CG A:HIS232 3.1 89.6 1.0
CB A:HIS232 3.5 85.4 1.0
CB A:CYS202 3.7 94.9 1.0
N A:CYS219 3.7 78.0 1.0
N A:CYS202 3.7 93.5 1.0
CA A:CYS219 4.0 80.5 1.0
NE2 A:HIS232 4.1 95.4 1.0
CB A:ASN230 4.1 0.4 1.0
CD2 A:HIS232 4.2 92.2 1.0
CA A:CYS202 4.2 95.5 1.0
N A:ASN230 4.5 0.8 1.0
CA A:CYS199 4.5 83.8 1.0
CG A:ASN230 4.6 0.3 1.0
N A:HIS232 4.6 86.8 1.0
CA A:HIS232 4.7 84.5 1.0
OD1 A:ASN230 4.7 0.9 1.0
CB A:MET204 4.7 0.7 1.0
CA A:ASN230 4.8 0.0 1.0
CB A:LYS201 4.8 90.7 1.0
C A:LYS201 4.8 93.5 1.0
C A:CYS202 4.9 96.4 1.0
C A:LEU218 4.9 75.2 1.0
C A:CYS219 4.9 80.9 1.0
C A:ASN230 5.0 97.7 1.0

Zinc binding site 2 out of 2 in 3ihp

Go back to Zinc Binding Sites List in 3ihp
Zinc binding site 2 out of 2 in the Covalent Ubiquitin-USP5 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Covalent Ubiquitin-USP5 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn836

b:94.8
occ:1.00
SG B:CYS199 2.0 0.3 1.0
SG B:CYS219 2.3 99.5 1.0
ND1 B:HIS232 2.3 0.2 1.0
SG B:CYS202 2.7 0.8 1.0
CB B:CYS202 3.0 0.6 1.0
CG B:HIS232 3.1 0.3 1.0
N B:CYS202 3.1 0.0 1.0
CB B:CYS199 3.2 0.1 1.0
CB B:HIS232 3.2 0.7 1.0
CE1 B:HIS232 3.3 0.9 1.0
CA B:CYS202 3.6 0.1 1.0
CB B:CYS219 3.7 0.5 1.0
N B:CYS219 3.9 93.6 1.0
CB B:LYS201 4.2 1.0 1.0
CD2 B:HIS232 4.2 0.3 1.0
C B:LYS201 4.2 0.0 1.0
NE2 B:HIS232 4.3 0.7 1.0
C B:CYS202 4.4 0.6 1.0
CA B:CYS219 4.4 96.5 1.0
CA B:LYS201 4.5 0.2 1.0
CA B:CYS199 4.6 0.7 1.0
CA B:HIS232 4.6 98.6 1.0
N B:LYS201 4.6 0.7 1.0
CB B:ASN230 4.6 0.1 1.0
N B:HIS232 4.8 0.4 1.0
O B:CYS202 4.9 0.3 1.0
O B:ASN230 4.9 0.8 1.0
C B:CYS199 4.9 0.1 1.0

Reference:

J.R.Walker, G.V.Avvakumov, S.Xue, C.Butler-Cole, J.Weigelt, C.Bountra, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon. Covalent Ubiquitin-USP5 Complex To Be Published.
Page generated: Wed Dec 16 04:26:23 2020

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