Zinc in PDB 7oje: Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa

The structure of Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa, PDB code: 7oje was solved by C.Pichlo, T.Hermanns, K.Hofmann, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.67 / 2.05
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	151.607, 151.607, 83.751, 90, 90, 120
R / Rfree (%)	18.5 / 21.9

The structure of Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa (pdb code 7oje). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa, PDB code: 7oje:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:54.8 occ:1.00 NE2 A:HIS246 2.1 51.8 1.0 NE2 A:HIS250 2.1 56.1 1.0 SG A:CYS227 2.4 54.5 1.0 SG A:CYS230 2.4 60.1 1.0 CE1 A:HIS246 2.5 50.5 1.0 CD2 A:HIS250 2.9 47.6 1.0 CB A:CYS227 3.2 61.9 1.0 CE1 A:HIS250 3.2 57.4 1.0 CB A:CYS230 3.3 63.5 1.0 CD2 A:HIS246 3.4 57.2 1.0 ND1 A:HIS246 3.8 49.3 1.0 N A:CYS230 3.8 64.3 1.0 CA A:CYS230 4.1 69.1 1.0 CG A:HIS250 4.1 56.4 1.0 CG A:HIS246 4.2 49.8 1.0 ND1 A:HIS250 4.3 56.6 1.0 CA A:CYS227 4.6 67.9 1.0 CB A:VAL229 4.7 61.8 1.0 O A:HIS246 4.7 51.0 1.0 C A:CYS230 4.8 69.2 1.0 C A:VAL229 4.8 71.9 1.0 CB A:MET232 4.9 67.5 1.0 N A:GLY231 4.9 73.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn602 b:101.1 occ:1.00 SG C:CYS227 2.3 110.2 1.0 NE2 C:HIS246 2.4 102.1 1.0 NE2 C:HIS250 2.4 88.2 1.0 SG C:CYS230 2.9 120.2 1.0 CE1 C:HIS246 2.9 102.2 1.0 CD2 C:HIS250 3.0 91.2 1.0 CB C:CYS230 3.4 116.8 1.0 CD2 C:HIS246 3.4 99.8 1.0 CE1 C:HIS250 3.6 84.6 1.0 N C:CYS230 3.7 117.1 1.0 CB C:CYS227 3.7 130.0 1.0 ND1 C:HIS246 4.0 94.6 1.0 CB C:VAL229 4.1 99.6 1.0 CA C:CYS230 4.1 123.3 1.0 CG C:HIS250 4.2 86.8 1.0 CG C:HIS246 4.3 96.7 1.0 ND1 C:HIS250 4.5 88.9 1.0 C C:VAL229 4.5 110.9 1.0 CA C:VAL229 4.7 108.1 1.0 O C:HIS246 4.7 85.0 1.0 N C:VAL229 4.8 111.3 1.0 CG2 C:VAL229 4.9 98.6 1.0 CG1 C:VAL229 4.9 93.4 1.0

T.Hermanns, C.Pichlo, U.Baumann, K.Hofmann. A Structural Basis For the Diverse Linkage Specificities Within the Zufsp Deubiquitinase Family. Nat Commun V. 13 401 2022.
ISSN: ESSN 2041-1723
PubMed: 35058438
DOI: 10.1038/S41467-022-28049-6