Sodium 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:

Zinc

(Zn)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa, PDB code: 7oje:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 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 Sodium with other atoms in the Na 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:Na605 b:30.7 occ:1.00 O A:HOH823 2.3 28.2 1.0 O A:ARG548 2.3 25.1 1.0 O A:ARG551 2.3 25.7 1.0 O2 A:CIT601 2.4 39.7 1.0 O6 A:CIT601 2.4 32.5 1.0 O7 A:CIT601 2.5 34.7 1.0 C6 A:CIT601 3.0 41.9 1.0 C3 A:CIT601 3.2 39.0 1.0 C1 A:CIT601 3.3 46.7 1.0 C A:ARG551 3.5 27.6 1.0 C A:ARG548 3.5 34.2 1.0 C2 A:CIT601 3.7 38.7 1.0 O A:HOH716 3.9 39.0 1.0 N A:ARG551 4.0 22.6 1.0 O A:LEU549 4.0 26.0 1.0 NZ A:LYS552 4.0 25.0 1.0 O5 A:CIT601 4.0 42.6 1.0 CE A:LYS552 4.1 27.5 1.0 CA A:ARG551 4.1 24.9 1.0 C A:LEU549 4.2 26.4 1.0 CD A:LYS552 4.3 24.3 1.0 O4 A:CIT601 4.3 35.7 1.0 O1 A:CIT601 4.4 45.8 1.0 CB A:ARG551 4.4 23.7 1.0 CA A:ARG548 4.4 33.9 1.0 O A:HOH785 4.4 33.5 1.0 N A:LEU549 4.5 28.2 1.0 CA A:LEU549 4.5 31.6 1.0 C4 A:CIT601 4.6 33.8 1.0 N A:LYS552 4.6 21.2 1.0 C A:LEU550 4.7 26.0 1.0 CB A:ARG548 4.8 39.4 1.0 N A:LEU550 4.8 23.1 1.0 CA A:LYS552 4.9 24.7 1.0 CG A:LYS552 4.9 22.1 1.0 C5 A:CIT601 4.9 36.1 1.0

Sodium binding site 2 out of 3 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 Sodium with other atoms in the Na 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 A:Na606 b:34.6 occ:1.00 O A:ASN283 2.3 40.8 1.0 O A:ASN439 2.3 33.5 1.0 O A:GLY285 2.5 38.6 1.0 O A:HOH901 2.6 45.8 1.0 O A:HOH900 2.6 47.0 1.0 O A:HOH866 2.6 48.0 1.0 C A:GLY285 3.4 40.2 1.0 N A:GLY285 3.4 40.7 1.0 C A:ASN439 3.5 34.8 1.0 C A:ASN283 3.5 41.9 1.0 C A:GLN284 3.9 43.3 1.0 NH2 A:ARG436 3.9 38.0 1.0 CA A:GLY285 3.9 42.3 1.0 CA A:THR440 4.0 31.1 1.0 CA A:GLN284 4.1 41.5 1.0 N A:THR440 4.2 31.4 1.0 N A:GLN284 4.2 43.6 1.0 N A:ASN286 4.4 37.0 1.0 CB A:ASN286 4.5 36.9 1.0 CA A:ASN283 4.5 40.7 1.0 ND2 A:ASN286 4.6 39.2 1.0 CA A:ASN439 4.6 36.0 1.0 CB A:ASN439 4.6 35.0 1.0 CB A:ASN283 4.6 38.1 1.0 O A:GLN284 4.6 37.9 1.0 O A:HOH962 4.8 52.5 1.0 CG2 A:THR440 4.8 31.6 1.0 CA A:ASN286 4.8 39.1 1.0 CB A:THR440 4.9 33.6 1.0

Sodium binding site 3 out of 3 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 Sodium with other atoms in the Na binding site number 3 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:Na603 b:63.3 occ:1.00 O C:ARG548 2.1 60.0 1.0 O C:ARG551 2.3 54.7 1.0 O5 C:CIT601 2.5 61.6 1.0 O7 C:CIT601 2.5 65.0 1.0 O3 C:CIT601 2.6 69.8 1.0 C6 C:CIT601 3.2 71.7 1.0 C3 C:CIT601 3.3 64.5 1.0 C C:ARG548 3.4 66.2 1.0 C C:ARG551 3.4 56.6 1.0 C5 C:CIT601 3.6 75.9 1.0 O C:LEU549 3.8 61.2 1.0 N C:ARG551 3.8 62.0 1.0 C4 C:CIT601 3.9 67.3 1.0 CE C:LYS552 3.9 57.9 1.0 NZ C:LYS552 3.9 55.6 1.0 C C:LEU549 4.0 61.6 1.0 CA C:ARG551 4.0 57.0 1.0 CD C:LYS552 4.2 53.0 1.0 CA C:LEU549 4.2 63.5 1.0 N C:LEU549 4.3 62.7 1.0 CB C:ARG551 4.3 57.3 1.0 O6 C:CIT601 4.3 73.8 1.0 CA C:ARG548 4.3 70.0 1.0 O1 C:CIT601 4.3 62.0 1.0 C C:LEU550 4.5 54.7 1.0 N C:LYS552 4.5 58.4 1.0 C2 C:CIT601 4.6 64.7 1.0 N C:LEU550 4.6 56.3 1.0 O4 C:CIT601 4.7 80.9 1.0 CG C:LYS552 4.8 53.2 1.0 CB C:ARG548 4.8 70.5 1.0 CA C:LYS552 4.9 59.9 1.0 C1 C:CIT601 4.9 67.0 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