Zinc in PDB 8qni: Crystal Structure of the E3 Ubiquitin Ligase Cbl-B with An Allosteric Inhibitor (Benzodiazepine Compound 25)

The structure of Crystal Structure of the E3 Ubiquitin Ligase Cbl-B with An Allosteric Inhibitor (Benzodiazepine Compound 25), PDB code: 8qni was solved by M.Schimpl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.37 / 2.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.125, 73.364, 102.741, 90, 90, 90
R / Rfree (%)	21.8 / 28.6

The structure of Crystal Structure of the E3 Ubiquitin Ligase Cbl-B with An Allosteric Inhibitor (Benzodiazepine Compound 25) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the E3 Ubiquitin Ligase Cbl-B with An Allosteric Inhibitor (Benzodiazepine Compound 25) (pdb code 8qni). 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 E3 Ubiquitin Ligase Cbl-B with An Allosteric Inhibitor (Benzodiazepine Compound 25), PDB code: 8qni:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the E3 Ubiquitin Ligase Cbl-B with An Allosteric Inhibitor (Benzodiazepine Compound 25)


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 E3 Ubiquitin Ligase Cbl-B with An Allosteric Inhibitor (Benzodiazepine Compound 25) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:67.5 occ:1.00 SG A:CYS393 2.2 75.4 1.0 SG A:CYS373 2.3 72.4 1.0 SG A:CYS396 2.4 77.6 1.0 SG A:CYS376 2.4 72.5 1.0 CB A:CYS376 3.0 69.9 1.0 CB A:CYS373 3.1 74.8 1.0 CB A:CYS396 3.4 74.6 1.0 N A:CYS376 3.4 69.4 1.0 CB A:CYS393 3.6 73.2 1.0 CA A:CYS376 3.8 69.5 1.0 OD1 A:ASN379 4.0 78.2 1.0 N A:CYS393 4.1 73.4 1.0 CA A:CYS393 4.3 73.0 1.0 N A:CYS396 4.4 73.6 1.0 CA A:CYS396 4.5 74.3 1.0 CA A:CYS373 4.5 76.2 1.0 CB A:ILE375 4.5 69.2 1.0 CB A:ASN379 4.5 72.8 1.0 C A:ILE375 4.5 69.8 1.0 CG A:ASN379 4.7 76.8 1.0 O A:CYS393 4.7 72.8 1.0 C A:CYS376 4.7 70.1 1.0 O A:CYS373 4.8 74.6 1.0 N A:ALA377 4.8 70.4 1.0 C A:CYS373 4.8 75.1 1.0 CA A:ILE375 4.8 70.0 1.0 O A:ASN379 4.8 71.5 1.0 C A:CYS393 4.9 72.9 1.0 N A:ILE375 4.9 71.2 1.0 N A:ASN379 4.9 71.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the E3 Ubiquitin Ligase Cbl-B with An Allosteric Inhibitor (Benzodiazepine Compound 25)


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 E3 Ubiquitin Ligase Cbl-B with An Allosteric Inhibitor (Benzodiazepine Compound 25) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:91.2 occ:1.00 ND1 A:HIS390 2.3 96.4 1.0 SG A:CYS411 2.5 97.4 1.0 SG A:CYS388 2.5 93.7 1.0 SG A:CYS408 2.5 94.2 1.0 CB A:CYS408 3.0 91.4 1.0 CG A:HIS390 3.1 93.8 1.0 CE1 A:HIS390 3.2 97.0 1.0 CB A:CYS411 3.4 95.4 1.0 CB A:HIS390 3.4 89.3 1.0 CB A:CYS388 3.6 90.5 1.0 N A:CYS411 3.9 93.8 1.0 CD2 A:HIS390 4.2 95.5 1.0 CA A:CYS411 4.2 95.0 1.0 NE2 A:HIS390 4.2 96.9 1.0 CA A:CYS408 4.6 90.8 1.0 CA A:HIS390 4.7 87.3 1.0 CG2 A:ILE385 4.7 86.5 1.0 CB A:PHE410 4.7 92.6 1.0 CB A:ILE385 4.8 86.0 1.0 N A:HIS390 4.8 87.7 1.0 CA A:CYS388 4.9 90.0 1.0 C A:PHE410 4.9 93.4 1.0 C A:CYS411 5.0 96.5 1.0

M.Schimpl, M.Schimpl. N/A N/A.