Zinc in PDB 8bdy: Crystal Structure of TRIM33 Alpha Phd-Bromo Domain in Complex with 9

All present enzymatic activity of Crystal Structure of TRIM33 Alpha Phd-Bromo Domain in Complex with 9:
2.3.2.27;

The structure of Crystal Structure of TRIM33 Alpha Phd-Bromo Domain in Complex with 9, PDB code: 8bdy was solved by G.Tassone, C.Pozzi, T.Palomba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.25 / 3.05
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	79.965, 79.965, 135.497, 90, 90, 120
R / Rfree (%)	22.9 / 33.4

The structure of Crystal Structure of TRIM33 Alpha Phd-Bromo Domain in Complex with 9 also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Crystal Structure of TRIM33 Alpha Phd-Bromo Domain in Complex with 9 (pdb code 8bdy). 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 TRIM33 Alpha Phd-Bromo Domain in Complex with 9, PDB code: 8bdy:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of TRIM33 Alpha Phd-Bromo Domain in Complex with 9


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 TRIM33 Alpha Phd-Bromo Domain in Complex with 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1103 b:176.2 occ:1.00 SG A:CYS905 2.3 77.5 1.0 SG A:CYS928 2.3 80.3 1.0 SG A:CYS902 2.3 83.0 1.0 SG A:CYS931 2.4 71.1 1.0 CB A:CYS902 3.1 75.3 1.0 CB A:CYS905 3.1 78.8 1.0 CB A:CYS931 3.5 61.9 1.0 CB A:CYS928 3.8 73.2 1.0 N A:CYS905 4.1 82.0 1.0 CA A:CYS905 4.2 88.5 1.0 N A:CYS931 4.2 86.3 1.0 N A:CYS928 4.4 83.2 1.0 CA A:CYS931 4.5 75.0 1.0 CA A:CYS928 4.5 77.4 1.0 CA A:CYS902 4.6 77.2 1.0 O A:CYS928 4.6 80.3 1.0 C A:LYS904 4.7 72.5 1.0 C A:CYS905 4.8 93.4 1.0 CB A:LYS907 4.8 87.1 1.0 CB A:PHE930 4.9 63.5 1.0 C A:CYS928 4.9 81.2 1.0 O A:CYS905 4.9 100.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of TRIM33 Alpha Phd-Bromo Domain in Complex with 9


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 TRIM33 Alpha Phd-Bromo Domain in Complex with 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1104 b:116.9 occ:1.00 SG A:CYS893 2.1 60.1 1.0 SG A:CYS890 2.4 60.9 1.0 ND1 A:HIS910 2.5 93.8 1.0 SG A:CYS913 2.5 58.2 1.0 CB A:CYS893 3.2 58.3 1.0 CB A:CYS913 3.3 56.1 1.0 CG A:HIS910 3.3 87.5 1.0 CB A:CYS890 3.3 75.6 1.0 CB A:HIS910 3.3 79.4 1.0 CE1 A:HIS910 3.5 91.3 1.0 N A:HIS910 3.9 66.1 1.0 N A:CYS893 4.1 84.4 1.0 CA A:CYS893 4.2 69.1 1.0 CA A:HIS910 4.2 69.9 1.0 O A:ASN895 4.4 86.6 1.0 CD2 A:HIS910 4.5 96.9 1.0 NE2 A:HIS910 4.6 97.0 1.0 CA A:CYS913 4.7 57.8 1.0 CA A:CYS890 4.7 78.2 1.0 C A:CYS893 4.9 70.4 1.0 CD2 A:LEU899 4.9 71.4 1.0 N A:GLN894 5.0 78.9 1.0

T.Palomba, G.Tassone, C.Vacca, M.Bartalucci, A.Valeri, C.Pozzi, S.Cross, L.Siragusa, J.Desantis. Exploiting Eliot For Scaffold-Repurposing Opportunities: TRIM33 A Possible Novel E3 Ligase to Expand the Toolbox For Protac Design. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 36430693
DOI: 10.3390/IJMS232214218