Zinc in PDB 8aw3: Cryo-Em Structure of the TBADAT2/3 Deaminase in Complex with Trna

The binding sites of Zinc atom in the Cryo-Em Structure of the TBADAT2/3 Deaminase in Complex with Trna (pdb code 8aw3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of the TBADAT2/3 Deaminase in Complex with Trna, PDB code: 8aw3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of the TBADAT2/3 Deaminase in Complex with Trna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the TBADAT2/3 Deaminase in Complex with Trna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Zn501 b:70.7 occ:1.00 ND1 2:HIS90 2.3 52.2 1.0 SG 2:CYS136 2.3 52.1 1.0 SG 2:CYS139 2.3 49.7 1.0 CG 2:HIS90 3.1 52.2 1.0 CB 2:CYS136 3.2 52.1 1.0 CE1 2:HIS90 3.2 52.2 1.0 OE1 2:GLU92 3.3 54.8 1.0 N 2:CYS136 3.3 52.1 1.0 CB 2:HIS90 3.5 52.2 1.0 N4 1:C34 3.5 54.1 1.0 CB 2:CYS139 3.5 49.7 1.0 C4 1:C34 3.8 54.1 1.0 N3 1:C34 3.8 54.1 1.0 CA 2:CYS136 3.8 52.1 1.0 CD 2:GLU92 4.0 54.8 1.0 NE2 2:HIS90 4.2 52.2 1.0 CD2 2:HIS90 4.2 52.2 1.0 N 2:CYS139 4.4 49.7 1.0 OE2 2:GLU92 4.4 54.8 1.0 C 2:PRO135 4.4 48.1 1.0 CA 2:PRO135 4.5 48.1 1.0 CA 2:CYS139 4.6 49.7 1.0 C2 1:C34 4.6 54.1 1.0 C 2:CYS136 4.6 52.1 1.0 C5 1:C34 4.7 54.1 1.0 O 2:CYS136 4.7 52.1 1.0 CA 2:HIS90 5.0 52.2 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of the TBADAT2/3 Deaminase in Complex with Trna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the TBADAT2/3 Deaminase in Complex with Trna within 5.0Å range: probe atom residue distance (Å) B Occ 3:Zn501 b:79.2 occ:1.00 OH 3:TYR236 1.9 50.6 1.0 SG 3:CYS294 2.3 55.9 1.0 ND1 3:HIS252 2.3 55.6 1.0 SG 3:CYS291 2.3 52.5 1.0 CZ 3:TYR236 3.2 50.6 1.0 CG 3:HIS252 3.2 55.6 1.0 CE1 3:HIS252 3.3 55.6 1.0 CB 3:CYS294 3.4 55.9 1.0 CB 3:HIS252 3.5 55.6 1.0 N 3:CYS294 3.5 55.9 1.0 CB 3:CYS291 3.6 52.5 1.0 N 3:CYS291 3.9 52.5 1.0 CE1 3:TYR236 3.9 50.6 1.0 CE 3:MET293 4.0 57.2 1.0 CA 3:CYS294 4.0 55.9 1.0 CE2 3:TYR236 4.1 50.6 1.0 CA 3:CYS291 4.2 52.5 1.0 CB 3:MET293 4.3 57.2 1.0 NE2 3:HIS252 4.4 55.6 1.0 CD2 3:HIS252 4.4 55.6 1.0 C 3:MET293 4.5 57.2 1.0 C 3:CYS291 4.7 52.5 1.0 N 3:MET293 4.8 57.2 1.0 CA 3:MET293 4.8 57.2 1.0 O 3:CYS291 4.9 52.5 1.0 CA 3:HIS252 5.0 55.6 1.0 C 3:PRO290 5.0 52.2 1.0 CG 3:MET293 5.0 57.2 1.0

L.G.Dolce, A.A.Zimmer, L.Tengo, F.Weis, M.A.T.Rubio, J.D.Alfonzo, E.Kowalinski. Structural Basis For Sequence-Independent Substrate Selection By Eukaryotic Wobble Base Trna Deaminase ADAT2/3 Nat Commun V. 13 6737 2022.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-022-34441-Z