Zinc in PDB 5ud5: Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Bound to Trna(Pyl)

All present enzymatic activity of Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Bound to Trna(Pyl):
6.1.1.26;

The structure of Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Bound to Trna(Pyl), PDB code: 5ud5 was solved by T.Suzuki, D.Soll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.22 / 2.35
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.280, 72.280, 238.970, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 24.2

The binding sites of Zinc atom in the Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Bound to Trna(Pyl) (pdb code 5ud5). 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 Trna Binding Domain of Pyrrolysyl-Trna Synthetase Bound to Trna(Pyl), PDB code: 5ud5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Bound to Trna(Pyl)


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 Trna Binding Domain of Pyrrolysyl-Trna Synthetase Bound to Trna(Pyl) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn200 b:70.0 occ:1.00 ND1 A:HIS24 2.0 68.2 1.0 SG A:CYS72 2.3 80.6 1.0 SG A:CYS42 2.4 73.7 1.0 SG A:CYS69 2.4 71.7 1.0 CE1 A:HIS24 3.0 68.6 1.0 CB A:CYS69 3.0 71.4 1.0 CG A:HIS24 3.1 67.5 1.0 CB A:CYS42 3.1 75.3 1.0 CB A:HIS24 3.5 67.4 1.0 CB A:CYS72 3.6 83.0 1.0 NE2 A:HIS24 4.1 67.9 1.0 CA A:HIS24 4.1 67.2 1.0 N A:CYS72 4.2 86.2 1.0 CD2 A:HIS24 4.2 66.9 1.0 N A:CYS42 4.3 75.1 1.0 CA A:CYS42 4.3 76.7 1.0 CA A:CYS72 4.4 86.2 1.0 CB A:MET40 4.4 73.3 1.0 CA A:CYS69 4.5 73.2 1.0 CG A:MET40 4.9 73.5 1.0 N A:LYS25 4.9 67.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Bound to Trna(Pyl)


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 Trna Binding Domain of Pyrrolysyl-Trna Synthetase Bound to Trna(Pyl) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn200 b:71.0 occ:1.00 ND1 B:HIS24 2.1 68.8 1.0 SG B:CYS72 2.3 86.4 1.0 SG B:CYS42 2.3 76.6 1.0 SG B:CYS69 2.3 79.9 1.0 CB B:CYS42 2.9 76.6 1.0 CE1 B:HIS24 3.0 70.5 1.0 CG B:HIS24 3.1 68.5 1.0 CB B:CYS69 3.1 79.9 1.0 CB B:CYS72 3.5 86.7 1.0 CB B:HIS24 3.5 66.7 1.0 N B:CYS72 4.0 88.8 1.0 NE2 B:HIS24 4.1 69.4 1.0 CA B:CYS42 4.1 77.2 1.0 N B:CYS42 4.1 76.6 1.0 CA B:HIS24 4.2 66.6 1.0 CD2 B:HIS24 4.2 68.0 1.0 CA B:CYS72 4.3 87.8 1.0 CB B:MET40 4.5 77.8 1.0 CA B:CYS69 4.6 82.0 1.0 N B:LYS25 5.0 63.5 1.0 C B:ARG71 5.0 91.6 1.0 CG B:MET40 5.0 77.6 1.0

T.Suzuki, C.Miller, L.T.Guo, J.M.L.Ho, D.I.Bryson, Y.S.Wang, D.R.Liu, D.Soll. Crystal Structures Reveal An Elusive Functional Domain of Pyrrolysyl-Trna Synthetase. Nat. Chem. Biol. V. 13 1261 2017.
ISSN: ESSN 1552-4469
PubMed: 29035363
DOI: 10.1038/NCHEMBIO.2497