Zinc in PDB 5v6x: Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Mutant (32A Ntd) Bound to Trna(Pyl)

All present enzymatic activity of Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Mutant (32A Ntd) Bound to Trna(Pyl):
6.1.1.26;

The structure of Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Mutant (32A Ntd) Bound to Trna(Pyl), PDB code: 5v6x 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)	49.33 / 2.76
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.620, 72.620, 238.580, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 24.9

The binding sites of Zinc atom in the Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Mutant (32A Ntd) Bound to Trna(Pyl) (pdb code 5v6x). 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 Mutant (32A Ntd) Bound to Trna(Pyl), PDB code: 5v6x:
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 Mutant (32A Ntd) 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 Mutant (32A Ntd) Bound to Trna(Pyl) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn200 b:74.3 occ:1.00 ND1 A:HIS24 2.0 71.4 1.0 SG A:CYS69 2.3 79.4 1.0 SG A:CYS42 2.4 70.3 1.0 SG A:CYS72 2.4 70.9 1.0 CE1 A:HIS24 2.9 70.5 1.0 CB A:CYS69 3.0 77.2 1.0 CG A:HIS24 3.1 68.6 1.0 CB A:CYS42 3.2 77.2 1.0 CB A:HIS24 3.5 66.3 1.0 CB A:CYS72 3.7 72.4 1.0 NE2 A:HIS24 4.0 69.7 1.0 CD2 A:HIS24 4.1 67.6 1.0 CA A:HIS24 4.1 68.9 1.0 N A:CYS42 4.3 81.5 1.0 CB A:MET40 4.4 77.2 1.0 CA A:CYS42 4.4 84.4 1.0 N A:CYS72 4.4 91.2 1.0 CA A:CYS69 4.5 78.5 1.0 CA A:CYS72 4.6 86.7 1.0 CG A:MET40 4.8 77.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Mutant (32A Ntd) 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 Mutant (32A Ntd) Bound to Trna(Pyl) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn200 b:74.8 occ:1.00 ND1 B:HIS24 2.1 66.0 1.0 SG B:CYS69 2.4 76.3 1.0 SG B:CYS72 2.4 95.0 1.0 SG B:CYS42 2.4 75.7 1.0 CB B:CYS42 3.0 77.1 1.0 CE1 B:HIS24 3.0 63.7 1.0 CB B:CYS69 3.1 73.7 1.0 CG B:HIS24 3.2 62.2 1.0 CB B:HIS24 3.5 60.6 1.0 CB B:CYS72 3.6 92.6 1.0 NE2 B:HIS24 4.2 62.3 1.0 CA B:CYS42 4.2 77.8 1.0 CA B:HIS24 4.2 63.9 1.0 N B:CYS42 4.2 74.2 1.0 N B:CYS72 4.2 91.7 1.0 CD2 B:HIS24 4.3 60.7 1.0 CA B:CYS72 4.4 92.1 1.0 CB B:MET40 4.5 77.1 1.0 CA B:CYS69 4.6 78.9 1.0 N B:LYS25 5.0 65.6 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