Zinc in PDB 1h4q: Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg), Atp and Prolinol

All present enzymatic activity of Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg), Atp and Prolinol:
6.1.1.15;

The structure of Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg), Atp and Prolinol, PDB code: 1h4q was solved by A.Yaremchuk, M.Tukalo, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20 / 3.0
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	141.290, 141.290, 237.560, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 25.4

The binding sites of Zinc atom in the Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg), Atp and Prolinol (pdb code 1h4q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg), Atp and Prolinol, PDB code: 1h4q:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg), Atp and Prolinol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg), Atp and Prolinol within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1479 b:59.6 occ:1.00 SG A:CYS432 2.3 57.6 1.0 SG A:CYS458 2.3 54.4 1.0 SG A:CYS427 2.3 59.8 1.0 SG A:CYS461 2.4 69.3 1.0 CB A:CYS432 3.1 57.4 1.0 CB A:CYS427 3.2 53.0 1.0 CB A:CYS458 3.2 53.0 1.0 CB A:CYS461 3.3 63.5 1.0 N A:CYS461 3.7 65.1 1.0 N A:CYS427 3.9 53.4 1.0 NE2 A:HIS426 3.9 47.0 1.0 CA A:CYS461 4.1 63.5 1.0 CE1 A:HIS426 4.1 45.9 1.0 CA A:CYS427 4.2 55.5 1.0 CD2 A:HIS426 4.3 49.8 1.0 NH2 A:ARG463 4.5 71.0 1.0 CA A:CYS432 4.6 60.6 1.0 ND1 A:HIS426 4.6 47.1 1.0 CA A:CYS458 4.7 56.6 1.0 CG A:HIS426 4.7 46.4 1.0 C A:ARG460 4.8 63.4 1.0 NE A:ARG463 4.8 63.0 1.0 CB A:ARG460 4.9 55.8 1.0 C A:CYS461 4.9 61.3 1.0 N A:ARG460 4.9 56.9 1.0

Zinc binding site 2 out of 2 in the Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg), Atp and Prolinol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with Trnapro(Cgg), Atp and Prolinol within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1479 b:88.0 occ:1.00 SG B:CYS427 2.3 79.2 1.0 SG B:CYS432 2.3 82.5 1.0 SG B:CYS458 2.3 88.0 1.0 SG B:CYS461 2.3 90.3 1.0 CB B:CYS427 3.2 77.7 1.0 CB B:CYS458 3.2 83.7 1.0 CB B:CYS432 3.2 79.3 1.0 CB B:CYS461 3.3 86.8 1.0 N B:CYS427 3.8 75.6 1.0 N B:CYS461 3.8 86.9 1.0 CA B:CYS461 4.1 87.0 1.0 CA B:CYS427 4.1 76.8 1.0 NE2 B:HIS426 4.2 73.5 1.0 CD2 B:HIS426 4.4 75.5 1.0 NH2 B:ARG463 4.4 98.0 0.0 CE1 B:HIS426 4.5 73.8 1.0 CA B:CYS458 4.6 82.9 1.0 CA B:CYS432 4.7 76.9 1.0 CG B:HIS426 4.8 76.5 1.0 ND1 B:HIS426 4.8 76.5 1.0 C B:ARG460 4.8 86.7 1.0 C B:CYS461 4.8 86.4 1.0 NE B:ARG463 4.8 94.7 0.0 N B:GLY462 4.8 83.3 1.0 C B:HIS426 5.0 75.8 1.0 C B:CYS458 5.0 82.0 1.0

A.Yaremchuk, M.Tukalo, M.Grotli, S.Cusack. A Succession of Substrate Induced Conformational Changes Ensures the Amino Acid Specificity of Thermus Thermophilus Prolyl-Trna Synthetase: Comparison with Histidyl-Trna Synthetase J.Mol.Biol. V. 309 989 2001.
ISSN: ISSN 0022-2836
PubMed: 11399074
DOI: 10.1006/JMBI.2001.4712