Zinc in PDB 1hc7: Prolyl-Trna Synthetase From Thermus Thermophilus

All present enzymatic activity of Prolyl-Trna Synthetase From Thermus Thermophilus:
6.1.1.15;

The structure of Prolyl-Trna Synthetase From Thermus Thermophilus, PDB code: 1hc7 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)	20.0 / 2.43
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	132.300, 191.100, 125.100, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 23.4

The binding sites of Zinc atom in the Prolyl-Trna Synthetase From Thermus Thermophilus (pdb code 1hc7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Prolyl-Trna Synthetase From Thermus Thermophilus, PDB code: 1hc7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Prolyl-Trna Synthetase From Thermus Thermophilus


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn490 b:42.5 occ:1.00 SG A:CYS458 2.3 39.4 1.0 SG A:CYS432 2.3 48.1 1.0 SG A:CYS427 2.3 46.6 1.0 SG A:CYS461 2.3 48.6 1.0 CB A:CYS458 3.2 38.9 1.0 CB A:CYS432 3.2 40.9 1.0 CB A:CYS427 3.3 44.8 1.0 CB A:CYS461 3.3 43.9 1.0 N A:CYS461 3.8 43.7 1.0 N A:CYS427 3.9 42.5 1.0 NE2 A:HIS426 4.0 43.8 1.0 CA A:CYS461 4.1 44.3 1.0 CA A:CYS427 4.2 43.3 1.0 NH2 A:ARG463 4.3 55.7 1.0 CD2 A:HIS426 4.3 43.6 1.0 CE1 A:HIS426 4.4 43.1 1.0 NE A:ARG463 4.6 53.1 1.0 CA A:CYS458 4.7 39.5 1.0 CB A:ARG460 4.7 44.0 1.0 CA A:CYS432 4.7 41.3 1.0 C A:CYS461 4.8 45.2 1.0 CG A:HIS426 4.8 43.2 1.0 ND1 A:HIS426 4.9 45.1 1.0 C A:ARG460 4.9 44.0 1.0 CZ A:ARG463 4.9 56.3 1.0 N A:GLY462 4.9 45.4 1.0

Zinc binding site 2 out of 4 in the Prolyl-Trna Synthetase From Thermus Thermophilus


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn490 b:55.3 occ:1.00 SG B:CYS432 2.3 51.8 1.0 SG B:CYS458 2.3 55.8 1.0 SG B:CYS427 2.3 52.1 1.0 SG B:CYS461 2.4 59.1 1.0 CB B:CYS458 3.2 51.5 1.0 CB B:CYS432 3.2 48.8 1.0 CB B:CYS427 3.2 49.4 1.0 CB B:CYS461 3.3 55.1 1.0 N B:CYS461 3.8 54.4 1.0 NE2 B:HIS426 3.8 37.8 1.0 N B:CYS427 3.9 48.6 1.0 CD2 B:HIS426 3.9 38.2 1.0 CA B:CYS461 4.1 54.8 1.0 CA B:CYS427 4.2 50.9 1.0 CE1 B:HIS426 4.5 43.4 1.0 CA B:CYS458 4.6 52.8 1.0 NH2 B:ARG463 4.6 73.0 1.0 CA B:CYS432 4.6 49.2 1.0 CG B:HIS426 4.7 41.2 1.0 C B:CYS461 4.8 54.4 1.0 NE B:ARG463 4.8 71.0 1.0 N B:GLY462 4.9 55.0 1.0 C B:ARG460 4.9 54.7 1.0 CB B:ARG460 5.0 54.8 1.0

Zinc binding site 3 out of 4 in the Prolyl-Trna Synthetase From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Prolyl-Trna Synthetase From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn490 b:35.0 occ:1.00 SG C:CYS458 2.3 32.2 1.0 SG C:CYS427 2.3 31.4 1.0 SG C:CYS432 2.3 33.2 1.0 SG C:CYS461 2.4 37.3 1.0 CB C:CYS427 3.2 27.8 1.0 CB C:CYS458 3.2 31.1 1.0 CB C:CYS432 3.2 30.3 1.0 CB C:CYS461 3.3 29.2 1.0 N C:CYS461 3.8 34.7 1.0 N C:CYS427 3.9 27.7 1.0 NE2 C:HIS426 3.9 28.8 1.0 CA C:CYS461 4.1 34.2 1.0 NH2 C:ARG463 4.1 47.2 1.0 CA C:CYS427 4.2 29.9 1.0 CD2 C:HIS426 4.2 28.9 1.0 CE1 C:HIS426 4.4 33.8 1.0 CA C:CYS458 4.7 31.0 1.0 NE C:ARG463 4.7 49.3 1.0 CA C:CYS432 4.7 32.3 1.0 CG C:HIS426 4.8 30.0 1.0 CZ C:ARG463 4.9 49.5 1.0 C C:CYS461 4.9 34.5 1.0 C C:ARG460 4.9 36.2 1.0 ND1 C:HIS426 4.9 29.2 1.0 N C:GLY462 5.0 34.2 1.0 CB C:ARG460 5.0 37.6 1.0

Zinc binding site 4 out of 4 in the Prolyl-Trna Synthetase From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Prolyl-Trna Synthetase From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn490 b:42.5 occ:1.00 SG D:CYS458 2.3 41.9 1.0 SG D:CYS432 2.3 46.2 1.0 SG D:CYS427 2.3 42.6 1.0 SG D:CYS461 2.4 50.0 1.0 CB D:CYS427 3.2 38.0 1.0 CB D:CYS458 3.2 42.2 1.0 CB D:CYS432 3.2 39.3 1.0 CB D:CYS461 3.3 46.0 1.0 N D:CYS461 3.8 48.0 1.0 NE2 D:HIS426 3.8 29.0 1.0 N D:CYS427 3.9 36.5 1.0 CA D:CYS461 4.1 47.2 1.0 NH2 D:ARG463 4.1 60.0 1.0 CA D:CYS427 4.2 38.3 1.0 CE1 D:HIS426 4.2 34.2 1.0 CD2 D:HIS426 4.2 30.0 1.0 NE D:ARG463 4.6 56.5 1.0 CG D:ARG460 4.6 49.2 1.0 CA D:CYS458 4.7 41.8 1.0 CA D:CYS432 4.7 40.1 1.0 ND1 D:HIS426 4.7 32.5 1.0 CG D:HIS426 4.8 31.6 1.0 CB D:ARG460 4.8 48.0 1.0 CZ D:ARG463 4.8 58.7 1.0 C D:CYS461 4.8 47.0 1.0 C D:ARG460 4.9 48.2 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