Zinc in PDB 1h4t: Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with L-Proline

All present enzymatic activity of Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with L-Proline:
6.1.1.15;

The structure of Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with L-Proline, PDB code: 1h4t 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)	15 / 2.9
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	132.570, 193.470, 125.240, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 24.3

The binding sites of Zinc atom in the Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with L-Proline (pdb code 1h4t). 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 Complexed with L-Proline, PDB code: 1h4t:
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 Complexed with L-Proline


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 L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn490 b:62.2 occ:1.00 SG A:CYS458 2.3 59.4 1.0 SG A:CYS432 2.3 54.0 1.0 SG A:CYS427 2.3 57.8 1.0 SG A:CYS461 2.3 62.3 1.0 CB A:CYS458 3.2 57.6 1.0 CB A:CYS427 3.2 51.7 1.0 CB A:CYS432 3.2 53.0 1.0 CB A:CYS461 3.2 60.1 1.0 N A:CYS461 3.7 58.8 1.0 N A:CYS427 3.8 49.6 1.0 NE2 A:HIS426 4.0 54.4 1.0 CA A:CYS461 4.1 60.0 1.0 NH2 A:ARG463 4.1 74.5 1.0 CA A:CYS427 4.2 51.1 1.0 CD2 A:HIS426 4.2 53.4 1.0 CE1 A:HIS426 4.4 53.2 1.0 NE A:ARG463 4.5 71.8 1.0 CA A:CYS458 4.6 55.7 1.0 CA A:CYS432 4.7 52.0 1.0 CG A:HIS426 4.8 52.2 1.0 CZ A:ARG463 4.8 72.4 1.0 C A:ARG460 4.8 58.5 1.0 CB A:ARG460 4.8 58.3 1.0 C A:CYS461 4.8 60.2 1.0 ND1 A:HIS426 4.9 54.8 1.0 N A:GLY462 5.0 60.9 1.0 C A:HIS426 5.0 49.4 1.0

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


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 L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn490 b:51.4 occ:1.00 SG B:CYS458 2.3 46.7 1.0 SG B:CYS432 2.3 47.7 1.0 SG B:CYS427 2.3 53.4 1.0 SG B:CYS461 2.3 56.4 1.0 CB B:CYS458 3.1 48.7 1.0 CB B:CYS432 3.2 47.6 1.0 CB B:CYS427 3.2 44.1 1.0 CB B:CYS461 3.2 53.0 1.0 N B:CYS461 3.8 51.8 1.0 N B:CYS427 3.9 43.8 1.0 NE2 B:HIS426 3.9 41.8 1.0 NH2 B:ARG463 4.0 59.4 1.0 CA B:CYS461 4.1 52.0 1.0 CA B:CYS427 4.2 46.1 1.0 CE1 B:HIS426 4.2 39.9 1.0 CD2 B:HIS426 4.3 39.8 1.0 NE B:ARG463 4.4 56.8 1.0 CA B:CYS458 4.6 51.1 1.0 CA B:CYS432 4.7 48.4 1.0 CZ B:ARG463 4.7 59.0 1.0 ND1 B:HIS426 4.8 40.9 1.0 C B:ARG460 4.8 51.9 1.0 CG B:HIS426 4.8 40.8 1.0 C B:CYS461 4.8 51.4 1.0 CB B:ARG460 4.9 51.9 1.0 N B:GLY462 4.9 50.2 1.0

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


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 Complexed with L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn490 b:57.6 occ:1.00 SG C:CYS461 2.3 65.5 1.0 SG C:CYS458 2.3 55.4 1.0 SG C:CYS427 2.3 53.3 1.0 SG C:CYS432 2.3 53.7 1.0 CB C:CYS432 3.2 52.9 1.0 CB C:CYS427 3.2 51.7 1.0 CB C:CYS458 3.2 53.3 1.0 CB C:CYS461 3.3 61.9 1.0 N C:CYS461 3.7 62.2 1.0 N C:CYS427 3.9 54.3 1.0 NH2 C:ARG463 4.0 78.7 1.0 NE2 C:HIS426 4.1 56.9 1.0 O C:HOH2105 4.1 56.6 1.0 CA C:CYS461 4.1 62.0 1.0 CD2 C:HIS426 4.2 58.5 1.0 CA C:CYS427 4.2 54.9 1.0 CA C:CYS432 4.6 53.8 1.0 NE C:ARG463 4.6 72.6 1.0 C C:ARG460 4.7 62.6 1.0 CA C:CYS458 4.7 54.3 1.0 CB C:ARG460 4.7 63.1 1.0 C C:CYS461 4.8 61.8 1.0 CE1 C:HIS426 4.8 56.9 1.0 CZ C:ARG463 4.8 76.1 1.0 CG C:HIS426 4.9 56.1 1.0 CG C:ARG460 4.9 66.5 1.0 N C:ARG460 5.0 61.6 1.0

Zinc binding site 4 out of 4 in the Prolyl-Trna Synthetase From Thermus Thermophilus Complexed with L-Proline


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 Complexed with L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn490 b:39.4 occ:1.00 SG D:CYS458 2.3 37.2 1.0 SG D:CYS432 2.3 38.4 1.0 SG D:CYS427 2.3 35.2 1.0 SG D:CYS461 2.4 42.6 1.0 CB D:CYS458 3.2 34.3 1.0 CB D:CYS427 3.2 32.6 1.0 CB D:CYS432 3.2 40.1 1.0 CB D:CYS461 3.3 42.1 1.0 N D:CYS461 3.7 40.6 1.0 N D:CYS427 3.9 34.9 1.0 NE2 D:HIS426 4.0 29.2 1.0 NH2 D:ARG463 4.0 61.1 1.0 CA D:CYS461 4.1 42.1 1.0 CE1 D:HIS426 4.1 27.4 1.0 CA D:CYS427 4.2 35.5 1.0 CD2 D:HIS426 4.5 27.9 1.0 NE D:ARG463 4.5 57.8 1.0 CA D:CYS458 4.6 34.3 1.0 ND1 D:HIS426 4.6 29.5 1.0 CB D:ARG460 4.7 36.5 1.0 CA D:CYS432 4.7 38.9 1.0 C D:ARG460 4.7 39.0 1.0 CZ D:ARG463 4.8 60.5 1.0 C D:CYS461 4.8 42.9 1.0 CG D:HIS426 4.9 27.1 1.0 N D:ARG460 5.0 35.6 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