Zinc in PDB 1nyr: Structure of Staphylococcus Aureus Threonyl-Trna Synthetase Complexed with Atp

All present enzymatic activity of Structure of Staphylococcus Aureus Threonyl-Trna Synthetase Complexed with Atp:
6.1.1.3;

The structure of Structure of Staphylococcus Aureus Threonyl-Trna Synthetase Complexed with Atp, PDB code: 1nyr was solved by A.Torres-Larios, R.Sankaranarayanan, B.Rees, A.C.Dock-Bregeon, D.Moras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.130, 122.521, 148.661, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 31.3

The binding sites of Zinc atom in the Structure of Staphylococcus Aureus Threonyl-Trna Synthetase Complexed with Atp (pdb code 1nyr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Staphylococcus Aureus Threonyl-Trna Synthetase Complexed with Atp, PDB code: 1nyr:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of Staphylococcus Aureus Threonyl-Trna Synthetase Complexed with Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Staphylococcus Aureus Threonyl-Trna Synthetase Complexed with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:45.2 occ:1.00 ND1 A:HIS517 1.8 41.2 1.0 OG1 A:THR1004 1.8 76.7 1.0 NE2 A:HIS387 2.1 33.4 1.0 N A:THR1004 2.4 75.6 1.0 SG A:CYS336 2.5 42.6 1.0 CA A:THR1004 2.6 75.6 1.0 CE1 A:HIS517 2.6 40.0 1.0 CB A:THR1004 2.7 75.2 1.0 CG A:HIS517 2.9 40.2 1.0 CD2 A:HIS387 3.0 35.0 1.0 CE1 A:HIS387 3.1 34.6 1.0 CB A:CYS336 3.4 39.8 1.0 CB A:HIS517 3.4 37.1 1.0 NE2 A:HIS517 3.8 37.8 1.0 CG2 A:THR1004 3.8 75.1 1.0 CD2 A:HIS517 3.9 40.7 1.0 OH A:TYR468 4.0 58.1 1.0 C A:THR1004 4.1 76.5 1.0 CA A:CYS336 4.1 38.5 1.0 N A:CYS336 4.1 39.2 1.0 CG A:HIS387 4.1 32.2 1.0 ND1 A:HIS387 4.1 31.9 1.0 CA A:HIS517 4.5 37.2 1.0 SD A:MET334 4.6 53.1 1.0 NE2 A:GLN490 4.6 46.4 1.0 CZ A:TYR468 4.7 55.9 1.0 OD1 A:ASP385 4.7 51.6 1.0 OXT A:THR1004 4.8 77.9 1.0 OD2 A:ASP385 4.8 48.5 1.0 O A:THR1004 4.9 77.0 1.0

Zinc binding site 2 out of 3 in the Structure of Staphylococcus Aureus Threonyl-Trna Synthetase Complexed with Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Staphylococcus Aureus Threonyl-Trna Synthetase Complexed with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:93.8 occ:1.00 NE2 A:HIS75 2.1 64.0 1.0 NE2 A:HIS79 2.2 56.0 1.0 NE2 A:HIS185 2.4 77.1 1.0 SG A:CYS181 2.4 84.0 1.0 CE1 A:HIS185 2.5 78.4 1.0 CB A:CYS181 2.7 82.6 1.0 CE1 A:HIS75 2.9 64.9 1.0 CD2 A:HIS79 2.9 54.4 1.0 CD2 A:HIS75 3.3 62.6 1.0 CE1 A:HIS79 3.3 54.3 1.0 O A:HOH1074 3.6 59.9 1.0 CD2 A:HIS185 3.6 75.4 1.0 ND1 A:HIS185 3.7 76.6 1.0 ND1 A:HIS75 4.1 62.3 1.0 CG A:HIS79 4.2 53.1 1.0 CA A:CYS181 4.2 82.0 1.0 CG A:HIS185 4.3 74.3 1.0 CG A:HIS75 4.3 61.4 1.0 ND1 A:HIS79 4.3 53.5 1.0 N A:GLY183 4.4 81.7 1.0 O A:GLY183 4.4 75.4 1.0 CA A:GLY183 4.5 78.0 1.0 C A:GLY183 4.7 75.7 1.0 C A:CYS181 4.7 82.4 1.0 CB A:TYR172 4.7 78.8 1.0 N A:ARG182 4.8 83.5 1.0 CG A:TYR172 5.0 77.8 1.0 N A:CYS181 5.0 80.9 1.0

Zinc binding site 3 out of 3 in the Structure of Staphylococcus Aureus Threonyl-Trna Synthetase Complexed with Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Staphylococcus Aureus Threonyl-Trna Synthetase Complexed with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2001 b:70.7 occ:1.00 SG B:CYS336 2.0 51.3 1.0 OG1 B:THR2004 2.0 1.0 1.0 ND1 B:HIS517 2.1 54.6 1.0 NE2 B:HIS387 2.2 55.2 1.0 N B:THR2004 2.3 0.1 1.0 CE1 B:HIS517 2.8 55.0 1.0 CB B:THR2004 3.0 0.5 1.0 CA B:THR2004 3.0 0.5 1.0 CE1 B:HIS387 3.0 57.5 1.0 CD2 B:HIS387 3.3 55.4 1.0 CG B:HIS517 3.3 55.7 1.0 CB B:CYS336 3.5 53.6 1.0 O B:HOH2016 3.8 36.4 1.0 CB B:HIS517 3.9 55.9 1.0 NE2 B:HIS517 4.0 54.2 1.0 CA B:CYS336 4.2 52.8 1.0 ND1 B:HIS387 4.2 56.6 1.0 CG2 B:THR2004 4.2 0.1 1.0 OD2 B:ASP385 4.2 52.5 1.0 CD2 B:HIS517 4.3 54.9 1.0 N B:CYS336 4.3 54.2 1.0 CG B:HIS387 4.4 54.4 1.0 C B:THR2004 4.4 0.6 1.0 OH B:TYR468 4.5 0.4 1.0 OD1 B:ASP385 4.7 53.5 1.0 O B:THR2004 4.7 1.0 1.0 CA B:HIS517 4.8 57.0 1.0 CZ B:TYR468 4.8 0.1 1.0 CG B:ASP385 4.9 52.1 1.0 CE2 B:TYR468 4.9 0.9 1.0

A.Torres-Larios, R.Sankaranarayanan, B.Rees, A.C.Dock-Bregeon, D.Moras. Conformational Movements and Cooperativity Upon Amino Acid, Atp and Trna Binding in Threonyl-Trna Synthetase J.Mol.Biol. V. 331 201 2003.
ISSN: ISSN 0022-2836
PubMed: 12875846
DOI: 10.1016/S0022-2836(03)00719-8