Zinc in PDB 5zy9: Structural Basis For A Trna Synthetase

All present enzymatic activity of Structural Basis For A Trna Synthetase:
6.1.1.3;

The structure of Structural Basis For A Trna Synthetase, PDB code: 5zy9 was solved by J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.212, 109.633, 133.766, 90.00, 99.46, 90.00
R / Rfree (%)	16.7 / 21

The binding sites of Zinc atom in the Structural Basis For A Trna Synthetase (pdb code 5zy9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structural Basis For A Trna Synthetase, PDB code: 5zy9:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structural Basis For A Trna Synthetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis For A Trna Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:48.8 occ:1.00 ND1 C:HIS272 2.0 58.0 1.0 SG C:CYS93 2.1 20.0 1.0 NE2 C:HIS144 2.3 20.0 1.0 CB C:CYS93 2.5 20.0 1.0 CD2 C:HIS144 2.6 20.0 1.0 CG C:HIS272 2.8 61.2 1.0 CE1 C:HIS272 3.0 44.7 1.0 CB C:HIS272 3.1 33.5 1.0 CE1 C:HIS144 3.4 20.0 1.0 C9 C:2CR501 3.4 35.1 1.0 CA C:CYS93 3.6 35.2 1.0 CG C:HIS144 3.8 20.0 1.0 CD2 C:HIS272 4.0 48.5 1.0 NE2 C:HIS272 4.0 34.5 1.0 C8 C:2CR501 4.1 31.4 1.0 ND1 C:HIS144 4.1 20.0 1.0 C10 C:2CR501 4.2 32.6 1.0 N C:CYS93 4.3 41.6 1.0 CA C:HIS272 4.3 29.2 1.0 C7 C:2CR501 4.4 36.3 1.0 OD1 C:ASP142 4.6 34.5 1.0 C5 C:2CR501 4.7 34.4 1.0 OD2 C:ASP142 4.7 32.3 1.0 C11 C:2CR501 4.9 34.4 1.0 C12 C:2CR501 4.9 32.5 1.0 C C:CYS93 5.0 36.7 1.0 SD C:MET91 5.0 34.0 1.0 CB C:HIS144 5.0 20.0 1.0

Zinc binding site 2 out of 3 in the Structural Basis For A Trna Synthetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis For A Trna Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:32.4 occ:1.00 SG D:CYS93 2.0 20.0 1.0 ND1 D:HIS272 2.1 44.0 1.0 NE2 D:HIS144 2.2 20.0 1.0 CB D:CYS93 2.2 20.0 1.0 CE1 D:HIS272 2.8 39.7 1.0 CD2 D:HIS144 2.9 20.0 1.0 CG D:HIS272 3.0 35.9 1.0 CA D:CYS93 3.0 30.6 1.0 CE1 D:HIS144 3.3 20.0 1.0 CB D:HIS272 3.5 31.7 1.0 NE2 D:HIS272 3.7 33.8 1.0 N D:CYS93 3.8 34.9 1.0 CD2 D:HIS272 3.8 27.1 1.0 OD1 D:ASP142 4.0 30.9 1.0 C9 D:2CR501 4.1 32.6 1.0 CG D:HIS144 4.2 20.0 1.0 ND1 D:HIS144 4.3 20.0 1.0 C D:CYS93 4.4 34.6 1.0 CA D:HIS272 4.4 29.9 1.0 OD2 D:ASP142 4.6 35.5 1.0 CG D:ASP142 4.7 35.9 1.0 C D:ASN92 4.8 30.4 1.0 C8 D:2CR501 4.9 34.8 1.0 C7 D:2CR501 4.9 37.0 1.0 O D:CYS93 5.0 38.8 1.0

Zinc binding site 3 out of 3 in the Structural Basis For A Trna Synthetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis For A Trna Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn802 b:80.4 occ:1.00 SG E:CYS93 2.1 20.0 1.0 ND1 E:HIS272 2.2 35.4 1.0 NE2 E:HIS144 2.5 20.0 1.0 CB E:CYS93 2.6 20.0 1.0 CG E:HIS272 2.7 33.0 1.0 CE1 E:HIS272 2.8 30.7 1.0 CD2 E:HIS144 2.9 20.0 1.0 CB E:HIS272 3.2 27.9 1.0 O E:HOH930 3.3 27.2 1.0 C9 E:2CR801 3.3 30.8 1.0 CD2 E:HIS272 3.4 27.8 1.0 NE2 E:HIS272 3.4 33.1 1.0 CA E:CYS93 3.6 29.7 1.0 CE1 E:HIS144 3.6 20.0 1.0 CG E:HIS144 4.1 20.0 1.0 C8 E:2CR801 4.1 32.8 1.0 C10 E:2CR801 4.2 24.9 1.0 N E:CYS93 4.3 30.7 1.0 ND1 E:HIS144 4.4 20.0 1.0 CA E:HIS272 4.4 29.3 1.0 C7 E:2CR801 4.5 34.7 1.0 OD1 E:ASP142 4.6 36.0 1.0 OD2 E:ASP142 4.6 34.6 1.0 C5 E:2CR801 4.7 26.2 1.0 SD E:MET91 4.7 32.1 1.0 C11 E:2CR801 4.9 31.2 1.0 C E:CYS93 4.9 36.6 1.0 C12 E:2CR801 5.0 28.9 1.0

J.Zhang, J.Zhang. N/A N/A.