Zinc in PDB 5ah5: Crystal Structure of the Ternary Complex of Agrobacterium Radiobacter K84 AGNB2 Leurs-Trna-Leuams

All present enzymatic activity of Crystal Structure of the Ternary Complex of Agrobacterium Radiobacter K84 AGNB2 Leurs-Trna-Leuams:
6.1.1.4;

The structure of Crystal Structure of the Ternary Complex of Agrobacterium Radiobacter K84 AGNB2 Leurs-Trna-Leuams, PDB code: 5ah5 was solved by A.Palencia, S.Chopra, C.Virus, S.Schulwitz, B.R.Temple, S.Cusack, J.S.Reader, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.58 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	169.910, 50.320, 170.520, 90.00, 93.48, 90.00
R / Rfree (%)	19.416 / 23.732

The structure of Crystal Structure of the Ternary Complex of Agrobacterium Radiobacter K84 AGNB2 Leurs-Trna-Leuams also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Ternary Complex of Agrobacterium Radiobacter K84 AGNB2 Leurs-Trna-Leuams (pdb code 5ah5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Ternary Complex of Agrobacterium Radiobacter K84 AGNB2 Leurs-Trna-Leuams, PDB code: 5ah5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Ternary Complex of Agrobacterium Radiobacter K84 AGNB2 Leurs-Trna-Leuams


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Ternary Complex of Agrobacterium Radiobacter K84 AGNB2 Leurs-Trna-Leuams within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn900 b:73.3 occ:1.00 SG A:CYS473 2.3 52.3 1.0 SG A:CYS435 2.4 64.9 1.0 SG A:CYS432 2.4 63.6 1.0 SG A:CYS476 2.7 75.1 1.0 CB A:CYS473 3.2 51.8 1.0 CB A:CYS432 3.3 61.3 1.0 CB A:CYS435 3.4 64.5 1.0 CB A:CYS476 3.4 71.6 1.0 N A:CYS476 3.8 69.9 1.0 N A:CYS435 4.0 71.8 1.0 CA A:CYS476 4.2 70.8 1.0 CA A:CYS435 4.3 66.3 1.0 CB A:GLU434 4.5 87.8 1.0 CB A:GLN475 4.6 63.0 1.0 CA A:CYS473 4.6 55.7 1.0 CA A:CYS432 4.7 56.4 1.0 CG A:GLU434 4.8 97.5 1.0 C A:GLN475 4.9 71.7 1.0 C A:CYS476 5.0 66.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Ternary Complex of Agrobacterium Radiobacter K84 AGNB2 Leurs-Trna-Leuams


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Ternary Complex of Agrobacterium Radiobacter K84 AGNB2 Leurs-Trna-Leuams within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn900 b:63.7 occ:1.00 SG B:CYS435 2.2 57.8 1.0 SG B:CYS473 2.3 51.4 1.0 SG B:CYS432 2.4 64.6 1.0 SG B:CYS476 2.6 67.4 1.0 CB B:CYS473 3.1 46.4 1.0 CB B:CYS476 3.3 65.8 1.0 CB B:CYS435 3.4 56.3 1.0 CB B:CYS432 3.4 54.2 1.0 N B:CYS476 3.7 65.8 1.0 N B:CYS435 3.8 70.2 1.0 CA B:CYS476 4.0 65.3 1.0 CB B:GLU434 4.2 81.0 1.0 CA B:CYS435 4.3 58.2 1.0 OE1 B:GLU434 4.4 95.6 1.0 CD B:GLU434 4.5 94.1 1.0 CA B:CYS473 4.5 48.2 1.0 CB B:GLN475 4.6 61.0 1.0 C B:GLN475 4.8 69.6 1.0 CA B:CYS432 4.8 52.4 1.0 CG B:GLU434 4.8 83.9 1.0 C B:GLU434 4.9 74.2 1.0 N B:GLY477 4.9 65.2 1.0 C B:CYS476 4.9 68.4 1.0 OE2 B:GLU434 4.9 88.7 1.0 CA B:GLU434 5.0 71.7 1.0 C B:CYS473 5.0 57.9 1.0

S.Chopra, A.Palencia, C.Virus, S.Schulwitz, B.R.Temple, S.Cusack, J.Reader. Structural Characterization of Antibiotic Self-Immunity Trna Synthetase in Plant Tumour Biocontrol Agent. Nat.Commun. V. 7 12928 2016.
ISSN: ISSN 2041-1723
PubMed: 27713402
DOI: 10.1038/NCOMMS12928