Zinc in PDB 5k2m: Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa

The structure of Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa, PDB code: 5k2m was solved by A.Yoshida, T.Tomita, M.Nishiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.150, 135.099, 136.977, 90.00, 97.49, 90.00
R / Rfree (%)	18 / 22

The structure of Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa also contains other interesting chemical elements:

Magnesium

(Mg)

9 atoms

The binding sites of Zinc atom in the Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa (pdb code 5k2m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa, PDB code: 5k2m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn102 b:57.5 occ:1.00 SG E:CYS7 2.4 79.0 1.0 SG E:CYS27 2.5 92.2 1.0 SG E:CYS24 2.5 81.8 1.0 SG E:CYS4 2.5 72.4 1.0 CB E:CYS27 3.2 93.2 1.0 CB E:CYS4 3.2 71.5 1.0 CB E:CYS7 3.2 80.8 1.0 CB E:CYS24 3.2 81.9 1.0 N E:CYS7 3.7 74.9 1.0 N E:CYS27 3.9 93.0 1.0 CA E:CYS27 4.1 92.8 1.0 CA E:CYS7 4.1 79.2 1.0 CG1 E:VAL26 4.1 93.2 1.0 CB E:VAL6 4.5 76.6 1.0 CA E:CYS4 4.7 72.3 1.0 C E:CYS27 4.7 89.2 1.0 CA E:CYS24 4.7 82.8 1.0 C E:VAL6 4.8 77.0 1.0 CB E:ALA29 4.8 80.1 1.0 N E:GLY28 4.8 87.1 1.0 N E:ALA29 5.0 81.8 1.0 C E:CYS7 5.0 79.2 1.0

Zinc binding site 2 out of 2 in the Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bifunctional Lysx/Argx From Thermococcus Kodakarensis with Lysw-Gamma- Aaa within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn102 b:54.1 occ:1.00 SG F:CYS27 2.3 76.0 1.0 SG F:CYS24 2.4 77.6 1.0 SG F:CYS4 2.5 74.5 1.0 CB F:CYS7 2.7 91.7 1.0 CB F:CYS24 3.2 77.0 1.0 CB F:CYS27 3.3 76.3 1.0 CB F:CYS4 3.3 75.7 1.0 SG F:CYS7 3.7 0.2 1.0 N F:CYS27 3.8 77.3 1.0 N F:CYS7 3.9 82.2 1.0 CA F:CYS7 3.9 88.0 1.0 CA F:CYS27 4.1 76.1 1.0 CB F:ALA29 4.4 69.9 1.0 CA F:CYS24 4.6 77.4 1.0 C F:CYS27 4.7 74.2 1.0 CA F:CYS4 4.8 76.4 1.0 CB F:VAL6 4.8 71.7 1.0 CB F:VAL26 4.8 86.5 1.0 N F:ALA29 4.9 68.7 1.0 N F:GLY28 4.9 72.5 1.0 C F:VAL26 4.9 81.2 1.0 C F:CYS7 5.0 89.1 1.0 C F:VAL6 5.0 78.7 1.0

A.Yoshida, T.Tomita, H.Atomi, T.Kuzuyama, M.Nishiyama. Lysine Biosynthesis of Thermococcus Kodakarensis with the Capacity to Function As An Ornithine Biosynthetic System. J. Biol. Chem. V. 291 21630 2016.
ISSN: ESSN 1083-351X
PubMed: 27566549
DOI: 10.1074/JBC.M116.743021