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

Protein crystallography data

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

Other elements in 5k2m:

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

Magnesium (Mg) 9 atoms

Zinc Binding Sites:

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 5k2m

Go back to Zinc Binding Sites List in 5k2m
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 5k2m

Go back to Zinc Binding Sites List in 5k2m
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

Reference:

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
Page generated: Wed Dec 16 06:26:13 2020

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