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Iodine in PDB 6s0t: The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide

Enzymatic activity of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide

All present enzymatic activity of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide:
1.14.11.37;

Protein crystallography data

The structure of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide, PDB code: 6s0t was solved by B.Mrugala, P.J.Porebski, E.Niedzialkowska, M.T.Cymborowski, W.Minor, T.Borowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.614, 186.468, 110.828, 90.00, 95.74, 90.00
R / Rfree (%) 16.9 / 20.4

Other elements in 6s0t:

The structure of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide also contains other interesting chemical elements:

Nickel (Ni) 6 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide (pdb code 6s0t). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide, PDB code: 6s0t:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 6s0t

Go back to Iodine Binding Sites List in 6s0t
Iodine binding site 1 out of 2 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I301

b:25.2
occ:1.00
 N B:ALA189 3.7 21.4 1.0
CB B:ALA189 3.9 23.8 1.0
CG B:LEU187 4.0 27.8 1.0
CD B:PRO188 4.1 20.8 1.0
CB B:PRO188 4.2 21.6 1.0
CD2 B:LEU187 4.3 29.1 1.0
CD1 B:LEU187 4.3 29.1 1.0
CA B:ALA189 4.3 22.6 1.0
N B:PRO188 4.4 20.2 1.0
CG B:PRO188 4.5 21.6 1.0
C B:PRO188 4.5 21.2 1.0
CA B:PRO188 4.6 20.6 1.0

Iodine binding site 2 out of 2 in 6s0t

Go back to Iodine Binding Sites List in 6s0t
Iodine binding site 2 out of 2 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I301

b:42.2
occ:0.50
 CG2 F:THR72 3.2 33.1 0.5
O C:HOH560 3.4 20.2 1.0
N F:GLY77 3.4 20.9 1.0
CB C:ALA189 3.5 29.3 1.0
O C:HOH603 3.8 45.5 1.0
CA F:GLY77 4.1 20.8 1.0
CA F:PRO76 4.2 22.3 1.0
CG2 F:VAL79 4.2 22.4 1.0
C F:PRO76 4.3 21.2 1.0
CB F:THR72 4.3 31.7 0.5
N C:ALA189 4.4 23.1 1.0
CA C:ALA189 4.4 25.1 1.0
CB F:THR72 4.4 31.5 0.5
OG1 F:THR72 4.5 31.1 0.5
CG1 F:VAL70 4.6 40.7 1.0
CB F:PRO76 4.7 23.6 1.0
C F:GLY77 4.9 20.0 1.0
CG2 F:THR72 4.9 33.5 0.5
OG1 F:THR72 4.9 34.2 0.5
CD1 F:LEU123 5.0 18.7 1.0
CG C:PRO188 5.0 24.5 1.0
CB F:VAL70 5.0 42.6 1.0

Reference:

B.Mrugala, A.Milaczewska, P.J.Porebski, E.Niedzialkowska, M.Guzik, W.Minor, T.Borowski. A Study on the Structure, Mechanism, and Biochemistry of Kanamycin B Dioxygenase (Kanj)-An Enzyme with A Broad Range of Substrates. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 32592631
DOI: 10.1111/FEBS.15462
Page generated: Mon Aug 12 00:14:12 2024

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