Chlorine in PDB 6s0u: The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel and 2-Oxoglutarate

Enzymatic activity of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel and 2-Oxoglutarate

All present enzymatic activity of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel and 2-Oxoglutarate:
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 and 2-Oxoglutarate, PDB code: 6s0u was solved by B.Mrugala, P.J.Porebski, E.Niedzialkowska, W.Minor, T.Borowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.73 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.825, 183.691, 110.169, 90.00, 96.55, 90.00
R / Rfree (%) 19.6 / 24.4

Other elements in 6s0u:

The structure of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel and 2-Oxoglutarate also contains other interesting chemical elements:

Nickel (Ni) 6 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel and 2-Oxoglutarate (pdb code 6s0u). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel and 2-Oxoglutarate, PDB code: 6s0u:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6s0u

Go back to Chlorine Binding Sites List in 6s0u
Chlorine binding site 1 out of 2 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel and 2-Oxoglutarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel and 2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl303

b:32.9
occ:1.00
 O F:HOH492 3.0 18.4 1.0
N C:ALA189 3.1 23.3 1.0
CB C:ALA189 3.3 27.1 1.0
O C:HOH571 3.6 27.3 1.0
CB C:LEU187 3.7 23.1 1.0
O C:HOH533 3.7 37.9 1.0
N C:PRO188 3.7 21.7 1.0
CA C:ALA189 3.7 25.1 1.0
CB F:PRO76 3.7 19.7 1.0
CD C:PRO188 3.8 22.6 1.0
CG C:PRO188 3.8 24.1 1.0
C C:LEU187 3.9 20.9 1.0
C C:PRO188 4.2 22.3 1.0
O F:HOH566 4.2 22.7 1.0
CA C:LEU187 4.3 21.3 1.0
N C:GLU190 4.3 24.0 1.0
CA C:PRO188 4.4 21.7 1.0
CA F:PRO76 4.4 19.6 1.0
O C:LEU187 4.4 19.7 1.0
CB C:PRO188 4.5 23.6 1.0
C C:ALA189 4.5 24.6 1.0
CG F:PRO76 4.6 19.9 1.0
CD2 C:LEU187 4.6 25.9 1.0
CG C:LEU187 4.6 24.4 1.0
N F:GLY77 4.6 19.7 1.0
C F:PRO76 4.9 19.8 1.0
CD1 C:LEU187 4.9 27.2 1.0

Chlorine binding site 2 out of 2 in 6s0u

Go back to Chlorine Binding Sites List in 6s0u
Chlorine binding site 2 out of 2 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel and 2-Oxoglutarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel and 2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl303

b:29.2
occ:1.00
 O E:HOH549 3.0 35.4 1.0
N E:GLY77 3.1 21.9 1.0
CA E:GLY77 3.7 21.3 1.0
O E:HOH539 3.9 33.7 1.0
C E:PRO76 3.9 23.1 1.0
CA E:PRO76 3.9 23.5 1.0
CB E:PRO76 4.1 24.7 1.0
CG2 E:THR72 4.3 33.2 1.0
CD1 E:LEU123 4.6 23.6 1.0
C E:GLY77 4.9 20.3 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: Sat Dec 12 13:38:06 2020

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