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Chlorine in PDB 6s0s: The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Ribostamycin B and 2-Oxoglutarate

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

All present enzymatic activity of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Ribostamycin B 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, Ribostamycin B and 2-Oxoglutarate, PDB code: 6s0s 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) 47.27 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.083, 184.582, 110.333, 90.00, 94.97, 90.00
R / Rfree (%) 17.3 / 20.4

Other elements in 6s0s:

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

Nickel (Ni) 6 atoms

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, Ribostamycin B and 2-Oxoglutarate (pdb code 6s0s). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Ribostamycin B and 2-Oxoglutarate, PDB code: 6s0s:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6s0s

Go back to Chlorine Binding Sites List in 6s0s
Chlorine binding site 1 out of 3 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Ribostamycin B 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, Ribostamycin B and 2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl304

b:58.0
occ:1.00
 OD2 B:ASP93 3.5 55.6 1.0
N B:ASP93 3.5 26.6 1.0
CD B:PRO92 3.6 26.7 1.0
CG B:ASP93 3.8 46.9 1.0
CB B:ASP93 3.8 36.4 1.0
N B:PRO92 3.8 25.7 1.0
CB B:PHE91 4.1 25.9 1.0
CG B:PRO92 4.2 27.2 1.0
CA B:ASP93 4.3 29.2 1.0
CD1 B:LEU49 4.3 30.1 1.0
C B:PHE91 4.3 24.9 1.0
CB B:PRO92 4.3 25.8 1.0
CA B:PHE91 4.4 26.8 1.0
C B:PRO92 4.4 25.2 1.0
CA B:PRO92 4.4 25.1 1.0
OD1 B:ASP93 4.6 48.8 1.0
CD1 B:PHE91 4.7 27.0 1.0
CD2 B:LEU49 4.7 33.8 1.0
CG B:PHE91 4.8 25.7 1.0

Chlorine binding site 2 out of 3 in 6s0s

Go back to Chlorine Binding Sites List in 6s0s
Chlorine binding site 2 out of 3 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Ribostamycin B 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, Ribostamycin B and 2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl304

b:63.2
occ:1.00
 N C:ALA189 3.1 36.1 1.0
O F:HOH454 3.2 24.7 1.0
CB C:ALA189 3.2 39.9 1.0
O C:HOH463 3.3 34.2 1.0
CB C:LEU187 3.6 36.6 1.0
CG C:PRO188 3.6 34.2 1.0
CD C:PRO188 3.7 34.2 1.0
N C:PRO188 3.7 32.6 1.0
CB F:PRO76 3.7 33.0 1.0
CA C:ALA189 3.7 37.8 1.0
C C:LEU187 3.9 34.3 1.0
O F:HOH485 4.1 37.4 1.0
C C:PRO188 4.2 34.5 1.0
CA C:LEU187 4.3 34.6 1.0
CA C:PRO188 4.3 32.7 1.0
CA F:PRO76 4.4 31.0 1.0
O C:LEU187 4.5 32.7 1.0
CB C:PRO188 4.5 33.0 1.0
N C:GLU190 4.5 37.3 1.0
CG C:LEU187 4.5 39.9 1.0
CG F:PRO76 4.6 33.7 1.0
N F:GLY77 4.6 29.8 1.0
C C:ALA189 4.6 36.4 1.0
CD1 C:LEU187 4.7 43.5 1.0
CD2 C:LEU187 4.7 41.0 1.0
C F:PRO76 4.9 29.2 1.0

Chlorine binding site 3 out of 3 in 6s0s

Go back to Chlorine Binding Sites List in 6s0s
Chlorine binding site 3 out of 3 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Ribostamycin B and 2-Oxoglutarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Ribostamycin B and 2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl304

b:41.5
occ:1.00
 N E:GLY77 3.1 40.8 1.0
CA E:GLY77 3.8 41.6 1.0
CA E:PRO76 3.8 40.7 1.0
C E:PRO76 3.9 41.2 1.0
CB E:PRO76 4.0 41.6 1.0
CG2 E:THR72 4.3 42.2 1.0
CD1 E:LEU123 4.8 38.4 1.0
CG2 E:VAL79 4.9 42.9 1.0
C E:GLY77 4.9 41.6 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 Jul 29 14:45:58 2024

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