Sodium 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
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel and 2-Oxoglutarate, PDB code: 6s0u:

Sodium binding site 1 out of 1 in 6s0u

Go back to Sodium Binding Sites List in 6s0u
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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
E:Na304

b:30.4
occ:1.00
 O E:ASP18 2.4 40.3 1.0
O E:HOH441 2.4 22.7 1.0
O E:HOH420 2.4 28.3 1.0
O E:HOH471 2.4 46.3 1.0
O E:PRO16 2.4 38.3 1.0
O E:HOH447 2.4 29.8 1.0
C E:PRO16 3.2 35.2 1.0
C E:ASP18 3.5 39.7 1.0
CA E:PRO16 3.8 34.2 1.0
N E:ASP18 3.9 37.0 1.0
O E:HOH456 3.9 33.6 1.0
O E:THR15 4.0 31.9 1.0
O E:MET44 4.1 28.1 1.0
CA E:ASP18 4.1 38.0 1.0
N E:ASP17 4.2 38.0 1.0
C E:ASP17 4.2 39.8 1.0
OD2 E:ASP93 4.3 36.6 1.0
ND2 E:ASN97 4.4 27.5 1.0
OD1 E:ASP93 4.5 42.2 1.0
N E:LYS19 4.6 44.0 1.0
CB E:ASP18 4.6 36.9 1.0
CA E:ASP17 4.7 40.7 1.0
NZ E:LYS19 4.7 58.2 1.0
O E:ASP17 4.7 45.4 1.0
CG E:PRO98 4.8 35.0 1.0
OD1 E:ASN97 4.8 31.0 1.0
N E:PRO16 4.8 34.1 1.0
C E:THR15 4.8 34.0 1.0
CG2 E:VAL99 4.8 31.5 1.0
CG E:ASP93 4.9 39.7 1.0
CB E:PRO16 4.9 33.7 1.0
CE E:LYS19 4.9 61.0 1.0
CA E:LYS19 5.0 42.4 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: Tue Dec 15 12:56:37 2020

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