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Nickel 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:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 6 binding sites of Nickel 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 Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 6s0u

Go back to Nickel Binding Sites List in 6s0u
Nickel binding site 1 out of 6 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 Nickel with other atoms in the Ni 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
A:Ni302

b:23.7
occ:1.00
 O A:HOH404 1.7 19.9 1.0
NE2 A:HIS219 2.0 22.1 1.0
O2 A:AKG301 2.0 22.9 1.0
NE2 A:HIS132 2.0 22.3 1.0
O5 A:AKG301 2.2 25.9 1.0
OD1 A:ASP134 2.2 20.9 1.0
C1 A:AKG301 2.7 29.4 1.0
C2 A:AKG301 2.8 26.4 1.0
CE1 A:HIS219 2.9 24.6 1.0
CD2 A:HIS219 3.0 22.2 1.0
CE1 A:HIS132 3.0 26.5 1.0
CG A:ASP134 3.0 23.3 1.0
CD2 A:HIS132 3.1 24.3 1.0
OD2 A:ASP134 3.2 29.5 1.0
O1 A:AKG301 3.9 31.6 1.0
O A:HOH524 4.0 32.0 1.0
ND1 A:HIS219 4.1 25.4 1.0
CG A:HIS219 4.1 22.7 1.0
ND1 A:HIS132 4.1 25.9 1.0
CG A:HIS132 4.2 23.9 1.0
C3 A:AKG301 4.2 28.4 1.0
CB A:ASP134 4.5 23.0 1.0
C4 A:AKG301 4.8 25.4 1.0
OE1 A:GLN129 4.8 24.0 1.0
CA A:ASP134 4.9 23.6 1.0
N A:ASP134 4.9 23.2 1.0

Nickel binding site 2 out of 6 in 6s0u

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Nickel binding site 2 out of 6 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 Nickel with other atoms in the Ni 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
B:Ni302

b:19.3
occ:1.00
 NE2 B:HIS219 1.9 16.2 1.0
O1 B:AKG301 1.9 13.7 1.0
O5 B:AKG301 2.1 19.5 1.0
OD1 B:ASP134 2.1 27.5 1.0
NE2 B:HIS132 2.1 20.6 1.0
O B:HOH413 2.4 21.9 1.0
C1 B:AKG301 2.7 13.3 1.0
C2 B:AKG301 2.8 15.6 1.0
CE1 B:HIS219 2.8 16.6 1.0
CG B:ASP134 2.9 24.1 1.0
CD2 B:HIS219 2.9 17.2 1.0
OD2 B:ASP134 3.0 19.5 1.0
CE1 B:HIS132 3.1 20.4 1.0
CD2 B:HIS132 3.1 20.5 1.0
O2 B:AKG301 3.9 17.4 1.0
ND1 B:HIS219 4.0 17.2 1.0
CG B:HIS219 4.0 17.6 1.0
O B:HOH521 4.0 21.0 1.0
O B:HOH554 4.1 38.0 1.0
ND1 B:HIS132 4.2 22.1 1.0
C3 B:AKG301 4.2 18.4 1.0
CG B:HIS132 4.2 20.8 1.0
CB B:ASP134 4.3 24.6 1.0
C4 B:AKG301 4.8 19.4 1.0
CA B:ASP134 4.8 25.1 1.0
NH2 B:ARG213 4.8 24.3 1.0
N B:ASP134 4.8 25.2 1.0
OE1 B:GLN129 4.9 22.6 1.0
NH1 B:ARG213 5.0 21.5 1.0

Nickel binding site 3 out of 6 in 6s0u

Go back to Nickel Binding Sites List in 6s0u
Nickel binding site 3 out of 6 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 Nickel with other atoms in the Ni binding site number 3 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:Ni302

b:17.6
occ:1.00
 NE2 C:HIS219 1.9 18.1 1.0
O5 C:AKG301 2.0 19.0 1.0
O2 C:AKG301 2.0 13.4 1.0
NE2 C:HIS132 2.0 16.8 1.0
OD1 C:ASP134 2.2 17.7 1.0
O C:HOH422 2.3 22.4 1.0
C2 C:AKG301 2.8 19.3 1.0
C1 C:AKG301 2.8 22.5 1.0
CE1 C:HIS219 2.9 19.6 1.0
CD2 C:HIS219 2.9 19.3 1.0
CE1 C:HIS132 3.0 16.9 1.0
CG C:ASP134 3.0 18.2 1.0
CD2 C:HIS132 3.1 17.4 1.0
OD2 C:ASP134 3.2 17.5 1.0
O1 C:AKG301 4.0 17.7 1.0
ND1 C:HIS219 4.0 18.8 1.0
O C:HOH541 4.0 24.1 1.0
CG C:HIS219 4.1 18.4 1.0
ND1 C:HIS132 4.1 17.2 1.0
O C:HOH523 4.1 31.6 1.0
CG C:HIS132 4.2 16.7 1.0
C3 C:AKG301 4.2 16.0 1.0
O C:HOH453 4.3 25.7 1.0
CB C:ASP134 4.4 19.3 1.0
C4 C:AKG301 4.7 16.2 1.0
OE1 C:GLN129 4.8 15.6 1.0
CA C:ASP134 4.9 19.6 1.0
N C:ASP134 4.9 19.9 1.0

Nickel binding site 4 out of 6 in 6s0u

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Nickel binding site 4 out of 6 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 Nickel with other atoms in the Ni binding site number 4 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
D:Ni302

b:17.5
occ:1.00
 O D:HOH402 1.8 24.5 1.0
NE2 D:HIS219 1.9 18.6 1.0
O1 D:AKG301 2.0 13.0 1.0
NE2 D:HIS132 2.0 16.6 1.0
O5 D:AKG301 2.1 22.1 1.0
OD1 D:ASP134 2.1 18.0 1.0
C1 D:AKG301 2.8 23.2 1.0
C2 D:AKG301 2.8 20.8 1.0
CE1 D:HIS219 2.9 19.4 1.0
CG D:ASP134 3.0 17.6 1.0
CD2 D:HIS219 3.0 17.7 1.0
CE1 D:HIS132 3.0 16.9 1.0
CD2 D:HIS132 3.0 18.3 1.0
OD2 D:ASP134 3.1 18.5 1.0
O D:HOH514 3.8 33.3 1.0
O2 D:AKG301 4.0 13.8 1.0
ND1 D:HIS219 4.0 18.7 1.0
CG D:HIS219 4.1 17.9 1.0
ND1 D:HIS132 4.1 17.3 1.0
CG D:HIS132 4.2 18.2 1.0
O D:HOH537 4.2 24.7 1.0
C3 D:AKG301 4.3 21.2 1.0
CB D:ASP134 4.4 18.1 1.0
O D:HOH564 4.6 36.4 1.0
C4 D:AKG301 4.7 20.9 1.0
OE1 D:GLN129 4.8 18.0 1.0
CA D:ASP134 4.8 19.0 1.0
N D:ASP134 4.8 18.2 1.0

Nickel binding site 5 out of 6 in 6s0u

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Nickel binding site 5 out of 6 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 Nickel with other atoms in the Ni binding site number 5 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:Ni302

b:19.2
occ:1.00
 O E:HOH412 2.0 18.9 1.0
NE2 E:HIS219 2.0 17.8 1.0
O2 E:AKG301 2.0 19.2 1.0
O5 E:AKG301 2.1 16.0 1.0
NE2 E:HIS132 2.1 17.1 1.0
OD1 E:ASP134 2.2 20.3 1.0
C2 E:AKG301 2.7 14.7 1.0
C1 E:AKG301 2.7 22.5 1.0
CE1 E:HIS219 2.9 18.4 1.0
CG E:ASP134 3.0 20.2 1.0
CD2 E:HIS219 3.0 18.3 1.0
CE1 E:HIS132 3.1 16.9 1.0
CD2 E:HIS132 3.1 18.4 1.0
OD2 E:ASP134 3.1 21.5 1.0
O1 E:AKG301 3.9 18.2 1.0
ND1 E:HIS219 4.1 18.2 1.0
C3 E:AKG301 4.1 15.1 1.0
CG E:HIS219 4.1 18.5 1.0
ND1 E:HIS132 4.2 17.1 1.0
CG E:HIS132 4.2 18.3 1.0
O E:HOH512 4.3 40.2 1.0
O E:HOH463 4.4 39.7 1.0
O E:HOH469 4.4 30.2 1.0
CB E:ASP134 4.4 21.3 1.0
C4 E:AKG301 4.7 16.6 1.0
OE1 E:GLN129 4.8 20.4 1.0
CA E:ASP134 4.9 20.8 1.0
N E:ASP134 4.9 20.0 1.0
NH2 E:ARG213 5.0 26.7 1.0

Nickel binding site 6 out of 6 in 6s0u

Go back to Nickel Binding Sites List in 6s0u
Nickel binding site 6 out of 6 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 Nickel with other atoms in the Ni binding site number 6 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
F:Ni302

b:17.9
occ:1.00
 NE2 F:HIS219 2.0 15.0 1.0
O1 F:AKG301 2.0 14.6 1.0
O5 F:AKG301 2.1 24.4 1.0
NE2 F:HIS132 2.1 16.5 1.0
OD1 F:ASP134 2.1 22.2 1.0
O F:HOH408 2.3 26.1 1.0
C1 F:AKG301 2.8 19.4 1.0
C2 F:AKG301 2.8 22.6 1.0
CG F:ASP134 2.9 20.4 1.0
CE1 F:HIS219 2.9 15.0 1.0
CD2 F:HIS219 3.0 15.9 1.0
CE1 F:HIS132 3.0 16.6 1.0
CD2 F:HIS132 3.1 16.6 1.0
OD2 F:ASP134 3.1 19.7 1.0
O2 F:AKG301 4.0 20.1 1.0
ND1 F:HIS219 4.1 15.1 1.0
CG F:HIS219 4.1 15.8 1.0
ND1 F:HIS132 4.1 17.3 1.0
CG F:HIS132 4.2 16.9 1.0
C3 F:AKG301 4.2 22.0 1.0
CB F:ASP134 4.3 20.9 1.0
O F:HOH548 4.3 33.4 1.0
C4 F:AKG301 4.7 21.8 1.0
CA F:ASP134 4.8 20.9 1.0
OE1 F:GLN129 4.8 16.5 1.0
N F:ASP134 4.9 20.1 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: Thu Oct 10 08:50:49 2024

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