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Nickel in PDB 6s0v: The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Neamine and Sulfate

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

All present enzymatic activity of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Neamine and Sulfate:
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, Neamine and Sulfate, PDB code: 6s0v was solved by B.Mrugala, 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) 48.54 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.467, 185.250, 110.460, 90.00, 94.68, 90.00
R / Rfree (%) 20 / 22.8

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, Neamine and Sulfate (pdb code 6s0v). 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, Neamine and Sulfate, PDB code: 6s0v:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 6s0v

Go back to Nickel Binding Sites List in 6s0v
Nickel binding site 1 out of 6 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Neamine and Sulfate


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, Neamine and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:43.0
occ:1.00
 OD1 A:ASP134 2.0 45.0 1.0
NE2 A:HIS219 2.0 47.3 1.0
NE2 A:HIS132 2.1 52.7 1.0
O A:HOH404 2.1 8.0 1.0
O A:HOH403 2.2 36.2 1.0
O A:HOH406 2.3 24.3 1.0
CE1 A:HIS219 2.9 46.1 1.0
CE1 A:HIS132 3.0 52.4 1.0
CG A:ASP134 3.0 42.9 1.0
CD2 A:HIS132 3.1 51.7 1.0
CD2 A:HIS219 3.1 46.0 1.0
OD2 A:ASP134 3.4 42.2 1.0
ND1 A:HIS219 4.0 45.8 1.0
O3 A:XXX305 4.1 0.8 1.0
CG A:HIS219 4.1 46.4 1.0
ND1 A:HIS132 4.1 51.9 1.0
CG A:HIS132 4.2 50.9 1.0
O4 A:SO4302 4.3 76.1 1.0
CB A:ASP134 4.4 42.8 1.0
C2 A:XXX305 4.4 0.8 1.0
N4 A:XXX305 4.5 0.5 1.0
OE1 A:GLN129 4.6 50.6 1.0
CA A:ASP134 4.7 43.6 1.0
C3 A:XXX305 4.7 0.6 1.0
N A:ASP134 4.8 44.6 1.0
NH2 A:ARG213 4.8 43.1 1.0
CE2 A:PHE74 5.0 47.5 1.0

Nickel binding site 2 out of 6 in 6s0v

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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, Neamine and Sulfate


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, Neamine and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni301

b:43.4
occ:1.00
 O B:HOH405 2.0 38.5 1.0
O B:HOH409 2.0 40.7 1.0
NE2 B:HIS132 2.0 46.4 1.0
NE2 B:HIS219 2.0 44.0 1.0
OD1 B:ASP134 2.1 47.3 1.0
O B:HOH406 2.2 54.0 1.0
CE1 B:HIS219 2.9 42.4 1.0
CE1 B:HIS132 3.0 45.1 1.0
CD2 B:HIS132 3.1 44.7 1.0
CG B:ASP134 3.1 44.2 1.0
CD2 B:HIS219 3.1 41.4 1.0
OD2 B:ASP134 3.4 44.0 1.0
ND1 B:HIS219 4.0 41.1 1.0
ND1 B:HIS132 4.1 45.3 1.0
CG B:HIS132 4.2 44.0 1.0
CG B:HIS219 4.2 40.2 1.0
O3 B:XXX304 4.3 0.6 1.0
CB B:ASP134 4.4 44.2 1.0
C2 B:XXX304 4.5 0.7 1.0
O3 B:SO4302 4.6 78.8 1.0
OE1 B:GLN129 4.7 39.4 1.0
CA B:ASP134 4.8 43.6 1.0
NH2 B:ARG213 4.8 41.9 1.0
N B:ASP134 4.8 42.9 1.0
C3 B:XXX304 4.9 0.3 1.0
CE2 B:PHE74 4.9 45.0 1.0
N4 B:XXX304 5.0 0.8 1.0

Nickel binding site 3 out of 6 in 6s0v

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Nickel binding site 3 out of 6 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Neamine and Sulfate


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, Neamine and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni301

b:45.7
occ:1.00
 O C:HOH410 2.0 44.9 1.0
O C:HOH412 2.0 49.1 1.0
NE2 C:HIS132 2.0 38.6 1.0
O C:HOH416 2.0 46.4 1.0
OD1 C:ASP134 2.0 45.4 1.0
NE2 C:HIS219 2.1 46.4 1.0
CE1 C:HIS219 2.9 44.9 1.0
CD2 C:HIS132 3.0 36.3 1.0
CE1 C:HIS132 3.0 36.0 1.0
CG C:ASP134 3.1 43.1 1.0
CD2 C:HIS219 3.2 44.2 1.0
OD2 C:ASP134 3.4 46.0 1.0
ND1 C:HIS219 4.1 42.9 1.0
ND1 C:HIS132 4.1 35.4 1.0
CG C:HIS132 4.1 35.4 1.0
CG C:HIS219 4.2 42.1 1.0
CB C:ASP134 4.4 42.7 1.0
O4 C:SO4302 4.6 81.2 1.0
OE1 C:GLN129 4.7 35.4 1.0
CA C:ASP134 4.7 41.4 1.0
C2 C:XXX304 4.8 63.1 0.7
N C:ASP134 4.8 39.6 1.0
NH2 C:ARG213 4.8 49.5 1.0
C1 C:XXX304 4.9 63.3 0.7
CE2 C:PHE74 5.0 37.0 1.0
O5 C:XXX304 5.0 64.2 0.7

Nickel binding site 4 out of 6 in 6s0v

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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, Neamine and Sulfate


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, Neamine and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni301

b:52.3
occ:1.00
 O D:HOH404 2.0 61.2 1.0
NE2 D:HIS219 2.0 49.9 1.0
O D:HOH410 2.0 52.6 1.0
OD1 D:ASP134 2.0 55.6 1.0
NE2 D:HIS132 2.1 47.7 1.0
O D:HOH402 2.1 52.1 1.0
CE1 D:HIS219 2.9 47.5 1.0
CE1 D:HIS132 3.0 45.4 1.0
CG D:ASP134 3.1 51.7 1.0
CD2 D:HIS132 3.1 45.0 1.0
CD2 D:HIS219 3.1 46.9 1.0
OD2 D:ASP134 3.4 55.5 1.0
ND1 D:HIS219 4.0 45.0 1.0
ND1 D:HIS132 4.1 44.7 1.0
CG D:HIS219 4.1 43.3 1.0
CG D:HIS132 4.2 44.4 1.0
CB D:ASP134 4.4 48.2 1.0
O D:HOH416 4.4 31.9 1.0
O2 D:SO4302 4.5 83.7 1.0
OE1 D:GLN129 4.6 38.2 1.0
C2 D:XXX306 4.7 53.4 0.8
CA D:ASP134 4.7 45.3 1.0
NH2 D:ARG213 4.8 43.3 1.0
N D:ASP134 4.8 44.1 1.0
N4 D:XXX306 4.8 53.4 0.8

Nickel binding site 5 out of 6 in 6s0v

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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, Neamine and Sulfate


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, Neamine and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni301

b:56.5
occ:1.00
 O E:HOH413 2.0 53.1 1.0
O E:HOH403 2.0 49.5 1.0
O E:HOH409 2.0 56.5 1.0
OD1 E:ASP134 2.0 60.7 1.0
NE2 E:HIS219 2.1 53.8 1.0
NE2 E:HIS132 2.1 53.9 1.0
CE1 E:HIS219 2.9 52.2 1.0
CE1 E:HIS132 3.0 52.2 1.0
CG E:ASP134 3.0 55.9 1.0
CD2 E:HIS132 3.1 50.9 1.0
CD2 E:HIS219 3.1 52.3 1.0
OD2 E:ASP134 3.4 56.5 1.0
ND1 E:HIS219 4.1 52.1 1.0
ND1 E:HIS132 4.1 51.0 1.0
CG E:HIS132 4.2 50.6 1.0
CG E:HIS219 4.2 51.8 1.0
CB E:ASP134 4.4 54.8 1.0
C2 E:XXX305 4.5 51.1 0.7
N4 E:XXX305 4.5 49.3 0.7
OE1 E:GLN129 4.6 50.1 1.0
O3 E:SO4302 4.7 86.9 1.0
CA E:ASP134 4.7 54.3 1.0
NH2 E:ARG213 4.8 50.0 1.0
N E:ASP134 4.8 53.5 1.0
CE2 E:PHE74 4.9 49.3 1.0

Nickel binding site 6 out of 6 in 6s0v

Go back to Nickel Binding Sites List in 6s0v
Nickel binding site 6 out of 6 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Neamine and Sulfate


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, Neamine and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni301

b:50.8
occ:1.00
 O F:HOH407 2.0 54.7 1.0
O F:HOH406 2.0 54.1 1.0
OD1 F:ASP134 2.0 51.1 1.0
NE2 F:HIS219 2.0 51.3 1.0
O F:HOH405 2.1 42.7 1.0
NE2 F:HIS132 2.1 45.9 1.0
CE1 F:HIS219 2.9 48.9 1.0
CE1 F:HIS132 3.0 44.5 1.0
CG F:ASP134 3.0 47.4 1.0
CD2 F:HIS132 3.1 43.3 1.0
CD2 F:HIS219 3.1 49.6 1.0
OD2 F:ASP134 3.4 50.0 1.0
ND1 F:HIS219 4.0 47.9 1.0
ND1 F:HIS132 4.1 43.5 1.0
CG F:HIS219 4.2 47.7 1.0
O2 F:SO4302 4.2 97.3 1.0
CG F:HIS132 4.2 42.4 1.0
CB F:ASP134 4.4 45.2 1.0
C2 F:XXX306 4.6 33.0 0.7
OE1 F:GLN129 4.7 47.5 1.0
CA F:ASP134 4.7 44.1 1.0
NH2 F:ARG213 4.8 45.0 1.0
N F:ASP134 4.8 43.4 1.0
N4 F:XXX306 4.9 33.5 0.7

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 08:50:56 2024

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