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Nickel in PDB 6s0t: The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide

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

All present enzymatic activity of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide:
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, Sulfate, Soaked with Iodide, PDB code: 6s0t was solved by B.Mrugala, P.J.Porebski, E.Niedzialkowska, M.T.Cymborowski, W.Minor, T.Borowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.614, 186.468, 110.828, 90.00, 95.74, 90.00
R / Rfree (%) 16.9 / 20.4

Other elements in 6s0t:

The structure of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide also contains other interesting chemical elements:

Iodine (I) 2 atoms

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, Sulfate, Soaked with Iodide (pdb code 6s0t). 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, Sulfate, Soaked with Iodide, PDB code: 6s0t:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 6s0t

Go back to Nickel Binding Sites List in 6s0t
Nickel binding site 1 out of 6 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide


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, Sulfate, Soaked with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:21.3
occ:1.00
 NE2 A:HIS219 2.1 18.5 1.0
O A:HOH407 2.2 15.0 1.0
O A:HOH560 2.2 18.3 1.0
OD1 A:ASP134 2.2 19.5 1.0
O A:HOH467 2.2 17.2 1.0
NE2 A:HIS132 2.2 18.1 1.0
CE1 A:HIS219 3.0 19.9 1.0
CD2 A:HIS219 3.1 18.4 1.0
CG A:ASP134 3.1 19.8 1.0
CE1 A:HIS132 3.1 18.4 1.0
CD2 A:HIS132 3.2 18.1 1.0
OD2 A:ASP134 3.4 17.0 1.0
O A:HOH574 4.0 44.5 1.0
O A:HOH584 4.1 34.8 1.0
ND1 A:HIS219 4.2 21.3 1.0
O4 A:SO4302 4.2 28.1 1.0
CG A:HIS219 4.2 20.4 1.0
O A:HOH474 4.2 23.2 1.0
ND1 A:HIS132 4.3 18.5 1.0
CG A:HIS132 4.4 18.6 1.0
OE1 A:GLN129 4.5 19.4 1.0
CB A:ASP134 4.5 19.9 1.0
O A:HOH412 4.7 24.4 1.0
NH2 A:ARG213 4.9 29.0 1.0
CA A:ASP134 5.0 18.7 1.0

Nickel binding site 2 out of 6 in 6s0t

Go back to Nickel Binding Sites List in 6s0t
Nickel binding site 2 out of 6 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide


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, Sulfate, Soaked with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni302

b:19.5
occ:1.00
 O B:HOH599 2.0 14.2 1.0
NE2 B:HIS219 2.1 13.8 1.0
NE2 B:HIS132 2.2 15.4 1.0
OD1 B:ASP134 2.2 18.2 1.0
O B:HOH463 2.2 21.2 1.0
O B:HOH442 2.3 16.9 1.0
CE1 B:HIS219 3.0 14.2 1.0
CE1 B:HIS132 3.1 15.3 1.0
CD2 B:HIS219 3.1 14.2 1.0
CG B:ASP134 3.2 17.5 1.0
CD2 B:HIS132 3.2 15.8 1.0
OD2 B:ASP134 3.4 19.9 1.0
O B:HOH659 3.8 40.2 1.0
O B:HOH656 3.9 37.5 1.0
ND1 B:HIS219 4.1 14.1 1.0
CG B:HIS219 4.2 14.3 1.0
ND1 B:HIS132 4.2 15.8 1.0
O1 B:SO4303 4.3 23.4 1.0
CG B:HIS132 4.3 16.4 1.0
O B:HOH453 4.4 26.7 1.0
O B:HOH462 4.4 21.0 1.0
OE1 B:GLN129 4.5 17.3 1.0
CB B:ASP134 4.6 17.7 1.0
NH2 B:ARG213 4.9 22.8 1.0
CA B:ASP134 5.0 17.8 1.0

Nickel binding site 3 out of 6 in 6s0t

Go back to Nickel Binding Sites List in 6s0t
Nickel binding site 3 out of 6 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide


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, Sulfate, Soaked with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni301

b:22.3
occ:1.00
 NE2 C:HIS219 2.1 18.2 1.0
O C:HOH587 2.2 29.1 1.0
NE2 C:HIS132 2.2 14.4 1.0
OD1 C:ASP134 2.2 21.8 1.0
O C:HOH481 2.3 25.4 1.0
O C:HOH467 2.3 18.1 1.0
CE1 C:HIS219 3.1 19.1 1.0
CE1 C:HIS132 3.1 14.7 1.0
CD2 C:HIS219 3.1 18.6 1.0
CG C:ASP134 3.1 22.1 1.0
CD2 C:HIS132 3.2 15.7 1.0
OD2 C:ASP134 3.4 22.4 1.0
O C:HOH625 3.9 32.5 1.0
ND1 C:HIS219 4.2 18.9 1.0
O C:HOH609 4.2 51.2 1.0
ND1 C:HIS132 4.2 14.6 1.0
O4 C:SO4302 4.2 25.1 1.0
CG C:HIS219 4.2 18.8 1.0
O C:HOH424 4.3 27.2 1.0
CG C:HIS132 4.3 15.9 1.0
OE1 C:GLN129 4.5 17.6 1.0
CB C:ASP134 4.6 22.3 1.0
O C:HOH458 4.7 25.0 1.0
NH2 C:ARG213 4.9 25.4 1.0
CA C:ASP134 5.0 22.3 1.0

Nickel binding site 4 out of 6 in 6s0t

Go back to Nickel Binding Sites List in 6s0t
Nickel binding site 4 out of 6 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide


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, Sulfate, Soaked with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni301

b:19.0
occ:1.00
 O D:HOH422 2.1 17.1 1.0
O D:HOH474 2.1 15.8 1.0
NE2 D:HIS219 2.1 14.0 1.0
NE2 D:HIS132 2.2 16.4 1.0
OD1 D:ASP134 2.2 16.6 1.0
O D:HOH619 2.3 19.8 1.0
CE1 D:HIS219 3.1 14.8 1.0
CE1 D:HIS132 3.1 17.6 1.0
CD2 D:HIS219 3.1 14.2 1.0
CG D:ASP134 3.1 17.9 1.0
CD2 D:HIS132 3.2 16.5 1.0
OD2 D:ASP134 3.4 16.4 1.0
O D:HOH642 4.1 38.2 1.0
O2 D:SO4302 4.2 23.3 1.0
ND1 D:HIS219 4.2 14.2 1.0
ND1 D:HIS132 4.2 17.8 1.0
CG D:HIS219 4.2 14.1 1.0
O D:HOH485 4.3 27.9 1.0
CG D:HIS132 4.3 17.1 1.0
OE1 D:GLN129 4.4 17.2 1.0
O D:HOH489 4.5 25.6 1.0
CB D:ASP134 4.6 17.4 1.0
NH2 D:ARG213 4.9 31.9 1.0
CA D:ASP134 5.0 17.5 1.0

Nickel binding site 5 out of 6 in 6s0t

Go back to Nickel Binding Sites List in 6s0t
Nickel binding site 5 out of 6 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide


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, Sulfate, Soaked with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni301

b:30.5
occ:1.00
 NE2 E:HIS219 2.1 22.8 1.0
O E:HOH549 2.2 26.6 1.0
O E:HOH456 2.2 32.4 1.0
OD1 E:ASP134 2.2 30.6 1.0
NE2 E:HIS132 2.2 23.6 1.0
O E:HOH473 2.3 25.3 1.0
CE1 E:HIS219 3.0 23.3 1.0
CD2 E:HIS219 3.1 22.5 1.0
CG E:ASP134 3.1 30.6 1.0
CE1 E:HIS132 3.1 25.0 1.0
CD2 E:HIS132 3.2 24.8 1.0
OD2 E:ASP134 3.4 31.5 1.0
O E:HOH476 4.1 27.1 1.0
ND1 E:HIS219 4.2 22.8 1.0
CG E:HIS219 4.2 22.3 1.0
O3 E:SO4302 4.3 32.0 1.0
ND1 E:HIS132 4.3 24.9 1.0
CG E:HIS132 4.3 24.6 1.0
OE1 E:GLN129 4.5 26.1 1.0
O E:HOH418 4.5 32.6 1.0
CB E:ASP134 4.6 30.4 1.0
NH2 E:ARG213 4.9 34.4 1.0
CA E:ASP134 5.0 29.9 1.0

Nickel binding site 6 out of 6 in 6s0t

Go back to Nickel Binding Sites List in 6s0t
Nickel binding site 6 out of 6 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel, Sulfate, Soaked with Iodide


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, Sulfate, Soaked with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni302

b:26.8
occ:1.00
 NE2 F:HIS219 2.1 23.4 1.0
NE2 F:HIS132 2.2 25.3 1.0
O F:HOH450 2.2 24.9 1.0
O F:HOH508 2.2 26.1 1.0
OD1 F:ASP134 2.2 24.7 1.0
O F:HOH433 2.2 21.5 1.0
CE1 F:HIS219 3.0 24.4 1.0
CE1 F:HIS132 3.1 26.7 1.0
CD2 F:HIS219 3.1 23.8 1.0
CG F:ASP134 3.2 22.4 1.0
CD2 F:HIS132 3.2 22.9 1.0
OD2 F:ASP134 3.4 23.0 1.0
O F:HOH522 4.0 43.5 1.0
O F:HOH519 4.0 29.5 1.0
O2 F:SO4303 4.1 37.5 1.0
ND1 F:HIS219 4.2 26.9 1.0
CG F:HIS219 4.2 25.8 1.0
ND1 F:HIS132 4.2 24.2 1.0
CG F:HIS132 4.3 23.1 1.0
O F:HOH487 4.4 32.7 1.0
O F:HOH417 4.5 37.8 1.0
OE1 F:GLN129 4.5 19.9 1.0
CB F:ASP134 4.6 21.4 1.0
NH2 F:ARG213 4.9 32.2 1.0
CA F:ASP134 5.0 21.6 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: Thu Oct 10 08:50:46 2024

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