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Nickel in PDB 6s0r: The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus Complex with Nickel, Sulfate and Chloride

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

All present enzymatic activity of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus Complex with Nickel, Sulfate and Chloride:
1.14.11.37;

Protein crystallography data

The structure of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus Complex with Nickel, Sulfate and Chloride, PDB code: 6s0r 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) 47.22 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.368, 184.213, 110.148, 90.00, 94.23, 90.00
R / Rfree (%) 17 / 20.8

Other elements in 6s0r:

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

Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus Complex with Nickel, Sulfate and Chloride (pdb code 6s0r). 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 Complex with Nickel, Sulfate and Chloride, PDB code: 6s0r:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 6s0r

Go back to Nickel Binding Sites List in 6s0r
Nickel binding site 1 out of 6 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus Complex with Nickel, Sulfate and Chloride


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 Complex with Nickel, Sulfate and Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:27.0
occ:1.00
 NE2 A:HIS219 2.0 27.4 1.0
O A:HOH406 2.1 19.7 1.0
NE2 A:HIS132 2.1 27.9 1.0
O A:HOH462 2.1 26.5 1.0
O A:HOH465 2.1 24.6 1.0
OD1 A:ASP134 2.1 30.1 1.0
CE1 A:HIS219 2.8 27.3 1.0
CE1 A:HIS132 3.0 27.3 1.0
CG A:ASP134 3.0 29.9 1.0
CD2 A:HIS219 3.1 26.4 1.0
CD2 A:HIS132 3.1 26.3 1.0
OD2 A:ASP134 3.3 30.5 1.0
O A:HOH497 3.7 31.6 1.0
ND1 A:HIS219 4.0 26.8 1.0
ND1 A:HIS132 4.1 27.1 1.0
O A:HOH425 4.1 27.7 1.0
CG A:HIS219 4.1 26.9 1.0
CG A:HIS132 4.2 27.3 1.0
O4 A:SO4302 4.4 56.6 1.0
CB A:ASP134 4.4 28.6 1.0
OE1 A:GLN129 4.5 27.8 1.0
NH2 A:ARG213 4.8 34.5 1.0
CA A:ASP134 4.8 28.4 1.0
O A:HOH427 4.9 39.0 1.0
N A:ASP134 5.0 27.0 1.0

Nickel binding site 2 out of 6 in 6s0r

Go back to Nickel Binding Sites List in 6s0r
Nickel binding site 2 out of 6 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus Complex with Nickel, Sulfate and Chloride


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 Complex with Nickel, Sulfate and Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni301

b:22.3
occ:1.00
 NE2 B:HIS132 2.0 25.2 1.0
NE2 B:HIS219 2.1 20.9 1.0
O B:HOH519 2.1 18.3 1.0
O B:HOH479 2.1 24.6 1.0
O B:HOH428 2.1 19.4 1.0
OD1 B:ASP134 2.1 26.2 1.0
CE1 B:HIS219 2.9 20.4 1.0
CE1 B:HIS132 2.9 23.9 1.0
CG B:ASP134 3.1 24.5 1.0
CD2 B:HIS132 3.1 24.5 1.0
CD2 B:HIS219 3.2 19.6 1.0
OD2 B:ASP134 3.3 24.9 1.0
ND1 B:HIS219 4.0 19.9 1.0
ND1 B:HIS132 4.1 24.4 1.0
CG B:HIS132 4.2 24.4 1.0
CG B:HIS219 4.2 19.3 1.0
CB B:ASP134 4.5 24.3 1.0
O1 B:SO4302 4.5 41.6 1.0
O B:HOH594 4.6 39.0 1.0
O B:HOH406 4.6 34.3 1.0
OE1 B:GLN129 4.7 24.1 1.0
NH2 B:ARG213 4.8 26.5 1.0
CA B:ASP134 4.9 25.4 1.0
N B:ASP134 5.0 24.9 1.0

Nickel binding site 3 out of 6 in 6s0r

Go back to Nickel Binding Sites List in 6s0r
Nickel binding site 3 out of 6 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus Complex with Nickel, Sulfate and Chloride


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 Complex with Nickel, Sulfate and Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni301

b:27.5
occ:1.00
 NE2 C:HIS132 2.0 30.9 1.0
NE2 C:HIS219 2.0 27.9 1.0
O C:HOH451 2.1 21.4 1.0
O C:HOH413 2.1 25.0 1.0
O C:HOH429 2.1 25.3 1.0
OD1 C:ASP134 2.1 35.4 1.0
CE1 C:HIS219 2.9 27.2 1.0
CE1 C:HIS132 2.9 28.9 1.0
CD2 C:HIS132 3.1 29.6 1.0
CG C:ASP134 3.1 36.0 1.0
CD2 C:HIS219 3.1 26.1 1.0
OD2 C:ASP134 3.4 35.3 1.0
O C:HOH468 4.0 39.1 1.0
ND1 C:HIS219 4.0 26.6 1.0
ND1 C:HIS132 4.0 28.6 1.0
O C:HOH488 4.1 38.6 1.0
CG C:HIS132 4.2 29.0 1.0
CG C:HIS219 4.2 25.8 1.0
O4 C:SO4302 4.2 52.5 1.0
CB C:ASP134 4.5 36.4 1.0
OE1 C:GLN129 4.6 24.3 1.0
CA C:ASP134 4.9 35.6 1.0
NH2 C:ARG213 4.9 39.1 1.0
N C:ASP134 5.0 34.6 1.0

Nickel binding site 4 out of 6 in 6s0r

Go back to Nickel Binding Sites List in 6s0r
Nickel binding site 4 out of 6 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus Complex with Nickel, Sulfate and Chloride


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 Complex with Nickel, Sulfate and Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni301

b:31.1
occ:1.00
 NE2 D:HIS219 2.0 27.9 1.0
NE2 D:HIS132 2.1 30.5 1.0
O D:HOH458 2.1 26.7 1.0
O D:HOH469 2.1 29.5 1.0
O D:HOH477 2.1 25.0 1.0
OD1 D:ASP134 2.1 32.2 1.0
CE1 D:HIS219 2.8 27.2 1.0
CE1 D:HIS132 3.0 29.4 1.0
CG D:ASP134 3.0 28.1 1.0
CD2 D:HIS219 3.1 26.6 1.0
CD2 D:HIS132 3.1 29.1 1.0
OD2 D:ASP134 3.3 28.1 1.0
ND1 D:HIS219 4.0 25.9 1.0
O D:HOH466 4.0 32.0 1.0
ND1 D:HIS132 4.1 29.4 1.0
CG D:HIS219 4.1 25.2 1.0
CG D:HIS132 4.2 28.9 1.0
O D:HOH515 4.3 31.6 1.0
O2 D:SO4302 4.4 41.6 1.0
CB D:ASP134 4.4 26.8 1.0
OE1 D:GLN129 4.6 25.9 1.0
NH2 D:ARG213 4.8 34.5 1.0
CA D:ASP134 4.8 27.2 1.0
O D:HOH470 4.8 35.5 1.0
N D:ASP134 4.9 25.7 1.0

Nickel binding site 5 out of 6 in 6s0r

Go back to Nickel Binding Sites List in 6s0r
Nickel binding site 5 out of 6 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus Complex with Nickel, Sulfate and Chloride


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 Complex with Nickel, Sulfate and Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni301

b:42.0
occ:1.00
 NE2 E:HIS132 2.0 46.5 1.0
NE2 E:HIS219 2.0 49.6 1.0
O E:HOH423 2.1 38.5 1.0
O E:HOH433 2.1 37.1 1.0
O E:HOH406 2.1 45.4 1.0
OD1 E:ASP134 2.1 55.0 1.0
CE1 E:HIS219 2.9 47.9 1.0
CE1 E:HIS132 2.9 45.5 1.0
CD2 E:HIS132 3.1 45.0 1.0
CG E:ASP134 3.1 51.4 1.0
CD2 E:HIS219 3.1 47.0 1.0
OD2 E:ASP134 3.4 52.0 1.0
ND1 E:HIS219 4.0 47.3 1.0
ND1 E:HIS132 4.1 46.2 1.0
CG E:HIS219 4.2 47.0 1.0
CG E:HIS132 4.2 45.3 1.0
O3 E:SO4302 4.2 71.8 1.0
CB E:ASP134 4.5 51.2 1.0
OE1 E:GLN129 4.6 44.6 1.0
CA E:ASP134 4.9 49.8 1.0
NH2 E:ARG213 4.9 57.8 1.0
N E:ASP134 5.0 47.5 1.0

Nickel binding site 6 out of 6 in 6s0r

Go back to Nickel Binding Sites List in 6s0r
Nickel binding site 6 out of 6 in the The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus Complex with Nickel, Sulfate and Chloride


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 Complex with Nickel, Sulfate and Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni301

b:31.1
occ:1.00
 NE2 F:HIS219 2.0 32.8 1.0
NE2 F:HIS132 2.0 29.4 1.0
O F:HOH451 2.1 25.9 1.0
O F:HOH410 2.1 27.5 1.0
OD1 F:ASP134 2.1 31.0 1.0
O F:HOH471 2.1 24.2 1.0
CE1 F:HIS219 2.8 32.3 1.0
CE1 F:HIS132 3.0 28.8 1.0
CG F:ASP134 3.0 30.2 1.0
CD2 F:HIS132 3.1 27.5 1.0
CD2 F:HIS219 3.1 32.0 1.0
OD2 F:ASP134 3.3 29.6 1.0
ND1 F:HIS219 4.0 30.6 1.0
ND1 F:HIS132 4.1 28.6 1.0
O2 F:SO4302 4.1 56.9 1.0
CG F:HIS219 4.1 30.7 1.0
CG F:HIS132 4.2 27.1 1.0
O F:HOH463 4.4 29.6 1.0
CB F:ASP134 4.4 29.2 1.0
OE1 F:GLN129 4.7 26.6 1.0
NH2 F:ARG213 4.8 35.6 1.0
CA F:ASP134 4.8 28.9 1.0
N F:ASP134 4.9 27.9 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 08:50:41 2024

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