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Nickel in PDB 6s0w: The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel and Kanamycin B Sulfate

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

All present enzymatic activity of The Crystal Structure of Kanamycin B Dioxygenase (Kanj) From Streptomyces Kanamyceticus in Complex with Nickel and Kanamycin B 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 and Kanamycin B Sulfate, PDB code: 6s0w 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) 44.22 / 2.36
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.444, 186.061, 110.168, 90.00, 95.20, 90.00
R / Rfree (%) 18.5 / 22.5

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 Kanamycin B Sulfate (pdb code 6s0w). 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 Kanamycin B Sulfate, PDB code: 6s0w:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 6s0w

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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 Kanamycin B 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 and Kanamycin B Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni302

b:44.3
occ:1.00
 O A:HOH404 2.0 30.9 1.0
O A:HOH449 2.0 47.8 1.0
O A:HOH456 2.0 47.3 1.0
OD1 A:ASP134 2.1 46.0 1.0
NE2 A:HIS132 2.1 45.8 1.0
NE2 A:HIS219 2.1 46.9 1.0
CE1 A:HIS219 2.9 44.8 1.0
CG A:ASP134 3.0 43.1 1.0
CE1 A:HIS132 3.0 44.4 1.0
CD2 A:HIS132 3.1 43.6 1.0
CD2 A:HIS219 3.2 45.8 1.0
OD2 A:ASP134 3.3 42.8 1.0
O A:HOH435 3.9 64.1 1.0
ND1 A:HIS219 4.0 46.9 1.0
ND1 A:HIS132 4.1 43.2 1.0
CG A:HIS219 4.2 47.4 1.0
CG A:HIS132 4.2 43.2 1.0
O4 A:SO4303 4.3 76.2 1.0
O7 A:9CS301 4.4 62.7 0.6
CB A:ASP134 4.4 42.2 1.0
OE1 A:GLN129 4.6 48.4 1.0
C2 A:9CS301 4.6 61.2 0.6
CA A:ASP134 4.8 42.5 1.0
NH2 A:ARG213 4.8 52.1 1.0
N A:ASP134 4.9 43.0 1.0
C3 A:9CS301 5.0 61.6 0.6

Nickel binding site 2 out of 6 in 6s0w

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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 Kanamycin B 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 and Kanamycin B Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni302

b:31.0
occ:0.80
 O B:HOH523 2.0 33.8 1.0
O B:HOH530 2.0 34.9 1.0
O B:HOH470 2.0 35.1 1.0
NE2 B:HIS132 2.0 39.6 1.0
OD1 B:ASP134 2.1 37.3 1.0
NE2 B:HIS219 2.1 38.1 1.0
CE1 B:HIS219 2.9 37.7 1.0
CE1 B:HIS132 3.0 39.4 1.0
CD2 B:HIS132 3.1 40.4 1.0
CG B:ASP134 3.1 36.4 1.0
CD2 B:HIS219 3.2 37.6 1.0
OD2 B:ASP134 3.4 37.9 1.0
O B:HOH520 3.7 61.5 1.0
ND1 B:HIS219 4.0 37.5 1.0
ND1 B:HIS132 4.1 39.7 1.0
CG B:HIS132 4.2 39.5 1.0
CG B:HIS219 4.2 37.3 1.0
O B:HOH579 4.3 74.3 1.0
O B:HOH421 4.4 60.4 1.0
CB B:ASP134 4.4 37.5 1.0
O1 B:SO4303 4.5 66.5 1.0
NH2 B:ARG213 4.7 45.3 1.0
OE1 B:GLN129 4.7 41.6 1.0
C2 B:9CS301 4.8 56.5 0.6
CA B:ASP134 4.8 38.7 1.0
N B:ASP134 4.8 40.3 1.0
C4 B:9CS301 4.9 55.2 0.6
O7 B:9CS301 5.0 59.1 0.6

Nickel binding site 3 out of 6 in 6s0w

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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 and Kanamycin B 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 and Kanamycin B Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni302

b:40.2
occ:1.00
 O C:HOH459 2.0 43.9 1.0
O C:HOH427 2.0 37.9 1.0
O C:HOH468 2.0 37.0 1.0
NE2 C:HIS132 2.0 39.2 1.0
OD1 C:ASP134 2.1 46.5 1.0
NE2 C:HIS219 2.1 41.3 1.0
CE1 C:HIS219 3.0 41.2 1.0
CE1 C:HIS132 3.0 36.5 1.0
CG C:ASP134 3.0 44.0 1.0
CD2 C:HIS132 3.1 38.5 1.0
CD2 C:HIS219 3.2 40.0 1.0
OD2 C:ASP134 3.3 45.0 1.0
O C:HOH476 4.0 48.7 1.0
ND1 C:HIS219 4.1 39.8 1.0
ND1 C:HIS132 4.1 36.4 1.0
CG C:HIS132 4.2 38.0 1.0
CG C:HIS219 4.2 39.8 1.0
O C:HOH412 4.2 55.1 1.0
O4 C:SO4303 4.4 61.7 1.0
C2 C:9CS301 4.4 68.5 0.8
CB C:ASP134 4.4 45.1 1.0
OE1 C:GLN129 4.7 36.3 1.0
O C:HOH474 4.8 56.1 1.0
NH2 C:ARG213 4.8 50.6 1.0
CA C:ASP134 4.8 45.3 1.0
N6 C:9CS301 4.9 67.8 0.8
N C:ASP134 4.9 43.9 1.0

Nickel binding site 4 out of 6 in 6s0w

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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 Kanamycin B 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 and Kanamycin B Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni302

b:38.7
occ:1.00
 O D:HOH474 2.0 30.4 1.0
OD1 D:ASP134 2.1 41.8 1.0
NE2 D:HIS132 2.1 42.9 1.0
NE2 D:HIS219 2.1 39.6 1.0
O D:HOH556 2.2 40.7 1.0
O D:HOH424 2.2 39.4 1.0
CG D:ASP134 3.0 39.8 1.0
CE1 D:HIS219 3.0 39.1 1.0
CE1 D:HIS132 3.1 42.9 1.0
CD2 D:HIS219 3.1 38.6 1.0
CD2 D:HIS132 3.1 41.8 1.0
OD2 D:ASP134 3.2 40.4 1.0
ND1 D:HIS219 4.1 38.7 1.0
O D:HOH423 4.1 55.2 1.0
O D:HOH411 4.1 60.0 1.0
CG D:HIS219 4.2 38.4 1.0
ND1 D:HIS132 4.2 42.7 1.0
CG D:HIS132 4.2 41.7 1.0
O2 D:SO4303 4.4 64.2 1.0
CB D:ASP134 4.4 39.0 1.0
C2 D:9CS301 4.6 78.9 0.9
OE1 D:GLN129 4.6 43.8 1.0
O D:HOH475 4.7 59.6 1.0
NH2 D:ARG213 4.8 45.0 1.0
CA D:ASP134 4.8 38.9 1.0
N D:ASP134 4.9 38.1 1.0
N6 D:9CS301 5.0 78.2 0.9

Nickel binding site 5 out of 6 in 6s0w

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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 Kanamycin B 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 and Kanamycin B Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni302

b:51.3
occ:1.00
 O E:HOH434 2.0 47.2 1.0
O E:HOH439 2.0 53.9 1.0
O E:HOH414 2.0 55.5 1.0
OD1 E:ASP134 2.1 62.2 1.0
NE2 E:HIS132 2.1 50.9 1.0
NE2 E:HIS219 2.1 61.9 1.0
CE1 E:HIS132 2.9 51.9 1.0
CE1 E:HIS219 2.9 60.9 1.0
CG E:ASP134 3.1 59.6 1.0
CD2 E:HIS219 3.1 60.2 1.0
CD2 E:HIS132 3.2 50.4 1.0
OD2 E:ASP134 3.3 58.6 1.0
ND1 E:HIS219 4.0 61.1 1.0
ND1 E:HIS132 4.1 53.8 1.0
CG E:HIS219 4.1 60.6 1.0
CG E:HIS132 4.2 52.8 1.0
C2 E:9CS301 4.3 60.7 0.7
O3 E:SO4303 4.4 92.2 1.0
CB E:ASP134 4.5 60.9 1.0
OE1 E:GLN129 4.6 51.5 1.0
N6 E:9CS301 4.7 59.4 0.7
NH2 E:ARG213 4.8 64.4 1.0
CA E:ASP134 4.8 59.6 1.0
O7 E:9CS301 4.9 64.8 0.7
N E:ASP134 4.9 59.1 1.0

Nickel binding site 6 out of 6 in 6s0w

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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 Kanamycin B 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 and Kanamycin B Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni302

b:41.9
occ:1.00
 O F:HOH458 2.0 40.1 1.0
O F:HOH463 2.0 44.1 1.0
O F:HOH488 2.0 41.6 1.0
OD1 F:ASP134 2.1 45.5 1.0
NE2 F:HIS132 2.1 41.7 1.0
NE2 F:HIS219 2.1 45.8 1.0
CE1 F:HIS219 3.0 45.0 1.0
CG F:ASP134 3.0 43.2 1.0
CD2 F:HIS132 3.1 40.2 1.0
CE1 F:HIS132 3.1 42.2 1.0
CD2 F:HIS219 3.2 45.7 1.0
OD2 F:ASP134 3.3 44.5 1.0
ND1 F:HIS219 4.1 45.3 1.0
O F:HOH471 4.1 55.4 1.0
ND1 F:HIS132 4.2 40.5 1.0
CG F:HIS219 4.2 45.3 1.0
CG F:HIS132 4.2 40.3 1.0
O F:HOH447 4.3 62.0 1.0
CB F:ASP134 4.4 42.5 1.0
O2 F:SO4303 4.5 77.8 1.0
C2 F:9CS301 4.6 41.0 0.7
OE1 F:GLN129 4.7 39.6 1.0
CA F:ASP134 4.8 42.0 1.0
NH2 F:ARG213 4.8 46.8 1.0
N6 F:9CS301 4.9 40.0 0.7
N F:ASP134 4.9 41.6 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 08:51:06 2024

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