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:
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
Go back to
Nickel Binding Sites List in 6s0u
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
Go back to
Nickel Binding Sites List in 6s0u
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
Go back to
Nickel Binding Sites List in 6s0u
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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