Nickel in PDB 5flj: Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase
Enzymatic activity of Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase
All present enzymatic activity of Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase:
1.13.11.24;
Protein crystallography data
The structure of Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase, PDB code: 5flj
was solved by
J.-H.Jeoung,
D.Nianios,
S.Fetzner,
H.Dobbek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
38.803 /
1.82
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
102.812,
114.586,
105.990,
90.00,
95.61,
90.00
|
|
R / Rfree (%)
|
16.41 /
20.76
|
Nickel Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Nickel atom in the Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase
(pdb code 5flj). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 12 binding sites of Nickel where determined in the
Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase, PDB code: 5flj:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Nickel binding site 1 out
of 12 in 5flj
Go back to
Nickel Binding Sites List in 5flj
Nickel binding site 1 out
of 12 in the Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni300
b:35.4
occ:1.00
|
NE2
|
A:HIS115
|
2.1
|
32.4
|
1.0
|
|
NE2
|
A:HIS69
|
2.1
|
47.8
|
1.0
|
|
NE2
|
A:HIS71
|
2.1
|
42.8
|
1.0
|
|
O27
|
A:QUE301
|
2.1
|
32.2
|
0.8
|
|
OE1
|
A:GLU76
|
2.1
|
44.5
|
1.0
|
|
O
|
A:HOH2069
|
2.2
|
39.2
|
0.8
|
|
CD
|
A:GLU76
|
2.9
|
44.5
|
1.0
|
|
CD2
|
A:HIS69
|
2.9
|
43.2
|
1.0
|
|
CE1
|
A:HIS115
|
2.9
|
36.3
|
1.0
|
|
C10
|
A:QUE301
|
2.9
|
41.9
|
0.8
|
|
OE2
|
A:GLU76
|
3.0
|
55.9
|
1.0
|
|
CE1
|
A:HIS71
|
3.1
|
41.0
|
1.0
|
|
CD2
|
A:HIS71
|
3.1
|
40.7
|
1.0
|
|
CD2
|
A:HIS115
|
3.1
|
35.2
|
1.0
|
|
CE1
|
A:HIS69
|
3.1
|
51.6
|
1.0
|
|
O13
|
A:QUE301
|
3.3
|
51.6
|
0.8
|
|
C9
|
A:QUE301
|
3.5
|
45.4
|
0.8
|
|
C11
|
A:QUE301
|
3.9
|
36.4
|
0.8
|
|
C19
|
A:QUE301
|
4.1
|
40.5
|
0.8
|
|
ND1
|
A:HIS115
|
4.1
|
38.1
|
1.0
|
|
CG
|
A:HIS69
|
4.1
|
45.7
|
1.0
|
|
ND1
|
A:HIS71
|
4.2
|
44.0
|
1.0
|
|
ND1
|
A:HIS69
|
4.2
|
44.0
|
1.0
|
|
CG
|
A:HIS115
|
4.2
|
37.7
|
1.0
|
|
CG
|
A:HIS71
|
4.2
|
42.6
|
1.0
|
|
CG
|
A:GLU76
|
4.3
|
42.1
|
1.0
|
|
C14
|
A:QUE301
|
4.4
|
36.2
|
0.8
|
|
C3
|
A:QUE301
|
4.7
|
48.1
|
0.8
|
|
CB
|
A:GLU76
|
4.9
|
32.3
|
1.0
|
|
CZ
|
A:PHE78
|
5.0
|
48.0
|
1.0
|
|
Nickel binding site 2 out
of 12 in 5flj
Go back to
Nickel Binding Sites List in 5flj
Nickel binding site 2 out
of 12 in the Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni300
b:34.3
occ:1.00
|
OE1
|
B:GLU76
|
2.0
|
37.4
|
1.0
|
|
NE2
|
B:HIS115
|
2.0
|
28.5
|
1.0
|
|
NE2
|
B:HIS69
|
2.0
|
40.7
|
1.0
|
|
NE2
|
B:HIS71
|
2.1
|
35.5
|
1.0
|
|
O27
|
B:QUE301
|
2.1
|
35.1
|
0.8
|
|
O
|
B:HOH2072
|
2.3
|
35.3
|
1.0
|
|
CD
|
B:GLU76
|
2.9
|
46.5
|
1.0
|
|
C10
|
B:QUE301
|
2.9
|
46.3
|
0.8
|
|
CE1
|
B:HIS115
|
2.9
|
37.5
|
1.0
|
|
CE1
|
B:HIS71
|
3.0
|
34.0
|
1.0
|
|
CD2
|
B:HIS69
|
3.0
|
38.0
|
1.0
|
|
CE1
|
B:HIS69
|
3.0
|
41.6
|
1.0
|
|
CD2
|
B:HIS115
|
3.1
|
35.2
|
1.0
|
|
CD2
|
B:HIS71
|
3.2
|
34.0
|
1.0
|
|
OE2
|
B:GLU76
|
3.2
|
50.2
|
1.0
|
|
O13
|
B:QUE301
|
3.3
|
62.4
|
0.8
|
|
C9
|
B:QUE301
|
3.4
|
53.1
|
0.8
|
|
C11
|
B:QUE301
|
3.9
|
42.9
|
0.8
|
|
ND1
|
B:HIS115
|
4.1
|
31.3
|
1.0
|
|
ND1
|
B:HIS71
|
4.1
|
36.9
|
1.0
|
|
C19
|
B:QUE301
|
4.1
|
38.1
|
0.8
|
|
ND1
|
B:HIS69
|
4.1
|
36.6
|
1.0
|
|
CG
|
B:HIS69
|
4.1
|
37.8
|
1.0
|
|
CG
|
B:HIS115
|
4.2
|
28.6
|
1.0
|
|
CG
|
B:GLU76
|
4.2
|
38.6
|
1.0
|
|
CG
|
B:HIS71
|
4.2
|
37.2
|
1.0
|
|
C14
|
B:QUE301
|
4.4
|
44.4
|
0.8
|
|
C3
|
B:QUE301
|
4.7
|
46.7
|
0.8
|
|
CB
|
B:GLU76
|
5.0
|
32.7
|
1.0
|
|
O12
|
B:QUE301
|
5.0
|
45.7
|
0.8
|
|
Nickel binding site 3 out
of 12 in 5flj
Go back to
Nickel Binding Sites List in 5flj
Nickel binding site 3 out
of 12 in the Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni300
b:30.8
occ:1.00
|
NE2
|
C:HIS71
|
2.1
|
34.4
|
1.0
|
|
NE2
|
C:HIS69
|
2.1
|
33.3
|
1.0
|
|
OE1
|
C:GLU76
|
2.2
|
29.8
|
1.0
|
|
O27
|
C:QUE301
|
2.3
|
29.2
|
0.8
|
|
NE2
|
C:HIS115
|
2.3
|
26.0
|
1.0
|
|
O1
|
C:OXY302
|
2.4
|
34.7
|
0.8
|
|
O2
|
C:OXY302
|
2.4
|
36.4
|
0.8
|
|
CD
|
C:GLU76
|
2.9
|
41.2
|
1.0
|
|
CE1
|
C:HIS71
|
3.0
|
32.6
|
1.0
|
|
CD2
|
C:HIS69
|
3.0
|
30.6
|
1.0
|
|
C10
|
C:QUE301
|
3.1
|
33.9
|
0.8
|
|
OE2
|
C:GLU76
|
3.1
|
44.3
|
1.0
|
|
CE1
|
C:HIS69
|
3.1
|
37.4
|
1.0
|
|
CD2
|
C:HIS71
|
3.2
|
30.5
|
1.0
|
|
CE1
|
C:HIS115
|
3.2
|
32.9
|
1.0
|
|
O13
|
C:QUE301
|
3.4
|
44.4
|
0.8
|
|
CD2
|
C:HIS115
|
3.4
|
30.2
|
1.0
|
|
C9
|
C:QUE301
|
3.6
|
42.1
|
0.8
|
|
ND1
|
C:HIS71
|
4.2
|
33.4
|
1.0
|
|
ND1
|
C:HIS69
|
4.2
|
41.1
|
1.0
|
|
C11
|
C:QUE301
|
4.2
|
37.8
|
0.8
|
|
CG
|
C:HIS69
|
4.2
|
35.4
|
1.0
|
|
C19
|
C:QUE301
|
4.2
|
33.0
|
0.8
|
|
CG
|
C:HIS71
|
4.3
|
34.3
|
1.0
|
|
CG
|
C:GLU76
|
4.3
|
38.1
|
1.0
|
|
ND1
|
C:HIS115
|
4.3
|
31.8
|
1.0
|
|
CG
|
C:HIS115
|
4.5
|
27.3
|
1.0
|
|
C14
|
C:QUE301
|
4.6
|
34.9
|
0.8
|
|
C3
|
C:QUE301
|
4.8
|
36.9
|
0.8
|
|
CB
|
C:GLU76
|
4.9
|
26.8
|
1.0
|
|
CZ
|
C:PHE78
|
5.0
|
45.9
|
1.0
|
|
Nickel binding site 4 out
of 12 in 5flj
Go back to
Nickel Binding Sites List in 5flj
Nickel binding site 4 out
of 12 in the Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni300
b:30.3
occ:1.00
|
NE2
|
D:HIS115
|
2.0
|
29.3
|
1.0
|
|
NE2
|
D:HIS71
|
2.0
|
32.2
|
1.0
|
|
OE1
|
D:GLU76
|
2.1
|
31.2
|
1.0
|
|
NE2
|
D:HIS69
|
2.1
|
32.7
|
1.0
|
|
O27
|
D:QUE301
|
2.2
|
26.5
|
0.8
|
|
O
|
D:HOH2065
|
2.3
|
36.1
|
1.0
|
|
CE1
|
D:HIS115
|
2.8
|
35.2
|
1.0
|
|
CE1
|
D:HIS71
|
2.9
|
29.0
|
1.0
|
|
CD
|
D:GLU76
|
2.9
|
44.1
|
1.0
|
|
CD2
|
D:HIS69
|
3.0
|
30.9
|
1.0
|
|
C10
|
D:QUE301
|
3.0
|
31.3
|
0.8
|
|
CD2
|
D:HIS115
|
3.1
|
31.3
|
1.0
|
|
CD2
|
D:HIS71
|
3.1
|
30.1
|
1.0
|
|
CE1
|
D:HIS69
|
3.1
|
32.2
|
1.0
|
|
OE2
|
D:GLU76
|
3.2
|
39.3
|
1.0
|
|
O13
|
D:QUE301
|
3.4
|
33.4
|
0.8
|
|
C9
|
D:QUE301
|
3.5
|
32.0
|
0.8
|
|
C11
|
D:QUE301
|
3.9
|
34.1
|
0.8
|
|
ND1
|
D:HIS115
|
4.0
|
37.8
|
1.0
|
|
ND1
|
D:HIS71
|
4.1
|
32.5
|
1.0
|
|
CG
|
D:HIS115
|
4.1
|
30.7
|
1.0
|
|
C19
|
D:QUE301
|
4.1
|
32.3
|
0.8
|
|
CG
|
D:HIS69
|
4.2
|
32.7
|
1.0
|
|
ND1
|
D:HIS69
|
4.2
|
31.8
|
1.0
|
|
CG
|
D:HIS71
|
4.2
|
32.7
|
1.0
|
|
CG
|
D:GLU76
|
4.3
|
41.4
|
1.0
|
|
C14
|
D:QUE301
|
4.5
|
33.9
|
0.8
|
|
C3
|
D:QUE301
|
4.7
|
27.2
|
0.8
|
|
CB
|
D:GLU76
|
4.9
|
31.4
|
1.0
|
|
CZ
|
D:PHE78
|
5.0
|
39.8
|
1.0
|
|
Nickel binding site 5 out
of 12 in 5flj
Go back to
Nickel Binding Sites List in 5flj
Nickel binding site 5 out
of 12 in the Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ni300
b:31.5
occ:1.00
|
NE2
|
E:HIS115
|
2.0
|
28.9
|
1.0
|
|
OE2
|
E:GLU76
|
2.0
|
59.0
|
1.0
|
|
NE2
|
E:HIS69
|
2.0
|
37.7
|
1.0
|
|
NE2
|
E:HIS71
|
2.1
|
28.5
|
1.0
|
|
O
|
E:HOH2070
|
2.3
|
33.0
|
1.0
|
|
O27
|
E:QUE301
|
2.3
|
22.0
|
0.5
|
|
OE1
|
E:GLU76
|
2.5
|
39.5
|
1.0
|
|
CD
|
E:GLU76
|
2.5
|
25.7
|
1.0
|
|
CE1
|
E:HIS115
|
2.8
|
27.9
|
1.0
|
|
CE1
|
E:HIS71
|
3.0
|
29.7
|
1.0
|
|
CE1
|
E:HIS69
|
3.0
|
37.0
|
1.0
|
|
CD2
|
E:HIS69
|
3.0
|
34.2
|
1.0
|
|
CD2
|
E:HIS115
|
3.1
|
32.1
|
1.0
|
|
C10
|
E:QUE301
|
3.1
|
44.3
|
0.5
|
|
CD2
|
E:HIS71
|
3.2
|
28.8
|
1.0
|
|
O13
|
E:QUE301
|
3.6
|
52.2
|
0.5
|
|
C9
|
E:QUE301
|
3.7
|
45.0
|
0.5
|
|
ND1
|
E:HIS115
|
4.0
|
28.8
|
1.0
|
|
CG
|
E:GLU76
|
4.0
|
48.4
|
1.0
|
|
C11
|
E:QUE301
|
4.0
|
43.0
|
0.5
|
|
ND1
|
E:HIS69
|
4.1
|
40.7
|
1.0
|
|
CG
|
E:HIS115
|
4.2
|
27.8
|
1.0
|
|
ND1
|
E:HIS71
|
4.2
|
32.8
|
1.0
|
|
CG
|
E:HIS69
|
4.2
|
36.4
|
1.0
|
|
C19
|
E:QUE301
|
4.2
|
37.2
|
0.5
|
|
CG
|
E:HIS71
|
4.3
|
30.5
|
1.0
|
|
C14
|
E:QUE301
|
4.5
|
38.4
|
0.5
|
|
CB
|
E:GLU76
|
4.9
|
30.3
|
1.0
|
|
C3
|
E:QUE301
|
4.9
|
39.5
|
0.5
|
|
Nickel binding site 6 out
of 12 in 5flj
Go back to
Nickel Binding Sites List in 5flj
Nickel binding site 6 out
of 12 in the Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 6 of Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ni300
b:31.6
occ:1.00
|
NE2
|
F:HIS71
|
2.1
|
35.8
|
1.0
|
|
NE2
|
F:HIS69
|
2.1
|
34.9
|
1.0
|
|
OE1
|
F:GLU76
|
2.1
|
33.7
|
1.0
|
|
O27
|
F:QUE301
|
2.2
|
35.4
|
0.8
|
|
NE2
|
F:HIS115
|
2.3
|
30.0
|
1.0
|
|
O2
|
F:OXY302
|
2.4
|
36.3
|
0.8
|
|
O1
|
F:OXY302
|
2.4
|
35.2
|
0.8
|
|
CD
|
F:GLU76
|
2.9
|
46.4
|
1.0
|
|
CE1
|
F:HIS71
|
3.0
|
33.9
|
1.0
|
|
OE2
|
F:GLU76
|
3.0
|
50.6
|
1.0
|
|
C10
|
F:QUE301
|
3.1
|
40.7
|
0.8
|
|
CD2
|
F:HIS69
|
3.1
|
36.6
|
1.0
|
|
CE1
|
F:HIS69
|
3.1
|
35.9
|
1.0
|
|
CD2
|
F:HIS71
|
3.2
|
32.3
|
1.0
|
|
CE1
|
F:HIS115
|
3.2
|
28.5
|
1.0
|
|
O13
|
F:QUE301
|
3.3
|
48.4
|
0.8
|
|
CD2
|
F:HIS115
|
3.3
|
30.1
|
1.0
|
|
C9
|
F:QUE301
|
3.5
|
47.5
|
0.8
|
|
ND1
|
F:HIS71
|
4.1
|
40.5
|
1.0
|
|
ND1
|
F:HIS69
|
4.2
|
39.8
|
1.0
|
|
C11
|
F:QUE301
|
4.2
|
42.2
|
0.8
|
|
CG
|
F:HIS69
|
4.2
|
39.0
|
1.0
|
|
CG
|
F:HIS71
|
4.3
|
33.0
|
1.0
|
|
CG
|
F:GLU76
|
4.3
|
38.7
|
1.0
|
|
C19
|
F:QUE301
|
4.3
|
40.5
|
0.8
|
|
ND1
|
F:HIS115
|
4.3
|
31.8
|
1.0
|
|
CG
|
F:HIS115
|
4.4
|
27.1
|
1.0
|
|
C14
|
F:QUE301
|
4.6
|
39.2
|
0.8
|
|
C3
|
F:QUE301
|
4.8
|
42.9
|
0.8
|
|
Nickel binding site 7 out
of 12 in 5flj
Go back to
Nickel Binding Sites List in 5flj
Nickel binding site 7 out
of 12 in the Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 7 of Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ni300
b:28.5
occ:1.00
|
NE2
|
G:HIS115
|
2.0
|
28.0
|
1.0
|
|
NE2
|
G:HIS71
|
2.1
|
31.1
|
1.0
|
|
O27
|
G:QUE301
|
2.1
|
27.8
|
0.8
|
|
NE2
|
G:HIS69
|
2.1
|
30.2
|
1.0
|
|
OE1
|
G:GLU76
|
2.1
|
33.9
|
1.0
|
|
O
|
G:HOH2061
|
2.3
|
26.9
|
1.0
|
|
CD
|
G:GLU76
|
2.9
|
33.6
|
1.0
|
|
CE1
|
G:HIS115
|
2.9
|
30.6
|
1.0
|
|
C10
|
G:QUE301
|
3.0
|
37.4
|
0.8
|
|
CE1
|
G:HIS71
|
3.0
|
29.1
|
1.0
|
|
CD2
|
G:HIS69
|
3.0
|
30.1
|
1.0
|
|
CD2
|
G:HIS115
|
3.1
|
27.1
|
1.0
|
|
CD2
|
G:HIS71
|
3.1
|
27.9
|
1.0
|
|
CE1
|
G:HIS69
|
3.1
|
32.7
|
1.0
|
|
OE2
|
G:GLU76
|
3.1
|
43.7
|
1.0
|
|
O13
|
G:QUE301
|
3.4
|
43.6
|
0.8
|
|
C9
|
G:QUE301
|
3.5
|
43.3
|
0.8
|
|
C11
|
G:QUE301
|
4.0
|
31.3
|
0.8
|
|
ND1
|
G:HIS115
|
4.1
|
30.0
|
1.0
|
|
ND1
|
G:HIS71
|
4.1
|
34.0
|
1.0
|
|
CG
|
G:HIS115
|
4.2
|
28.9
|
1.0
|
|
CG
|
G:HIS69
|
4.2
|
30.8
|
1.0
|
|
C19
|
G:QUE301
|
4.2
|
33.9
|
0.8
|
|
ND1
|
G:HIS69
|
4.2
|
36.9
|
1.0
|
|
CG
|
G:HIS71
|
4.2
|
32.8
|
1.0
|
|
CG
|
G:GLU76
|
4.3
|
31.9
|
1.0
|
|
C14
|
G:QUE301
|
4.5
|
32.7
|
0.8
|
|
C3
|
G:QUE301
|
4.8
|
25.9
|
0.8
|
|
CB
|
G:GLU76
|
5.0
|
26.0
|
1.0
|
|
Nickel binding site 8 out
of 12 in 5flj
Go back to
Nickel Binding Sites List in 5flj
Nickel binding site 8 out
of 12 in the Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 8 of Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ni300
b:30.9
occ:1.00
|
OE1
|
H:GLU76
|
2.1
|
28.8
|
0.6
|
|
NE2
|
H:HIS71
|
2.1
|
28.6
|
1.0
|
|
NE2
|
H:HIS115
|
2.1
|
33.5
|
1.0
|
|
NE2
|
H:HIS69
|
2.1
|
33.4
|
1.0
|
|
OE1
|
H:GLU76
|
2.1
|
33.5
|
0.4
|
|
O27
|
H:QUE301
|
2.2
|
27.7
|
0.7
|
|
O
|
H:HOH2059
|
2.3
|
31.4
|
1.0
|
|
CD
|
H:GLU76
|
2.8
|
19.9
|
0.4
|
|
OE2
|
H:GLU76
|
2.8
|
43.1
|
0.4
|
|
CE1
|
H:HIS71
|
2.9
|
29.1
|
1.0
|
|
C10
|
H:QUE301
|
3.0
|
41.0
|
0.7
|
|
CE1
|
H:HIS115
|
3.0
|
34.0
|
1.0
|
|
CD
|
H:GLU76
|
3.0
|
34.5
|
0.6
|
|
CD2
|
H:HIS69
|
3.0
|
33.7
|
1.0
|
|
CD2
|
H:HIS115
|
3.1
|
28.5
|
1.0
|
|
CE1
|
H:HIS69
|
3.1
|
38.9
|
1.0
|
|
CD2
|
H:HIS71
|
3.2
|
30.6
|
1.0
|
|
O13
|
H:QUE301
|
3.4
|
48.4
|
0.7
|
|
OE2
|
H:GLU76
|
3.5
|
37.9
|
0.6
|
|
C9
|
H:QUE301
|
3.5
|
45.8
|
0.7
|
|
C11
|
H:QUE301
|
4.0
|
42.2
|
0.7
|
|
ND1
|
H:HIS71
|
4.1
|
31.9
|
1.0
|
|
ND1
|
H:HIS115
|
4.1
|
28.4
|
1.0
|
|
CG
|
H:HIS115
|
4.2
|
28.6
|
1.0
|
|
CG
|
H:HIS69
|
4.2
|
34.3
|
1.0
|
|
ND1
|
H:HIS69
|
4.2
|
40.5
|
1.0
|
|
CG
|
H:HIS71
|
4.2
|
30.1
|
1.0
|
|
CG
|
H:GLU76
|
4.3
|
26.7
|
0.6
|
|
CG
|
H:GLU76
|
4.3
|
25.8
|
0.4
|
|
C19
|
H:QUE301
|
4.4
|
40.3
|
0.7
|
|
C14
|
H:QUE301
|
4.5
|
40.1
|
0.7
|
|
C3
|
H:QUE301
|
4.7
|
36.9
|
0.7
|
|
CB
|
H:GLU76
|
4.9
|
28.7
|
0.4
|
|
CB
|
H:GLU76
|
5.0
|
23.3
|
0.6
|
|
Nickel binding site 9 out
of 12 in 5flj
Go back to
Nickel Binding Sites List in 5flj
Nickel binding site 9 out
of 12 in the Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 9 of Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ni300
b:35.4
occ:1.00
|
NE2
|
I:HIS69
|
2.0
|
49.8
|
1.0
|
|
OE1
|
I:GLU76
|
2.0
|
45.5
|
1.0
|
|
NE2
|
I:HIS115
|
2.1
|
41.4
|
1.0
|
|
NE2
|
I:HIS71
|
2.1
|
35.5
|
1.0
|
|
O27
|
I:QUE301
|
2.2
|
40.8
|
0.8
|
|
O
|
I:HOH2051
|
2.3
|
29.7
|
0.7
|
|
CD
|
I:GLU76
|
2.9
|
47.5
|
1.0
|
|
CD2
|
I:HIS69
|
2.9
|
45.4
|
1.0
|
|
C10
|
I:QUE301
|
3.0
|
47.3
|
0.8
|
|
CE1
|
I:HIS71
|
3.0
|
38.3
|
1.0
|
|
CE1
|
I:HIS115
|
3.0
|
41.5
|
1.0
|
|
CE1
|
I:HIS69
|
3.0
|
55.0
|
1.0
|
|
CD2
|
I:HIS115
|
3.1
|
35.1
|
1.0
|
|
CD2
|
I:HIS71
|
3.2
|
43.1
|
1.0
|
|
OE2
|
I:GLU76
|
3.3
|
51.9
|
1.0
|
|
O13
|
I:QUE301
|
3.4
|
56.5
|
0.8
|
|
C9
|
I:QUE301
|
3.5
|
49.9
|
0.8
|
|
C11
|
I:QUE301
|
4.0
|
44.5
|
0.8
|
|
CG
|
I:HIS69
|
4.1
|
47.5
|
1.0
|
|
ND1
|
I:HIS69
|
4.1
|
50.0
|
1.0
|
|
ND1
|
I:HIS71
|
4.1
|
41.6
|
1.0
|
|
ND1
|
I:HIS115
|
4.1
|
41.6
|
1.0
|
|
C19
|
I:QUE301
|
4.2
|
44.9
|
0.8
|
|
CG
|
I:HIS115
|
4.2
|
39.2
|
1.0
|
|
CG
|
I:HIS71
|
4.3
|
44.5
|
1.0
|
|
CG
|
I:GLU76
|
4.3
|
42.4
|
1.0
|
|
C14
|
I:QUE301
|
4.5
|
38.9
|
0.8
|
|
C3
|
I:QUE301
|
4.7
|
47.2
|
0.8
|
|
CB
|
I:GLU76
|
4.9
|
37.7
|
1.0
|
|
Nickel binding site 10 out
of 12 in 5flj
Go back to
Nickel Binding Sites List in 5flj
Nickel binding site 10 out
of 12 in the Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 10 of Enzyme-Substrate-Dioxygen Complex of Ni-Quercetinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Ni300
b:42.7
occ:1.00
|
NE2
|
J:HIS69
|
2.0
|
45.7
|
1.0
|
|
NE2
|
J:HIS115
|
2.0
|
46.3
|
1.0
|
|
NE2
|
J:HIS71
|
2.1
|
61.5
|
1.0
|
|
OE1
|
J:GLU76
|
2.1
|
50.6
|
1.0
|
|
O27
|
J:QUE301
|
2.1
|
39.2
|
0.8
|
|
O
|
J:HOH2044
|
2.3
|
49.3
|
1.0
|
|
CD
|
J:GLU76
|
2.9
|
51.1
|
1.0
|
|
CD2
|
J:HIS69
|
2.9
|
48.6
|
1.0
|
|
C10
|
J:QUE301
|
3.0
|
51.1
|
0.8
|
|
CE1
|
J:HIS115
|
3.0
|
44.8
|
1.0
|
|
CD2
|
J:HIS71
|
3.0
|
45.3
|
1.0
|
|
CD2
|
J:HIS115
|
3.0
|
42.8
|
1.0
|
|
OE2
|
J:GLU76
|
3.0
|
50.3
|
1.0
|
|
CE1
|
J:HIS71
|
3.1
|
45.8
|
1.0
|
|
CE1
|
J:HIS69
|
3.1
|
46.1
|
1.0
|
|
O13
|
J:QUE301
|
3.4
|
56.5
|
0.8
|
|
C9
|
J:QUE301
|
3.5
|
55.9
|
0.8
|
|
C11
|
J:QUE301
|
3.9
|
50.0
|
0.8
|
|
C19
|
J:QUE301
|
4.0
|
50.6
|
0.8
|
|
CG
|
J:HIS69
|
4.1
|
50.8
|
1.0
|
|
ND1
|
J:HIS115
|
4.1
|
48.8
|
1.0
|
|
ND1
|
J:HIS69
|
4.1
|
54.1
|
1.0
|
|
ND1
|
J:HIS71
|
4.2
|
47.7
|
1.0
|
|
CG
|
J:HIS115
|
4.2
|
45.1
|
1.0
|
|
CG
|
J:HIS71
|
4.2
|
47.4
|
1.0
|
|
CG
|
J:GLU76
|
4.3
|
48.8
|
1.0
|
|
C14
|
J:QUE301
|
4.4
|
47.8
|
0.8
|
|
C3
|
J:QUE301
|
4.8
|
56.5
|
0.8
|
|
CB
|
J:GLU76
|
4.9
|
38.1
|
1.0
|
|
CZ
|
J:PHE78
|
5.0
|
51.1
|
1.0
|
|
Reference:
J.Jeoung,
D.Nianios,
S.Fetzner,
H.Dobbek.
Quercetin 2,4-Dioxygenase Activates Dioxygen in A Side-on O2 -Ni Complex. Angew.Chem.Int.Ed.Engl. V. 55 3281 2016.
ISSN: ISSN 1433-7851
PubMed: 26846734
DOI: 10.1002/ANIE.201510741
Page generated: Thu Oct 10 06:22:40 2024
|
