Magnesium in PDB 2zpe: Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile
Enzymatic activity of Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile
All present enzymatic activity of Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile:
4.2.1.84;
Protein crystallography data
The structure of Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, PDB code: 2zpe
was solved by
K.Hashimoto,
H.Suzuki,
K.Taniguchi,
T.Noguchi,
M.Yohda,
M.Odaka,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
1.48
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
113.976,
60.002,
81.707,
90.00,
125.08,
90.00
|
R / Rfree (%)
|
16.5 /
19.3
|
Other elements in 2zpe:
The structure of Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile
(pdb code 2zpe). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, PDB code: 2zpe:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 2zpe
Go back to
Magnesium Binding Sites List in 2zpe
Magnesium binding site 1 out
of 6 in the Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1602
b:13.9
occ:0.50
|
O
|
A:HOH1832
|
1.9
|
25.8
|
1.0
|
O
|
A:HOH1792
|
2.0
|
28.1
|
1.0
|
O
|
A:HOH1749
|
2.1
|
25.5
|
1.0
|
O
|
A:HOH1701
|
2.1
|
24.8
|
1.0
|
O
|
A:HOH1670
|
2.1
|
17.4
|
1.0
|
O
|
A:HOH1769
|
2.1
|
25.6
|
1.0
|
O
|
A:HOH1677
|
4.1
|
21.2
|
1.0
|
O
|
A:HOH1678
|
4.2
|
22.2
|
1.0
|
O
|
A:HOH1732
|
4.2
|
21.5
|
1.0
|
O
|
A:HOH1898
|
4.4
|
44.4
|
1.0
|
NH1
|
A:ARG174
|
4.8
|
14.6
|
1.0
|
CG
|
A:GLU179
|
4.9
|
15.8
|
1.0
|
CD
|
A:ARG174
|
4.9
|
16.4
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 2zpe
Go back to
Magnesium Binding Sites List in 2zpe
Magnesium binding site 2 out
of 6 in the Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1603
b:21.3
occ:0.50
|
O
|
A:HOH1817
|
2.1
|
32.5
|
1.0
|
O
|
A:HOH1753
|
2.1
|
27.1
|
1.0
|
O
|
A:HOH1925
|
2.3
|
38.2
|
1.0
|
OE2
|
A:GLU92
|
4.1
|
21.8
|
1.0
|
O
|
A:HOH1891
|
4.1
|
30.9
|
1.0
|
O
|
B:HOH1923
|
4.2
|
31.6
|
1.0
|
O
|
A:HOH1844
|
4.3
|
35.8
|
1.0
|
OE1
|
A:GLU92
|
4.3
|
23.6
|
1.0
|
O
|
A:HOH1840
|
4.3
|
37.3
|
1.0
|
CD
|
A:GLU92
|
4.7
|
20.4
|
1.0
|
O
|
A:HOH1954
|
4.9
|
44.1
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 2zpe
Go back to
Magnesium Binding Sites List in 2zpe
Magnesium binding site 3 out
of 6 in the Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1604
b:14.4
occ:0.50
|
O
|
A:HOH1928
|
2.0
|
41.8
|
1.0
|
O
|
A:HOH1685
|
2.0
|
21.6
|
1.0
|
O
|
A:HOH1885
|
2.2
|
36.9
|
1.0
|
O
|
A:HOH1934
|
2.3
|
46.6
|
1.0
|
O
|
A:HOH1702
|
2.6
|
22.2
|
1.0
|
O
|
A:GLY180
|
4.0
|
15.8
|
1.0
|
OE1
|
A:GLN185
|
4.1
|
19.8
|
1.0
|
O
|
A:HOH1671
|
4.2
|
21.8
|
1.0
|
O
|
A:HOH1910
|
4.5
|
41.6
|
1.0
|
C
|
A:GLY180
|
4.9
|
15.2
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 2zpe
Go back to
Magnesium Binding Sites List in 2zpe
Magnesium binding site 4 out
of 6 in the Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1606
b:24.2
occ:0.50
|
O
|
B:HOH1786
|
1.9
|
26.4
|
1.0
|
O
|
B:HOH1740
|
1.9
|
25.7
|
1.0
|
O
|
A:HOH1886
|
2.0
|
42.0
|
1.0
|
O
|
B:HOH1768
|
2.2
|
24.9
|
1.0
|
OE1
|
A:GLU139
|
2.5
|
22.3
|
1.0
|
O
|
A:HOH1834
|
2.6
|
32.3
|
1.0
|
O
|
B:HOH1878
|
3.4
|
29.7
|
1.0
|
CD
|
A:GLU139
|
3.5
|
16.0
|
1.0
|
O
|
A:HOH1687
|
4.0
|
26.0
|
1.0
|
OE2
|
A:GLU139
|
4.1
|
18.2
|
1.0
|
OD1
|
B:ASP193
|
4.1
|
21.6
|
1.0
|
O
|
B:HOH1789
|
4.1
|
31.2
|
1.0
|
NE2
|
B:GLN11
|
4.4
|
9.8
|
1.0
|
CG
|
A:GLU139
|
4.5
|
12.6
|
1.0
|
CB
|
A:GLU139
|
4.5
|
10.7
|
1.0
|
O
|
A:HOH1816
|
4.8
|
30.7
|
1.0
|
CG
|
B:ASP193
|
5.0
|
19.8
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 2zpe
Go back to
Magnesium Binding Sites List in 2zpe
Magnesium binding site 5 out
of 6 in the Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1601
b:7.5
occ:0.50
|
O
|
B:HOH1686
|
1.9
|
17.6
|
1.0
|
O
|
B:HOH1726
|
2.0
|
16.6
|
1.0
|
O
|
B:HOH1685
|
2.0
|
16.3
|
1.0
|
O
|
B:HOH1734
|
2.0
|
19.9
|
1.0
|
O
|
B:HOH1697
|
2.1
|
11.9
|
0.5
|
O
|
B:HOH1627
|
2.4
|
12.3
|
1.0
|
O
|
B:HOH1895
|
3.7
|
29.9
|
1.0
|
O
|
B:HOH1692
|
4.1
|
16.3
|
1.0
|
O
|
B:HOH1654
|
4.3
|
14.8
|
1.0
|
O
|
B:ASP6
|
4.4
|
8.1
|
1.0
|
OD2
|
B:ASP6
|
4.4
|
8.7
|
1.0
|
CB
|
B:ALA144
|
4.5
|
9.7
|
1.0
|
CB
|
B:ASP6
|
4.5
|
7.5
|
1.0
|
O
|
B:GLY3
|
4.5
|
7.7
|
1.0
|
O
|
B:ASP2
|
4.5
|
8.3
|
1.0
|
CB
|
B:ASP2
|
4.6
|
8.4
|
1.0
|
CG
|
B:ASP6
|
4.7
|
8.5
|
1.0
|
OD1
|
B:ASP2
|
4.7
|
11.6
|
1.0
|
C
|
B:ASP2
|
4.7
|
7.8
|
1.0
|
CG
|
B:ASP2
|
4.7
|
10.2
|
1.0
|
CA
|
B:ASP2
|
4.8
|
8.4
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 2zpe
Go back to
Magnesium Binding Sites List in 2zpe
Magnesium binding site 6 out
of 6 in the Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Nitrosylated Fe-Type Nitrile Hydratase with Tert- Butylisonitrile within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1605
b:23.3
occ:1.00
|
O
|
B:HOH1704
|
2.0
|
19.2
|
1.0
|
O
|
B:HOH1699
|
2.1
|
17.8
|
1.0
|
O
|
B:HOH1757
|
2.1
|
28.0
|
1.0
|
O
|
B:HOH1848
|
2.2
|
30.2
|
1.0
|
O
|
B:HOH1812
|
2.3
|
31.0
|
1.0
|
O
|
B:HOH1792
|
3.1
|
29.6
|
1.0
|
O
|
B:HOH1906
|
4.1
|
41.1
|
1.0
|
O
|
B:HOH1629
|
4.1
|
10.8
|
1.0
|
O
|
A:HOH1818
|
4.2
|
32.4
|
1.0
|
OE1
|
B:GLU74
|
4.3
|
10.6
|
1.0
|
O
|
A:HOH1664
|
4.3
|
19.8
|
1.0
|
O
|
B:HOH1733
|
4.4
|
24.4
|
1.0
|
CE
|
B:MET69
|
4.4
|
12.3
|
0.8
|
CD
|
B:PRO71
|
4.5
|
7.8
|
1.0
|
O
|
B:MET69
|
4.5
|
8.3
|
1.0
|
CE
|
B:MET69
|
4.8
|
10.8
|
0.2
|
O
|
B:HOH1847
|
4.9
|
31.4
|
1.0
|
CG
|
B:PRO71
|
5.0
|
9.0
|
1.0
|
OE2
|
B:GLU74
|
5.0
|
8.4
|
1.0
|
|
Reference:
K.Hashimoto,
H.Suzuki,
K.Taniguchi,
T.Noguchi,
M.Yohda,
M.Odaka.
Catalytic Mechanism of Nitrile Hydratase Proposed By Time-Resolved X-Ray Crystallography Using A Novel Substrate, Tert-Butylisonitrile J.Biol.Chem. V. 283 36617 2008.
ISSN: ISSN 0021-9258
PubMed: 18948265
DOI: 10.1074/JBC.M806577200
Page generated: Wed Aug 14 07:55:08 2024
|