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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:

Iron (Fe) 1 atom

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

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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

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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

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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

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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

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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

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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: Mon Dec 14 07:50:49 2020

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