Atomistry » Magnesium » PDB 2zjp-2zvj » 2zpe
Atomistry »
  Magnesium »
    PDB 2zjp-2zvj »
      2zpe »

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

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

Last articles

Mg in 8G7N
Mg in 8GIY
Mg in 8GHF
Mg in 8GIP
Mg in 8GIM
Mg in 8GIN
Mg in 8GFT
Mg in 8GI6
Mg in 8GCQ
Mg in 8GI3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy