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Magnesium in PDB 2zpi: Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 440MIN at 293K

Enzymatic activity of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 440MIN at 293K

All present enzymatic activity of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 440MIN at 293K:
4.2.1.84;

Protein crystallography data

The structure of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 440MIN at 293K, PDB code: 2zpi 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 / 1.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.046, 60.230, 81.480, 90.00, 125.12, 90.00
R / Rfree (%) 15.7 / 18.2

Other elements in 2zpi:

The structure of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 440MIN at 293K also contains other interesting chemical elements:

Iron (Fe) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 440MIN at 293K (pdb code 2zpi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 440MIN at 293K, PDB code: 2zpi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2zpi

Go back to Magnesium Binding Sites List in 2zpi
Magnesium binding site 1 out of 4 in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 440MIN at 293K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 440MIN at 293K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:22.8
occ:1.00
 O A:HOH1608 1.9 25.0 1.0
O A:HOH1605 2.0 22.7 1.0
O A:HOH1610 2.0 26.5 1.0
O A:HOH1607 2.1 17.7 1.0
O A:HOH1609 2.1 27.5 1.0
O A:HOH1606 2.2 27.2 1.0
O A:HOH1713 4.1 22.5 1.0
O A:HOH1687 4.1 20.9 1.0
O A:HOH1670 4.1 18.7 1.0
O A:HOH1762 4.5 28.7 1.0
CG A:GLU179 4.8 15.1 1.0
NH1 A:ARG174 4.9 13.2 1.0

Magnesium binding site 2 out of 4 in 2zpi

Go back to Magnesium Binding Sites List in 2zpi
Magnesium binding site 2 out of 4 in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 440MIN at 293K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 440MIN at 293K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:23.9
occ:1.00
 O A:HOH1613 1.9 40.1 1.0
O A:HOH1614 2.0 17.4 1.0
O A:HOH1611 2.1 27.7 1.0
O A:HOH1612 2.4 23.6 1.0
O A:GLY180 3.9 13.7 1.0
OE1 A:GLN185 4.2 17.6 1.0
O A:HOH1678 4.3 22.1 1.0
NE2 A:GLN185 4.7 19.9 1.0
C A:GLY180 4.8 13.4 1.0
CD A:GLN185 4.9 16.5 1.0
N A:SER182 5.0 13.2 1.0

Magnesium binding site 3 out of 4 in 2zpi

Go back to Magnesium Binding Sites List in 2zpi
Magnesium binding site 3 out of 4 in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 440MIN at 293K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 440MIN at 293K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1601

b:17.1
occ:1.00
 O B:HOH1792 2.0 18.5 1.0
O B:HOH1790 2.0 15.6 1.0
O B:HOH1795 2.0 18.4 1.0
O B:HOH1794 2.0 25.1 1.0
O B:HOH1791 2.2 18.0 1.0
O B:HOH1793 2.3 10.8 1.0
O B:HOH1900 4.1 18.7 1.0
O B:HOH1925 4.1 26.0 1.0
O B:ASP6 4.3 7.8 1.0
OD2 B:ASP6 4.5 8.2 1.0
O B:GLY3 4.5 6.5 1.0
CB B:ASP6 4.5 6.3 1.0
CB B:ALA144 4.5 8.2 1.0
O B:ASP2 4.5 7.3 1.0
CB B:ASP2 4.6 7.3 1.0
C B:ASP2 4.7 6.8 1.0
CG B:ASP6 4.7 6.9 1.0
CA B:ASP2 4.7 7.1 1.0
OD1 B:ASP2 4.7 10.2 1.0
CG B:ASP2 4.8 9.4 1.0

Magnesium binding site 4 out of 4 in 2zpi

Go back to Magnesium Binding Sites List in 2zpi
Magnesium binding site 4 out of 4 in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 440MIN at 293K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 440MIN at 293K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1604

b:25.5
occ:1.00
 O B:HOH1800 2.0 21.2 1.0
O B:HOH1798 2.0 30.2 1.0
O B:HOH1797 2.2 37.1 1.0
O B:HOH1796 2.2 23.5 1.0
O B:HOH1799 2.2 34.9 1.0
O B:HOH1984 3.9 41.1 1.0
O B:HOH1830 4.2 10.0 1.0
CE B:MET69 4.2 14.8 0.4
OE1 B:GLU74 4.4 11.0 1.0
O A:HOH1672 4.4 21.1 1.0
O B:MET69 4.5 8.8 1.0
CD B:PRO71 4.6 8.1 1.0
CE B:MET69 4.7 14.5 0.6
O B:HOH2034 4.9 38.7 1.0
OE2 B:GLU74 5.0 8.1 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 07:50:52 2020

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