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Magnesium in PDB 2zpf: Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 18MIN at 293K

Enzymatic activity of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 18MIN at 293K

All present enzymatic activity of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 18MIN at 293K:
4.2.1.84;

Protein crystallography data

The structure of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 18MIN at 293K, PDB code: 2zpf 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 (°) 114.045, 59.995, 81.710, 90.00, 125.06, 90.00
R / Rfree (%) 16.8 / 19

Other elements in 2zpf:

The structure of Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 18MIN 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 18MIN at 293K (pdb code 2zpf). 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 18MIN at 293K, PDB code: 2zpf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2zpf

Go back to Magnesium Binding Sites List in 2zpf
Magnesium binding site 1 out of 4 in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 18MIN 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 18MIN at 293K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:23.8
occ:1.00
 O A:HOH1607 2.2 25.1 1.0
O A:HOH1609 2.2 24.9 1.0
O A:HOH1604 2.2 24.2 1.0
O A:HOH1606 2.2 21.8 1.0
O A:HOH1608 2.2 24.4 1.0
O A:HOH1605 2.2 24.3 1.0
O A:HOH1674 4.1 20.2 1.0
O A:HOH1684 4.2 23.1 1.0
O A:HOH1737 4.2 23.4 1.0
O A:HOH1850 4.5 38.2 1.0
O A:HOH1875 4.5 42.0 1.0
NH1 A:ARG174 4.8 16.0 1.0
CG A:GLU179 4.9 16.8 1.0
CD A:ARG174 4.9 17.2 1.0

Magnesium binding site 2 out of 4 in 2zpf

Go back to Magnesium Binding Sites List in 2zpf
Magnesium binding site 2 out of 4 in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 18MIN 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 18MIN at 293K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:28.6
occ:1.00
 O A:HOH1615 2.2 28.5 1.0
O A:HOH1612 2.2 30.4 1.0
O A:HOH1614 2.2 30.4 1.0
O A:HOH1610 2.2 30.4 1.0
O A:HOH1611 2.2 30.0 1.0
O A:HOH1613 2.2 28.6 1.0
O A:GLY180 3.9 16.8 1.0
OE1 A:GLN185 4.1 20.1 1.0
O A:HOH1676 4.3 23.2 1.0
O A:HOH1872 4.6 39.4 1.0
NE2 A:GLN185 4.7 23.8 1.0
CD A:GLN185 4.8 19.0 1.0
C A:GLY180 4.8 16.1 1.0
N A:SER182 4.9 16.1 1.0

Magnesium binding site 3 out of 4 in 2zpf

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Magnesium binding site 3 out of 4 in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 18MIN 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 18MIN at 293K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1601

b:17.9
occ:1.00
 O B:HOH1608 2.2 18.5 1.0
O B:HOH1611 2.2 18.5 1.0
O B:HOH1607 2.2 18.8 1.0
O B:HOH1610 2.2 19.7 1.0
O B:HOH1606 2.2 17.7 1.0
O B:HOH1609 2.2 15.1 1.0
O B:HOH1870 4.2 29.7 1.0
O B:HOH1664 4.3 17.4 1.0
O B:ASP6 4.4 8.9 1.0
OD2 B:ASP6 4.4 9.7 1.0
CB B:ALA144 4.4 10.3 1.0
CB B:ASP6 4.5 8.0 1.0
O B:ASP2 4.5 8.9 1.0
O B:GLY3 4.5 8.4 1.0
CB B:ASP2 4.6 9.4 1.0
CG B:ASP6 4.6 9.2 1.0
OD1 B:ASP2 4.6 12.7 1.0
C B:ASP2 4.6 8.8 1.0
CG B:ASP2 4.7 11.0 1.0
CA B:ASP2 4.7 8.9 1.0

Magnesium binding site 4 out of 4 in 2zpf

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Magnesium binding site 4 out of 4 in the Complex of Fe-Type Nitrile Hydratase with Tert- Butylisonitrile, Photo-Activated For 18MIN 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 18MIN at 293K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1604

b:25.4
occ:1.00
 O B:HOH1617 2.2 24.3 1.0
O B:HOH1615 2.2 24.7 1.0
O B:HOH1612 2.2 26.1 1.0
O B:HOH1616 2.2 27.3 1.0
O B:HOH1614 2.2 26.8 1.0
O B:HOH1613 2.2 26.9 1.0
O B:HOH1781 3.9 34.7 1.0
O A:HOH1801 4.2 33.5 1.0
O B:HOH1638 4.2 11.0 1.0
O A:HOH1664 4.3 20.3 1.0
OE1 B:GLU74 4.4 11.9 1.0
O B:HOH1739 4.4 26.0 1.0
CE B:MET69 4.5 12.1 0.6
CD B:PRO71 4.6 9.3 1.0
O B:MET69 4.6 9.6 1.0
CE B:MET69 4.6 15.1 0.5

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 07:55:44 2024

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