Magnesium in PDB 2zpb: Nitrosylated Fe-Type Nitrile Hydratase

All present enzymatic activity of Nitrosylated Fe-Type Nitrile Hydratase:
4.2.1.84;

The structure of Nitrosylated Fe-Type Nitrile Hydratase, PDB code: 2zpb 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)	7.96 / 1.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.657, 60.548, 81.920, 90.00, 124.97, 90.00
R / Rfree (%)	16.7 / 18.6

The structure of Nitrosylated Fe-Type Nitrile Hydratase also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Magnesium atom in the Nitrosylated Fe-Type Nitrile Hydratase (pdb code 2zpb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Nitrosylated Fe-Type Nitrile Hydratase, PDB code: 2zpb:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Nitrosylated Fe-Type Nitrile Hydratase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1302 b:15.7 occ:0.50 O A:HOH1525 1.9 32.1 1.0 O A:HOH1557 2.0 32.6 1.0 O A:HOH1384 2.1 17.3 1.0 O A:HOH1476 2.1 27.0 1.0 O A:HOH1510 2.1 26.1 1.0 O A:HOH1466 2.2 25.0 1.0 O A:HOH1583 3.2 48.7 1.0 O A:HOH1366 4.1 19.1 1.0 O A:HOH1413 4.1 24.9 1.0 O A:HOH1429 4.3 21.9 1.0 NH1 A:ARG174 4.6 14.8 1.0 O A:HOH1670 4.7 58.2 1.0 CD A:ARG174 4.9 16.2 1.0 CZ A:ARG174 4.9 13.8 1.0 NE A:ARG174 5.0 14.2 1.0

Magnesium binding site 2 out of 3 in the Nitrosylated Fe-Type Nitrile Hydratase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1303 b:14.9 occ:0.50 O A:HOH1582 2.0 37.7 1.0 O A:HOH1574 2.0 37.5 1.0 O A:HOH1374 2.0 18.9 1.0 O A:HOH1549 2.2 36.9 1.0 O A:HOH1559 2.5 42.5 1.0 O A:HOH1411 2.7 23.8 1.0 O A:GLY180 4.0 13.9 1.0 OE1 A:GLN185 4.1 17.0 1.0 O A:HOH1370 4.2 18.6 1.0 O A:HOH1522 4.4 35.4 1.0 C A:GLY180 4.9 13.6 1.0 CD A:GLN185 5.0 17.9 1.0

Magnesium binding site 3 out of 3 in the Nitrosylated Fe-Type Nitrile Hydratase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1301 b:6.2 occ:0.50 O B:HOH1392 2.0 12.4 1.0 O B:HOH1399 2.0 14.1 1.0 O B:HOH1405 2.1 13.7 1.0 O B:HOH1390 2.1 8.6 0.5 O B:HOH1435 2.1 8.8 0.5 O B:HOH1390 2.2 6.7 0.5 O B:HOH1321 2.3 9.6 1.0 O B:HOH1435 3.0 8.8 0.5 O B:HOH1483 3.8 21.1 1.0 O B:HOH1371 4.1 13.5 1.0 OD2 B:ASP6 4.4 7.0 1.0 O B:HOH1336 4.4 11.5 1.0 O B:ASP6 4.4 6.5 1.0 CB B:ALA144 4.4 7.5 1.0 CB B:ASP6 4.5 6.3 1.0 O B:ASP2 4.5 6.6 1.0 O B:GLY3 4.5 5.8 1.0 CB B:ASP2 4.6 6.6 1.0 OD1 B:ASP2 4.6 8.8 1.0 CG B:ASP6 4.7 6.3 1.0 C B:ASP2 4.7 6.3 1.0 CG B:ASP2 4.7 7.4 1.0 CA B:ASP2 4.7 6.5 1.0

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