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Magnesium in PDB 3a8g: Crystal Structure of Nitrile Hydratase Mutant S113A Complexed with Trimethylacetonitrile

Enzymatic activity of Crystal Structure of Nitrile Hydratase Mutant S113A Complexed with Trimethylacetonitrile

All present enzymatic activity of Crystal Structure of Nitrile Hydratase Mutant S113A Complexed with Trimethylacetonitrile:
4.2.1.84;

Protein crystallography data

The structure of Crystal Structure of Nitrile Hydratase Mutant S113A Complexed with Trimethylacetonitrile, PDB code: 3a8g was solved by Y.Yamanaka, K.Hashimoto, A.Ohtaki, K.Noguchi, M.Yohda, M.Odaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.01 / 1.11
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.411, 60.268, 81.810, 90.00, 124.92, 90.00
R / Rfree (%) 14.2 / 16.9

Other elements in 3a8g:

The structure of Crystal Structure of Nitrile Hydratase Mutant S113A Complexed with Trimethylacetonitrile also contains other interesting chemical elements:

Iron (Fe) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Nitrile Hydratase Mutant S113A Complexed with Trimethylacetonitrile (pdb code 3a8g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Nitrile Hydratase Mutant S113A Complexed with Trimethylacetonitrile, PDB code: 3a8g:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3a8g

Go back to Magnesium Binding Sites List in 3a8g
Magnesium binding site 1 out of 3 in the Crystal Structure of Nitrile Hydratase Mutant S113A Complexed with Trimethylacetonitrile


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Nitrile Hydratase Mutant S113A Complexed with Trimethylacetonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:9.9
occ:0.50
 O B:HOH433 1.9 19.9 1.0
O B:HOH434 2.0 21.2 1.0
O B:HOH436 2.1 16.6 1.0
O B:HOH432 2.1 21.0 1.0
O B:HOH435 2.3 15.0 1.0
O B:HOH324 2.5 20.6 0.5
O B:HOH342 4.2 17.8 1.0
O B:HOH319 4.3 15.7 1.0
O B:ASP6 4.4 8.6 1.0
OD2 B:ASP6 4.4 9.2 1.0
CB B:ALA144 4.4 10.1 1.0
O B:GLY3 4.5 7.9 1.0
O B:ASP2 4.5 8.9 1.0
CB B:ASP6 4.5 8.1 1.0
CB B:ASP2 4.6 9.4 1.0
CG B:ASP6 4.6 8.2 1.0
C B:ASP2 4.7 7.7 1.0
OD1 B:ASP2 4.7 11.9 1.0
CA B:ASP2 4.7 8.4 1.0
CG B:ASP2 4.8 10.5 1.0

Magnesium binding site 2 out of 3 in 3a8g

Go back to Magnesium Binding Sites List in 3a8g
Magnesium binding site 2 out of 3 in the Crystal Structure of Nitrile Hydratase Mutant S113A Complexed with Trimethylacetonitrile


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Nitrile Hydratase Mutant S113A Complexed with Trimethylacetonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:15.7
occ:0.50
 O B:HOH427 1.8 27.0 1.0
O B:HOH425 2.0 24.9 1.0
O B:HOH429 2.0 26.7 1.0
O B:HOH430 2.1 26.1 1.0
O B:HOH426 2.2 19.6 1.0
O B:HOH428 2.2 26.5 1.0
O B:HOH325 4.3 16.0 1.0
OE1 B:GLU96 4.3 14.5 1.0
O B:HOH423 4.3 26.1 1.0
O B:HOH323 4.5 36.6 1.0

Magnesium binding site 3 out of 3 in 3a8g

Go back to Magnesium Binding Sites List in 3a8g
Magnesium binding site 3 out of 3 in the Crystal Structure of Nitrile Hydratase Mutant S113A Complexed with Trimethylacetonitrile


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Nitrile Hydratase Mutant S113A Complexed with Trimethylacetonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:16.6
occ:0.50
 O B:HOH388 1.8 28.6 1.0
O B:HOH389 1.9 36.4 1.0
O B:HOH405 2.0 31.7 1.0
O B:HOH381 2.1 18.2 1.0
O B:HOH386 2.2 26.5 1.0
O B:HOH401 2.3 22.5 1.0
OE2 B:GLU119 3.9 48.2 1.0
OE1 B:GLU119 4.1 43.4 1.0
O B:HOH300 4.2 40.9 1.0
CD B:GLU119 4.4 39.2 1.0

Reference:

Y.Yamanaka, K.Hashimoto, A.Ohtaki, K.Noguchi, M.Yohda, M.Odaka. Kinetic and Structural Studies on Roles of the Serine Ligand and A Strictly Conserved Tyrosine Residue in Nitrile Hydratase J.Biol.Inorg.Chem. V. 15 655 2010.
ISSN: ISSN 0949-8257
PubMed: 20221653
DOI: 10.1007/S00775-010-0632-3
Page generated: Wed Aug 14 08:30:44 2024

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