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Magnesium in PDB 3x24: Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 120 Min

Enzymatic activity of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 120 Min

All present enzymatic activity of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 120 Min:
4.2.1.84;

Protein crystallography data

The structure of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 120 Min, PDB code: 3x24 was solved by Y.Yamanaka, K.Hashimoto, 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) 24.55 / 1.24
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.910, 59.913, 81.585, 90.00, 125.05, 90.00
R / Rfree (%) 13.8 / 16.3

Other elements in 3x24:

The structure of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 120 Min 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 BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 120 Min (pdb code 3x24). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 120 Min, PDB code: 3x24:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3x24

Go back to Magnesium Binding Sites List in 3x24
Magnesium binding site 1 out of 2 in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 120 Min


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 BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 120 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:18.4
occ:0.50
O A:HOH480 4.1 25.0 1.0
O A:HOH483 4.1 28.0 1.0
O A:HOH550 4.2 27.4 1.0
O A:HOH592 4.4 38.2 1.0
NH1 A:ARG174 4.8 20.3 1.0
CD A:ARG174 4.8 22.4 1.0

Magnesium binding site 2 out of 2 in 3x24

Go back to Magnesium Binding Sites List in 3x24
Magnesium binding site 2 out of 2 in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 120 Min


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 BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 120 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:12.5
occ:0.50
O B:HOH402 2.4 16.6 1.0
O B:HOH466 4.1 19.9 1.0
O B:HOH561 4.3 24.3 1.0
O B:HOH446 4.4 20.0 1.0
O B:ASP6 4.4 13.2 1.0
OD2 B:ASP6 4.4 12.7 1.0
CB B:ALA144 4.5 14.4 1.0
O B:GLY3 4.5 11.7 1.0
O B:ASP2 4.5 12.6 1.0
CB B:ASP6 4.6 11.6 1.0
CB B:ASP2 4.6 12.2 1.0
OD1 B:ASP2 4.7 16.0 1.0
CG B:ASP6 4.7 11.8 1.0
C B:ASP2 4.7 12.2 1.0
CA B:ASP2 4.7 12.4 1.0
CG B:ASP2 4.7 13.6 1.0

Reference:

Y.Yamanaka, Y.Kato, K.Hashimoto, K.Iida, K.Nagasawa, H.Nakayama, N.Dohmae, K.Noguchi, T.Noguchi, M.Yohda, M.Odaka. Time-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing A Role For the Cysteinesulfenic Acid Ligand As A Catalytic Nucleophile. Angew.Chem.Int.Ed.Engl. V. 54 10763 2015.
ISSN: ISSN 1433-7851
PubMed: 26333053
DOI: 10.1002/ANIE.201502731
Page generated: Mon Dec 14 09:02:41 2020

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