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Magnesium in PDB 3x26: Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 5 Min

Enzymatic activity of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 5 Min

All present enzymatic activity of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 5 Min:
4.2.1.84;

Protein crystallography data

The structure of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 5 Min, PDB code: 3x26 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) 24.67 / 1.34
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.861, 59.953, 81.594, 90.00, 125.08, 90.00
R / Rfree (%) 17.3 / 19.4

Other elements in 3x26:

The structure of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 5 Min also contains other interesting chemical elements:

Iron (Fe) 1 atom
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 5 Min (pdb code 3x26). 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 5 Min, PDB code: 3x26:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3x26

Go back to Magnesium Binding Sites List in 3x26
Magnesium binding site 1 out of 2 in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 5 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 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:16.1
occ:0.50
O A:HOH474 4.1 22.3 1.0
O A:HOH460 4.2 25.1 1.0
O A:HOH508 4.2 24.8 1.0
NH1 A:ARG174 4.8 17.5 1.0
CG A:GLU179 5.0 18.5 1.0
CD A:ARG174 5.0 20.7 1.0

Magnesium binding site 2 out of 2 in 3x26

Go back to Magnesium Binding Sites List in 3x26
Magnesium binding site 2 out of 2 in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 5 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 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:11.6
occ:0.50
O B:HOH408 2.4 15.9 1.0
O B:HOH467 4.1 18.6 1.0
O B:HOH446 4.2 19.6 1.0
O B:HOH552 4.4 27.9 1.0
O B:ASP6 4.4 11.9 1.0
OD2 B:ASP6 4.4 11.2 1.0
CB B:ALA144 4.5 13.4 1.0
O B:GLY3 4.5 10.6 1.0
CB B:ASP6 4.5 10.7 1.0
O B:ASP2 4.6 11.2 1.0
CB B:ASP2 4.6 12.0 1.0
CG B:ASP6 4.7 10.5 1.0
C B:ASP2 4.7 11.5 1.0
OD1 B:ASP2 4.7 15.3 1.0
CA B:ASP2 4.8 12.0 1.0
CG B:ASP2 4.8 13.9 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: Thu Aug 15 13:49:38 2024

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