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Magnesium in PDB 3wve: Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Before Photo-Activation

Enzymatic activity of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Before Photo-Activation

All present enzymatic activity of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Before Photo-Activation:
4.2.1.84;

Protein crystallography data

The structure of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Before Photo-Activation, PDB code: 3wve 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) 29.91 / 1.57
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.742, 59.829, 81.464, 90.00, 125.21, 90.00
R / Rfree (%) 13 / 17.1

Other elements in 3wve:

The structure of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Before Photo-Activation 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, Before Photo-Activation (pdb code 3wve). 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, Before Photo-Activation, PDB code: 3wve:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3wve

Go back to Magnesium Binding Sites List in 3wve
Magnesium binding site 1 out of 2 in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Before Photo-Activation


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, Before Photo-Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:17.4
occ:0.50
 O A:HOH519 1.8 32.3 1.0
O A:HOH523 2.0 32.4 1.0
O A:HOH522 2.1 28.3 1.0
O A:HOH524 2.1 32.9 1.0
O A:HOH520 2.1 35.2 1.0
O A:HOH521 2.1 23.1 1.0
O A:HOH474 4.1 24.9 1.0
O A:HOH479 4.2 24.3 1.0
O A:HOH532 4.2 30.8 1.0
O A:HOH480 4.3 20.9 1.0
NH1 A:ARG174 4.8 19.4 1.0
CG A:GLU179 4.9 21.2 1.0
CD A:ARG174 4.9 21.2 1.0

Magnesium binding site 2 out of 2 in 3wve

Go back to Magnesium Binding Sites List in 3wve
Magnesium binding site 2 out of 2 in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Before Photo-Activation


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, Before Photo-Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:13.8
occ:0.50
 O B:HOH564 2.0 28.8 1.0
O B:HOH538 2.5 25.5 0.5
O B:HOH509 4.3 17.6 1.0
O B:HOH539 4.8 21.6 1.0
O B:HOH515 4.9 19.8 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 13:38:00 2024

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