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Magnesium in PDB 3wvd: Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 50 Min

Enzymatic activity of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 50 Min

All present enzymatic activity of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 50 Min:
4.2.1.84;

Protein crystallography data

The structure of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 50 Min, PDB code: 3wvd 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) 18.19 / 1.18
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.084, 59.965, 81.720, 90.00, 125.05, 90.00
R / Rfree (%) 14.2 / 16.3

Other elements in 3wvd:

The structure of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 50 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 50 Min (pdb code 3wvd). 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 BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 50 Min, PDB code: 3wvd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3wvd

Go back to Magnesium Binding Sites List in 3wvd
Magnesium binding site 1 out of 3 in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 50 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 50 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:21.1
occ:0.50
 O A:HOH491 2.0 30.2 1.0
O A:HOH490 2.0 35.3 1.0
O A:HOH492 2.0 29.3 1.0
O A:HOH538 2.1 29.9 1.0
O A:HOH489 2.1 30.2 1.0
O A:HOH481 2.2 24.4 1.0
O A:HOH477 4.1 24.4 1.0
O A:HOH461 4.2 28.3 1.0
O A:HOH542 4.2 27.0 1.0
NH1 A:ARG174 4.8 21.9 1.0
CD A:ARG174 4.9 23.5 1.0
CG A:GLU179 5.0 22.4 1.0

Magnesium binding site 2 out of 3 in 3wvd

Go back to Magnesium Binding Sites List in 3wvd
Magnesium binding site 2 out of 3 in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 50 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 50 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:15.9
occ:0.50
 O B:HOH455 1.9 24.3 1.0
O B:HOH473 2.0 21.1 1.0
O B:HOH447 2.0 20.5 1.0
O B:HOH475 2.1 18.2 0.5
O B:HOH511 2.1 22.6 1.0
O B:HOH413 2.4 18.5 1.0
O B:HOH464 4.1 21.4 1.0
O B:HOH549 4.2 25.8 1.0
MG B:MG302 4.3 22.5 0.5
O B:ASP6 4.4 14.3 1.0
O B:HOH449 4.4 21.1 1.0
OD2 B:ASP6 4.4 14.8 1.0
O B:GLY3 4.5 13.7 1.0
CB B:ALA144 4.5 15.6 1.0
CB B:ASP6 4.5 13.6 1.0
O B:ASP2 4.5 14.3 1.0
CB B:ASP2 4.6 14.5 1.0
CG B:ASP6 4.7 14.1 1.0
C B:ASP2 4.7 13.3 1.0
OD1 B:ASP2 4.7 17.6 1.0
CG B:ASP2 4.7 15.3 1.0
CA B:ASP2 4.7 13.8 1.0

Magnesium binding site 3 out of 3 in 3wvd

Go back to Magnesium Binding Sites List in 3wvd
Magnesium binding site 3 out of 3 in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 50 Min


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 BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 50 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:22.5
occ:0.50
 O B:HOH444 2.7 16.3 1.0
O B:HOH475 2.8 18.2 0.5
O B:HOH473 3.5 21.1 1.0
O B:HOH464 3.6 21.4 1.0
CG2 B:VAL10 3.6 14.4 1.0
MG B:MG301 4.3 15.9 0.5
CA B:VAL10 4.7 13.5 1.0
O A:HOH439 4.7 21.3 1.0
O B:HOH447 4.8 20.5 1.0
CB B:VAL10 4.8 13.8 1.0
N B:VAL10 4.8 13.5 1.0
O B:ASP6 4.9 14.3 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 13:37:50 2024

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