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Iron 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:

Magnesium (Mg) 3 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total only one binding site of Iron was determined in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 50 Min, PDB code: 3wvd:

Iron binding site 1 out of 1 in 3wvd

Go back to Iron Binding Sites List in 3wvd
Iron binding site 1 out of 1 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 Iron with other atoms in the Fe 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:Fe301

b:12.4
occ:0.90
 N A:TAN303 2.0 12.7 1.0
N A:CSO114 2.0 13.2 1.0
N A:SER113 2.0 12.9 1.0
SG A:CSD112 2.2 13.1 1.0
SG A:CSO114 2.2 14.8 1.0
SG A:CYS109 2.3 13.6 1.0
C A:SER113 2.8 13.5 1.0
CA A:SER113 2.9 13.4 1.0
C A:TAN303 2.9 18.3 1.0
CA A:CSO114 3.0 14.0 1.0
CB A:CSO114 3.0 14.9 1.0
OD A:CSO114 3.0 19.0 1.0
C A:CSD112 3.1 12.6 1.0
OD1 A:CSD112 3.1 14.0 1.0
OD2 A:CSD112 3.1 13.8 1.0
CB A:CSD112 3.2 13.2 1.0
CB A:CYS109 3.3 13.6 1.0
CA A:CSD112 3.4 12.6 1.0
OG A:SER113 3.7 16.1 1.0
N A:CSD112 3.9 12.6 1.0
CB A:SER113 3.9 14.0 1.0
O A:SER113 4.0 14.0 1.0
O A:CSD112 4.2 13.3 1.0
C2 A:TAN303 4.3 18.2 1.0
C A:CSO114 4.3 13.7 1.0
CA A:CYS109 4.7 13.7 1.0
O A:CSO114 4.7 14.0 1.0
NH2 B:ARG141 4.7 14.6 1.0
C1 A:TAN303 4.7 21.1 1.0
C A:LEU111 4.9 12.3 1.0
O A:CYS109 4.9 13.6 1.0
C4 A:TAN303 4.9 20.4 1.0
O A:THR162 4.9 15.6 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: Sun Aug 4 22:52:09 2024

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