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Chlorine 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:

Magnesium (Mg) 2 atoms
Iron (Fe) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 5 Min, PDB code: 3x26:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3x26

Go back to Chlorine Binding Sites List in 3x26
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl303

b:21.6
occ:1.00
 OG A:SER19 2.9 14.6 0.5
NE1 A:TRP23 3.2 14.6 1.0
CB A:SER19 3.6 14.8 0.5
CB B:GLU31 3.6 20.7 1.0
N B:TRP32 3.6 14.1 1.0
CD1 B:TRP32 3.6 14.0 1.0
CB A:SER19 3.9 13.6 0.5
CB B:TRP32 3.9 14.0 1.0
CD1 A:TRP23 3.9 14.0 1.0
C B:GLU31 3.9 15.8 1.0
O B:HOH503 4.0 28.2 1.0
CA B:GLU31 4.1 17.2 1.0
N B:GLU31 4.1 17.8 1.0
CG B:TRP32 4.2 12.5 1.0
CA B:TRP32 4.3 14.2 1.0
CE2 A:TRP23 4.4 15.1 1.0
OG A:SER19 4.5 18.9 0.5
O B:GLU31 4.7 16.3 1.0
CA A:SER19 4.7 13.8 0.5
CA A:SER19 4.7 12.6 0.5
CG B:GLU31 4.8 23.6 1.0
NE1 B:TRP32 4.8 14.4 1.0
CZ2 A:TRP23 5.0 16.3 1.0
O A:HOH510 5.0 29.2 1.0

Chlorine binding site 2 out of 4 in 3x26

Go back to Chlorine Binding Sites List in 3x26
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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
A:Cl304

b:18.5
occ:1.00
 O B:HOH523 2.9 28.7 1.0
O B:HOH474 3.0 22.6 1.0
O B:HOH480 3.1 22.7 1.0
N A:TRP126 3.4 11.1 1.0
CD1 A:TRP126 3.5 10.6 1.0
CB A:THR125 3.6 15.4 1.0
N A:THR125 3.7 13.3 1.0
CG2 B:ILE24 3.8 17.2 1.0
CB A:TRP126 4.0 11.7 1.0
CA A:THR125 4.0 12.7 1.0
CG A:TRP126 4.1 11.7 1.0
O A:HOH501 4.2 25.5 1.0
C A:THR125 4.2 12.3 1.0
CB B:ILE24 4.2 17.7 1.0
CA A:TRP126 4.3 10.8 1.0
OG1 A:THR125 4.4 20.0 1.0
CB A:PRO124 4.4 14.8 1.0
O B:PRO17 4.5 13.5 1.0
C A:PRO124 4.5 12.7 1.0
CG2 A:THR125 4.5 18.4 1.0
NE1 A:TRP126 4.7 11.4 1.0
CA B:ILE24 4.7 22.4 1.0
ND1 B:HIS18 4.7 13.2 1.0
CA A:PRO124 4.9 13.6 1.0
O B:ILE24 5.0 24.1 1.0

Chlorine binding site 3 out of 4 in 3x26

Go back to Chlorine Binding Sites List in 3x26
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl303

b:22.9
occ:1.00
 OG B:SER192 3.2 29.2 1.0
N B:SER192 3.2 20.1 1.0
CB B:SER192 3.8 27.3 1.0
CA B:GLY191 3.8 14.9 1.0
C B:GLY191 4.0 18.1 1.0
CA B:SER192 4.1 20.9 1.0
O B:PHE190 4.8 15.2 1.0
N B:ASP193 4.8 18.8 1.0
C B:SER192 4.9 23.9 1.0

Chlorine binding site 4 out of 4 in 3x26

Go back to Chlorine Binding Sites List in 3x26
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl304

b:23.0
occ:1.00
 OG1 B:THR121 3.0 24.4 1.0
NH2 B:ARG132 3.2 24.7 1.0
O B:HOH472 3.4 21.2 1.0
O B:LEU208 3.6 18.2 1.0
CD B:PRO210 3.8 22.4 1.0
CB B:THR121 3.8 25.9 1.0
N B:THR121 3.9 22.8 1.0
CA B:GLU209 3.9 17.2 1.0
CA B:THR120 4.0 24.4 1.0
C B:THR120 4.1 26.7 1.0
CB B:GLU209 4.2 18.9 1.0
CZ B:ARG132 4.3 22.1 1.0
C B:LEU208 4.5 15.4 1.0
CA B:THR121 4.5 23.4 1.0
CZ B:PHE123 4.5 24.5 1.0
NE B:ARG132 4.5 18.7 1.0
O B:GLU119 4.6 28.2 1.0
N B:GLU209 4.7 15.9 1.0
N B:THR120 4.8 27.1 1.0
N B:PRO210 4.8 20.1 1.0
CG B:PRO210 4.9 21.6 1.0
O B:THR120 4.9 28.0 1.0
C B:GLU209 4.9 19.2 1.0
C B:GLU119 5.0 31.8 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: Sun Jul 21 07:53:42 2024

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