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Chlorine in PDB 3x20: Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 25 Min

Enzymatic activity of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 25 Min

All present enzymatic activity of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 25 Min:
4.2.1.84;

Protein crystallography data

The structure of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 25 Min, PDB code: 3x20 was solved by Y.Yamanaka, K.Hashimoto, N.Noguchi, M.Yohda, M.Odaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.13 / 1.18
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.796, 60.381, 82.086, 90.00, 124.97, 90.00
R / Rfree (%) 14.2 / 16.2

Other elements in 3x20:

The structure of Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 25 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 25 Min (pdb code 3x20). 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 25 Min, PDB code: 3x20:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3x20

Go back to Chlorine Binding Sites List in 3x20
Chlorine binding site 1 out of 4 in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 25 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 25 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:28.2
occ:1.00
 OG A:SER19 2.9 26.5 1.0
O B:HOH588 3.2 46.5 1.0
NE1 A:TRP23 3.3 21.4 1.0
CB B:GLU31 3.6 26.6 1.0
N B:TRP32 3.7 21.1 1.0
CD1 B:TRP32 3.7 21.3 1.0
CB A:SER19 3.8 21.7 1.0
C B:GLU31 3.9 23.2 1.0
CB B:TRP32 3.9 19.4 1.0
CD1 A:TRP23 3.9 19.9 1.0
CA B:GLU31 4.0 23.0 1.0
O B:HOH575 4.1 45.2 1.0
N B:GLU31 4.1 23.7 1.0
CG B:TRP32 4.2 18.8 1.0
CA B:TRP32 4.3 19.9 1.0
CE2 A:TRP23 4.5 21.5 1.0
O B:GLU31 4.7 25.3 1.0
CA A:SER19 4.7 18.4 1.0
CG B:GLU31 4.8 33.2 1.0
NE1 B:TRP32 4.9 20.4 1.0
O A:HOH503 5.0 34.9 1.0

Chlorine binding site 2 out of 4 in 3x20

Go back to Chlorine Binding Sites List in 3x20
Chlorine binding site 2 out of 4 in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 25 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 25 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:23.0
occ:1.00
 O B:HOH568 2.8 39.2 1.0
O B:HOH488 3.0 28.8 1.0
O B:HOH534 3.1 28.4 1.0
N A:TRP126 3.4 16.6 1.0
CD1 A:TRP126 3.5 17.2 1.0
CB A:THR125 3.6 21.0 1.0
N A:THR125 3.8 18.9 1.0
CG2 B:ILE24 3.9 23.1 1.0
CB A:TRP126 4.0 17.2 1.0
CA A:THR125 4.1 18.6 1.0
O A:HOH500 4.1 32.7 1.0
CG A:TRP126 4.2 16.4 1.0
CB B:ILE24 4.2 22.0 1.0
C A:THR125 4.2 18.1 1.0
CA A:TRP126 4.3 16.8 1.0
OG1 A:THR125 4.3 25.2 1.0
CB A:PRO124 4.4 20.1 1.0
O B:PRO17 4.5 20.6 1.0
CA B:ILE24 4.5 24.3 1.0
CG2 A:THR125 4.5 24.5 1.0
C A:PRO124 4.6 17.5 1.0
O A:HOH601 4.6 44.0 1.0
NE1 A:TRP126 4.6 17.7 1.0
ND1 B:HIS18 4.7 19.9 1.0
O B:ILE24 4.9 29.2 1.0
CA A:PRO124 4.9 19.9 1.0

Chlorine binding site 3 out of 4 in 3x20

Go back to Chlorine Binding Sites List in 3x20
Chlorine binding site 3 out of 4 in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 25 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 25 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:26.6
occ:1.00
 O B:HOH610 3.0 54.2 1.0
OG B:SER192 3.2 34.1 1.0
N B:SER192 3.2 23.6 1.0
CB B:SER192 3.9 31.9 1.0
CA B:GLY191 3.9 20.9 1.0
C B:GLY191 4.1 22.7 1.0
CA B:SER192 4.1 25.0 1.0
O B:HOH617 4.5 40.6 1.0
O B:PHE190 4.8 19.8 1.0
O B:HOH600 4.8 57.0 1.0
N B:ASP193 4.8 23.1 1.0
O B:HOH597 5.0 55.4 1.0
C B:SER192 5.0 27.2 1.0

Chlorine binding site 4 out of 4 in 3x20

Go back to Chlorine Binding Sites List in 3x20
Chlorine binding site 4 out of 4 in the Crystal Structure of Nitrile Hydratase Mutant BR56K Complexed with Trimethylacetonitrile, Photo-Activated For 25 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 25 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:26.0
occ:1.00
 OG1 B:THR121 3.1 27.5 1.0
NH2 B:ARG132 3.3 24.1 1.0
O B:HOH439 3.3 25.9 1.0
O B:LEU208 3.7 20.3 1.0
CD B:PRO210 3.8 25.0 1.0
CB B:THR121 3.8 25.9 1.0
N B:THR121 3.9 24.6 1.0
CA B:GLU209 3.9 20.8 1.0
CA B:THR120 4.1 25.1 1.0
C B:THR120 4.1 26.0 1.0
CB B:GLU209 4.2 22.9 1.0
CZ B:ARG132 4.4 22.0 1.0
CA B:THR121 4.5 24.6 1.0
O B:GLU119 4.5 29.0 1.0
CZ B:PHE123 4.6 31.3 1.0
C B:LEU208 4.6 19.7 1.0
N B:PRO210 4.7 22.2 1.0
NE B:ARG132 4.7 21.6 1.0
CG B:PRO210 4.7 26.7 1.0
N B:GLU209 4.8 20.1 1.0
N B:THR120 4.8 25.5 1.0
C B:GLU209 4.8 21.2 1.0
O B:THR120 4.9 30.5 1.0
C B:GLU119 5.0 26.8 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: Sat Dec 12 10:20:21 2020

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