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Chlorine 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:

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, Before Photo-Activation (pdb code 3wve). 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, Before Photo-Activation, PDB code: 3wve:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3wve

Go back to Chlorine Binding Sites List in 3wve
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl304

b:17.4
occ:1.00
 O B:HOH484 3.0 22.8 1.0
O B:HOH489 3.2 21.0 1.0
N A:TRP126 3.4 11.2 1.0
CD1 A:TRP126 3.5 11.3 1.0
CB A:THR125 3.7 14.9 1.0
N A:THR125 3.8 13.2 1.0
CG2 B:ILE24 3.9 20.6 1.0
O A:HOH485 4.0 28.4 1.0
CB A:TRP126 4.0 11.5 1.0
CA A:THR125 4.1 12.4 1.0
CG A:TRP126 4.2 12.5 1.0
C A:THR125 4.2 11.3 1.0
CB B:ILE24 4.2 19.9 1.0
CA A:TRP126 4.3 11.3 1.0
CB A:PRO124 4.4 15.9 1.0
O B:PRO17 4.4 14.8 1.0
OG1 A:THR125 4.4 19.4 1.0
C A:PRO124 4.6 13.1 1.0
CG2 A:THR125 4.6 18.2 1.0
CA B:ILE24 4.6 22.9 1.0
NE1 A:TRP126 4.7 12.5 1.0
ND1 B:HIS18 4.7 14.4 1.0
CA A:PRO124 4.9 15.0 1.0
O B:ILE24 4.9 24.6 1.0

Chlorine binding site 2 out of 4 in 3wve

Go back to Chlorine Binding Sites List in 3wve
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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
A:Cl305

b:35.8
occ:1.00
 N A:LYS192 3.1 15.0 1.0
O B:HOH569 3.4 31.1 1.0
NH1 A:ARG54 3.6 39.6 1.0
CA A:THR191 3.7 15.9 1.0
CB A:LYS192 3.8 14.3 1.0
CB A:THR191 3.9 15.3 1.0
C A:THR191 3.9 14.0 1.0
CA A:LYS192 4.1 13.8 1.0
O A:HOH454 4.1 17.1 1.0
CG A:PRO53 4.3 13.6 1.0
CG2 A:THR191 4.5 17.3 1.0
CZ A:ARG54 4.7 55.5 1.0
CB A:PRO53 4.7 14.4 1.0

Chlorine binding site 3 out of 4 in 3wve

Go back to Chlorine Binding Sites List in 3wve
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl306

b:25.1
occ:1.00
 OG A:SER19 2.9 26.3 1.0
NE1 A:TRP23 3.3 17.3 1.0
CB B:GLU31 3.7 21.1 1.0
N B:TRP32 3.7 14.7 1.0
CD1 B:TRP32 3.7 13.8 1.0
CB A:SER19 3.8 17.7 1.0
CB B:TRP32 3.9 14.3 1.0
CD1 A:TRP23 3.9 14.8 1.0
O B:HOH507 4.0 28.4 1.0
C B:GLU31 4.0 16.9 1.0
CA B:GLU31 4.1 17.0 1.0
N B:GLU31 4.1 16.4 1.0
CG B:TRP32 4.2 12.8 1.0
CA B:TRP32 4.3 15.0 1.0
CE2 A:TRP23 4.5 17.5 1.0
CA A:SER19 4.7 13.4 1.0
O B:GLU31 4.7 18.2 1.0
CG B:GLU31 4.8 26.1 1.0
NE1 B:TRP32 4.9 14.9 1.0
CZ2 A:TRP23 5.0 18.5 1.0

Chlorine binding site 4 out of 4 in 3wve

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

b:24.2
occ:1.00
 OG1 B:THR121 3.1 29.6 1.0
NH2 B:ARG132 3.2 27.3 1.0
O B:HOH488 3.3 21.6 1.0
O B:LEU208 3.6 19.0 1.0
CD B:PRO210 3.8 24.6 1.0
CB B:THR121 3.8 27.7 1.0
CA B:GLU209 3.8 18.1 1.0
N B:THR121 3.9 23.9 1.0
CA B:THR120 4.1 26.9 1.0
C B:THR120 4.2 28.7 1.0
CB B:GLU209 4.2 20.4 1.0
CZ B:ARG132 4.3 22.4 1.0
C B:LEU208 4.5 16.1 1.0
CA B:THR121 4.5 25.7 1.0
O B:GLU119 4.6 30.6 1.0
NE B:ARG132 4.6 20.4 1.0
CZ B:PHE123 4.6 24.6 1.0
N B:GLU209 4.7 19.7 1.0
N B:PRO210 4.7 21.9 1.0
C B:GLU209 4.8 19.0 1.0
CG B:PRO210 4.8 24.3 1.0
N B:THR120 4.9 28.9 1.0
O B:THR120 5.0 29.2 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 07:48:38 2024

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