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Chlorine in PDB 5jsr: New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq

Enzymatic activity of New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq

All present enzymatic activity of New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq:
4.4.1.3;

Protein crystallography data

The structure of New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq, PDB code: 5jsr was solved by A.E.Brummett, M.Dey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.66 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.724, 88.170, 93.082, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 24.7

Other elements in 5jsr:

The structure of New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Iron (Fe) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq (pdb code 5jsr). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq, PDB code: 5jsr:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5jsr

Go back to Chlorine Binding Sites List in 5jsr
Chlorine binding site 1 out of 5 in the New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:36.4
occ:1.00
 O A:HOH465 2.7 30.6 1.0
NE A:ARG75 3.0 20.0 1.0
NH2 A:ARG75 3.1 22.2 1.0
NH1 A:ARG38 3.3 25.1 1.0
NH2 A:ARG38 3.4 21.8 1.0
CZ A:ARG75 3.5 24.8 1.0
N A:ARG75 3.6 19.0 1.0
CB A:ARG75 3.8 17.7 1.0
CZ A:ARG38 3.8 26.3 1.0
O A:HOH456 4.0 33.9 1.0
CD A:ARG75 4.2 15.0 1.0
CG A:ARG75 4.2 15.0 1.0
CA A:ARG75 4.3 19.4 1.0
C A:LYS74 4.3 18.0 1.0
CA A:LYS74 4.4 14.8 1.0
NH1 A:ARG87 4.5 28.7 1.0
N A:THR76 4.6 25.4 1.0
NH1 A:ARG75 4.8 21.8 1.0
CG2 A:ILE40 4.8 11.6 1.0
C A:ARG75 4.9 21.0 1.0
NH2 A:ARG87 4.9 27.8 1.0

Chlorine binding site 2 out of 5 in 5jsr

Go back to Chlorine Binding Sites List in 5jsr
Chlorine binding site 2 out of 5 in the New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:47.4
occ:1.00
 O A:HOH427 2.9 19.2 1.0
CB A:ALA32 3.4 17.1 1.0
N A:GLY34 3.4 16.3 1.0
O A:HIS101 3.7 12.3 1.0
N A:THR33 3.8 13.8 1.0
CA A:ALA32 3.9 19.1 1.0
CA A:GLY34 4.0 15.7 1.0
C A:ALA32 4.2 18.7 1.0
CE1 A:PHE102 4.5 17.1 1.0
C A:THR33 4.5 18.7 1.0
C A:GLY34 4.7 20.4 1.0
CA A:THR33 4.7 14.4 1.0
N A:LEU35 4.7 12.7 1.0
C A:HIS101 4.8 14.8 1.0
CZ A:PHE102 4.8 15.2 1.0
CD1 A:PHE102 4.9 18.2 1.0
OG1 A:THR33 5.0 12.3 1.0

Chlorine binding site 3 out of 5 in 5jsr

Go back to Chlorine Binding Sites List in 5jsr
Chlorine binding site 3 out of 5 in the New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:18.2
occ:1.00
 O A:HOH471 2.9 17.6 1.0
OH A:TYR113 3.2 12.5 1.0
O A:HOH406 3.3 14.6 1.0
CG A:PRO171 3.5 15.8 1.0
CB A:PRO171 3.9 13.8 1.0
O A:HOH446 4.1 9.5 1.0
CZ A:TYR113 4.2 16.1 1.0
CE1 A:TYR113 4.2 13.5 1.0
CD1 A:LEU49 4.3 15.1 1.0
CD A:PRO171 4.4 18.1 1.0
O A:LEU45 4.6 14.8 1.0
CB A:LEU45 5.0 10.2 1.0
OE1 A:GLN51 5.0 17.6 1.0

Chlorine binding site 4 out of 5 in 5jsr

Go back to Chlorine Binding Sites List in 5jsr
Chlorine binding site 4 out of 5 in the New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl304

b:38.5
occ:1.00
 NH2 B:ARG75 3.1 22.8 1.0
NE B:ARG75 3.2 17.7 1.0
NH1 B:ARG38 3.3 30.1 1.0
N B:ARG75 3.4 21.9 1.0
NH2 B:ARG38 3.5 21.2 1.0
CZ B:ARG75 3.6 23.1 1.0
CZ B:ARG38 3.8 32.0 1.0
CB B:ARG75 3.8 19.2 1.0
O B:HOH476 3.8 32.7 1.0
CA B:LYS74 4.1 21.3 1.0
CA B:ARG75 4.1 21.3 1.0
C B:LYS74 4.1 16.4 1.0
CD B:ARG75 4.3 17.9 1.0
N B:THR76 4.4 26.8 1.0
CG B:ARG75 4.4 16.7 1.0
NH1 B:ARG87 4.5 20.3 1.0
CB B:LYS74 4.6 13.9 1.0
C B:ARG75 4.8 28.5 1.0
NH1 B:ARG75 4.8 19.2 1.0
CG2 B:ILE40 4.9 10.4 1.0
O B:HOH486 4.9 32.8 1.0

Chlorine binding site 5 out of 5 in 5jsr

Go back to Chlorine Binding Sites List in 5jsr
Chlorine binding site 5 out of 5 in the New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of New Mechanistic Insight From Substrate and Product Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl305

b:14.8
occ:1.00
 O B:HOH428 2.6 12.1 1.0
O B:HOH467 3.1 20.3 1.0
O B:HOH415 3.2 14.8 1.0
OH B:TYR113 3.2 16.2 1.0
CG B:PRO171 3.7 20.5 1.0
CB B:PRO171 4.1 12.3 1.0
O B:HOH455 4.2 16.4 1.0
CZ B:TYR113 4.2 13.9 1.0
CE1 B:TYR113 4.3 10.9 1.0
CD1 B:LEU49 4.5 16.8 1.0
O B:LEU45 4.5 17.7 1.0
CD B:PRO171 4.6 16.4 1.0
CB B:LEU45 4.9 12.7 1.0
CD2 B:LEU45 5.0 16.3 1.0

Reference:

A.E.Brummett, M.Dey. New Mechanistic Insight From Substrate- and Product-Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase Dddq. Biochemistry V. 55 6162 2016.
ISSN: ISSN 1520-4995
PubMed: 27755868
DOI: 10.1021/ACS.BIOCHEM.6B00585
Page generated: Fri Jul 26 10:13:01 2024

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