Atomistry » Chlorine » PDB 5jkc-5jsr » 5jsr
Atomistry »
  Chlorine »
    PDB 5jkc-5jsr »
      5jsr »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy