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Bromine in PDB 5jsp: 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: 5jsp 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) 38.77 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.745, 88.101, 92.998, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22.8

Other elements in 5jsp:

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:

Iron (Fe) 2 atoms
Chlorine (Cl) 6 atoms

Bromine Binding Sites:

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

Bromine binding site 1 out of 2 in 5jsp

Go back to Bromine Binding Sites List in 5jsp
Bromine binding site 1 out of 2 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 Bromine with other atoms in the Br 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:Br303

b:21.0
occ:1.00
 N A:GLY53 3.3 15.6 1.0
O A:HOH540 3.3 26.5 1.0
N A:GLY136 3.5 11.5 1.0
O A:HOH415 3.5 13.0 1.0
CA A:GLY53 3.5 11.9 1.0
O A:HOH522 3.8 36.5 1.0
CA A:ALA135 3.9 12.1 1.0
CD A:PRO52 3.9 14.8 1.0
C A:GLY53 4.0 18.4 1.0
CB A:GLN51 4.0 15.1 1.0
N A:PRO52 4.1 14.8 1.0
CB A:ALA135 4.1 15.5 1.0
C A:ALA135 4.2 11.1 1.0
O A:GLY53 4.3 18.3 1.0
C A:GLN51 4.4 11.5 1.0
CA A:GLY136 4.4 13.3 1.0
C A:PRO52 4.5 16.2 1.0
CB A:ALA151 4.5 15.9 1.0
CA A:GLN51 4.5 14.3 1.0
CG A:PRO52 4.7 13.9 1.0
CG A:GLN51 4.7 13.9 1.0
N A:SER54 4.7 17.9 1.0
O A:GLY136 4.8 12.2 1.0
O A:HOH419 4.8 19.3 1.0
O A:LEU134 4.8 9.4 1.0
CA A:PRO52 4.9 7.5 1.0

Bromine binding site 2 out of 2 in 5jsp

Go back to Bromine Binding Sites List in 5jsp
Bromine binding site 2 out of 2 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 Bromine with other atoms in the Br 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
B:Br303

b:19.3
occ:1.00
 O B:HOH545 3.1 28.6 1.0
N B:GLY53 3.3 13.5 1.0
O B:HOH413 3.3 19.7 1.0
N B:GLY136 3.4 10.4 1.0
CA B:GLY53 3.6 12.6 1.0
CD B:PRO52 3.8 13.9 1.0
CA B:ALA135 3.9 12.5 1.0
CB B:GLN51 3.9 17.2 1.0
N B:PRO52 4.0 16.7 1.0
C B:GLY53 4.1 14.6 1.0
C B:ALA135 4.1 10.2 1.0
CA B:GLY136 4.3 11.1 1.0
CB B:ALA135 4.3 10.6 1.0
C B:GLN51 4.3 15.7 1.0
CB B:ALA151 4.3 11.0 1.0
O B:GLY53 4.4 13.0 1.0
C B:PRO52 4.5 16.6 1.0
CA B:GLN51 4.5 15.4 1.0
CG B:GLN51 4.6 13.6 1.0
CG B:PRO52 4.6 14.6 1.0
O B:GLY136 4.6 11.6 1.0
N B:SER54 4.7 12.1 1.0
O B:HOH418 4.8 13.2 1.0
O B:LEU134 4.8 8.7 1.0
CA B:PRO52 4.8 16.0 1.0
C B:GLY136 5.0 14.6 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: Thu Jul 11 00:07:25 2024

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