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Chlorine 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:

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 5jsp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 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: 5jsp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5jsp

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Chlorine binding site 1 out of 6 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:22.6
occ:1.00
 O A:HOH467 2.6 31.3 1.0
O A:HOH508 2.7 16.6 1.0
NH1 A:ARG38 3.1 15.5 1.0
NE A:ARG75 3.1 20.0 1.0
NH2 A:ARG75 3.2 18.0 1.0
NH2 A:ARG38 3.2 25.9 1.0
N A:ARG75 3.5 12.1 1.0
CZ A:ARG38 3.6 23.8 1.0
CZ A:ARG75 3.6 19.2 1.0
CB A:ARG75 3.9 11.8 1.0
CA A:LYS74 3.9 9.9 1.0
C A:LYS74 4.1 13.9 1.0
CD A:ARG75 4.3 13.8 1.0
CA A:ARG75 4.3 12.9 1.0
CG A:ARG75 4.3 12.0 1.0
CB A:LYS74 4.5 12.0 1.0
CG2 A:ILE40 4.5 10.4 1.0
N A:THR76 4.7 14.3 1.0
NH1 A:ARG87 4.7 19.0 1.0
NE A:ARG38 4.9 18.7 1.0
NH1 A:ARG75 4.9 14.5 1.0
O A:TRP73 5.0 8.6 1.0
C A:ARG75 5.0 12.8 1.0

Chlorine binding site 2 out of 6 in 5jsp

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Chlorine binding site 2 out of 6 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:29.8
occ:1.00
 O A:HOH468 2.8 21.4 1.0
O1 A:GOL307 2.9 50.8 1.0
NE1 A:TRP26 3.1 19.3 1.0
C1 A:GOL307 3.6 30.9 1.0
CD1 A:LEU30 3.7 12.3 1.0
CD1 A:TRP26 4.0 17.7 1.0
CD A:ARG11 4.0 19.6 1.0
CD2 A:LEU7 4.0 16.0 1.0
CE2 A:TRP26 4.1 15.1 1.0
CG A:LEU7 4.3 12.4 1.0
CZ2 A:TRP26 4.4 15.6 1.0
CG A:ARG11 4.6 11.9 1.0
O A:HOH469 4.7 17.0 1.0
CB A:ARG11 4.8 13.6 1.0
CD1 A:LEU7 4.9 7.0 1.0
OE2 A:GLU8 5.0 30.2 1.0
NE A:ARG11 5.0 30.7 1.0
C2 A:GOL307 5.0 44.2 1.0

Chlorine binding site 3 out of 6 in 5jsp

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Chlorine binding site 3 out of 6 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:12.3
occ:1.00
 OH A:TYR113 3.0 9.7 1.0
O A:HOH510 3.0 10.0 1.0
O A:HOH424 3.2 16.2 1.0
O A:HOH420 3.3 12.8 1.0
CG A:PRO171 3.7 10.2 1.0
CB A:PRO171 3.9 11.8 1.0
O A:HOH511 4.1 8.4 1.0
CZ A:TYR113 4.1 9.6 1.0
O A:HOH513 4.2 20.1 1.0
CE1 A:TYR113 4.3 6.7 1.0
CD1 A:LEU49 4.4 8.1 1.0
CD A:PRO171 4.7 11.6 1.0
O A:LEU45 4.8 12.2 1.0
CB A:LEU45 4.9 11.1 1.0
OE1 A:GLN51 5.0 8.2 1.0

Chlorine binding site 4 out of 6 in 5jsp

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Chlorine binding site 4 out of 6 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:9.1
occ:1.00
 OH B:TYR113 3.1 13.0 1.0
O B:HOH494 3.1 14.3 1.0
O B:HOH453 3.3 11.4 1.0
CG B:PRO171 3.9 9.6 1.0
CB B:PRO171 4.0 7.5 1.0
O B:HOH498 4.0 11.1 1.0
CZ B:TYR113 4.2 10.9 1.0
CE1 B:TYR113 4.4 10.7 1.0
O B:HOH490 4.5 24.3 1.0
CD1 B:LEU49 4.6 11.7 1.0
CD B:PRO171 4.8 10.5 1.0
O B:LEU45 4.9 14.0 1.0
CB B:LEU45 5.0 9.9 1.0

Chlorine binding site 5 out of 6 in 5jsp

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Chlorine binding site 5 out of 6 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:27.7
occ:1.00
 O B:HOH480 2.9 28.1 1.0
NH1 B:ARG38 3.0 12.8 1.0
NE B:ARG75 3.1 13.2 1.0
NH2 B:ARG75 3.1 19.8 1.0
NH2 B:ARG38 3.3 19.1 1.0
CZ B:ARG75 3.5 24.5 1.0
O B:HOH511 3.5 35.8 1.0
N B:ARG75 3.6 14.3 1.0
CZ B:ARG38 3.6 32.9 1.0
CB B:ARG75 3.9 12.9 1.0
CA B:LYS74 4.0 15.6 1.0
C B:LYS74 4.1 13.6 1.0
CD B:ARG75 4.2 18.3 1.0
CG B:ARG75 4.3 16.0 1.0
CA B:ARG75 4.3 15.5 1.0
CG2 B:ILE40 4.6 15.8 1.0
CB B:LYS74 4.6 12.2 1.0
N B:THR76 4.7 20.6 1.0
NH1 B:ARG87 4.7 20.7 1.0
NH1 B:ARG75 4.8 13.5 1.0
NH2 B:ARG87 4.9 19.9 1.0
NE B:ARG38 4.9 19.1 1.0

Chlorine binding site 6 out of 6 in 5jsp

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Chlorine binding site 6 out of 6 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 6 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:Cl306

b:30.2
occ:1.00
 O B:HOH483 2.6 22.1 1.0
NE1 B:TRP26 3.1 14.7 1.0
CD1 B:LEU30 3.5 10.2 1.0
CD1 B:TRP26 4.0 14.2 1.0
CD B:ARG11 4.0 17.9 1.0
CD2 B:LEU7 4.0 11.8 1.0
CE2 B:TRP26 4.1 13.6 1.0
CG B:LEU7 4.2 12.7 1.0
CG B:ARG11 4.5 15.4 1.0
CZ2 B:TRP26 4.5 8.7 1.0
CB B:ARG11 4.7 11.6 1.0
CD1 B:LEU7 4.7 6.9 1.0
O B:HOH444 4.8 15.6 1.0
O B:HOH486 4.9 28.1 1.0
CG B:LEU30 4.9 13.7 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 10:12:46 2024

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