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Chlorine in PDB 5jso: Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound

Enzymatic activity of Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound

All present enzymatic activity of Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound:
4.4.1.3;

Protein crystallography data

The structure of Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound, PDB code: 5jso 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) 48.82 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.870, 87.761, 48.900, 90.00, 93.37, 90.00
R / Rfree (%) 18.5 / 23.6

Other elements in 5jso:

The structure of Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound (pdb code 5jso). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound, PDB code: 5jso:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5jso

Go back to Chlorine Binding Sites List in 5jso
Chlorine binding site 1 out of 5 in the Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:13.6
occ:1.00
 O A:HOH568 2.9 25.2 1.0
N A:GLY53 3.2 13.6 1.0
O A:HOH440 3.4 16.2 1.0
N A:GLY136 3.4 11.4 1.0
CA A:GLY53 3.5 16.4 1.0
CA A:ALA135 3.8 8.9 1.0
CB A:GLN51 3.9 15.0 1.0
C A:GLY53 4.0 17.6 1.0
CD A:PRO52 4.1 17.7 1.0
N A:PRO52 4.1 15.4 1.0
C A:ALA135 4.1 10.8 1.0
CB A:ALA135 4.2 8.3 1.0
O A:GLY53 4.2 21.4 1.0
C A:GLN51 4.3 16.2 1.0
CB A:ALA151 4.3 13.2 1.0
CA A:GLY136 4.4 13.4 1.0
C A:PRO52 4.4 20.7 1.0
CA A:GLN51 4.4 17.2 1.0
CG A:GLN51 4.6 14.0 1.0
O A:HOH439 4.6 21.7 1.0
CG A:PRO52 4.7 18.7 1.0
O A:GLY136 4.8 11.4 1.0
N A:SER54 4.8 15.6 1.0
O A:LEU134 4.8 10.2 1.0
CA A:PRO52 4.9 10.8 1.0
O A:GLN51 5.0 12.9 1.0

Chlorine binding site 2 out of 5 in 5jso

Go back to Chlorine Binding Sites List in 5jso
Chlorine binding site 2 out of 5 in the Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:26.4
occ:1.00
 O A:HOH519 2.4 24.7 1.0
NH1 A:ARG38 3.1 18.2 1.0
O A:HOH428 3.1 29.6 1.0
NE A:ARG75 3.2 16.3 1.0
NH2 A:ARG75 3.4 19.0 1.0
N A:ARG75 3.4 14.6 1.0
NH2 A:ARG38 3.5 19.8 1.0
CZ A:ARG38 3.7 28.2 1.0
CZ A:ARG75 3.8 15.3 1.0
CB A:ARG75 3.9 13.1 1.0
CA A:LYS74 4.0 9.9 1.0
C A:LYS74 4.0 17.4 1.0
CG A:ARG75 4.2 13.4 1.0
CA A:ARG75 4.2 16.2 1.0
CD A:ARG75 4.2 14.4 1.0
CG2 A:ILE40 4.4 12.9 1.0
CB A:LYS74 4.6 11.0 1.0
N A:THR76 4.7 18.0 1.0
NH1 A:ARG87 4.7 16.9 1.0
C A:ARG75 5.0 16.1 1.0

Chlorine binding site 3 out of 5 in 5jso

Go back to Chlorine Binding Sites List in 5jso
Chlorine binding site 3 out of 5 in the Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:16.3
occ:1.00
 O B:HOH561 3.1 19.8 1.0
O B:HOH451 3.2 15.6 1.0
N B:GLY136 3.3 10.7 1.0
N B:GLY53 3.3 16.3 1.0
CA B:GLY53 3.5 13.4 1.0
CA B:ALA135 3.8 9.7 1.0
CB B:GLN51 3.8 13.8 1.0
C B:ALA135 4.0 11.8 1.0
C B:GLY53 4.1 18.6 1.0
CD B:PRO52 4.1 20.5 1.0
CB B:ALA135 4.2 7.8 1.0
N B:PRO52 4.2 17.9 1.0
CA B:GLY136 4.3 9.2 1.0
O B:GLY53 4.3 18.5 1.0
CB B:ALA151 4.3 15.5 1.0
C B:GLN51 4.4 18.6 1.0
CG B:GLN51 4.4 16.8 1.0
CA B:GLN51 4.5 14.6 1.0
C B:PRO52 4.5 18.1 1.0
O B:HOH415 4.6 23.0 1.0
O B:GLY136 4.7 12.8 1.0
O B:LEU134 4.8 10.9 1.0
CG B:PRO52 4.8 15.6 1.0
N B:SER54 4.8 12.9 1.0
N B:ALA135 5.0 10.9 1.0
CA B:PRO52 5.0 12.6 1.0

Chlorine binding site 4 out of 5 in 5jso

Go back to Chlorine Binding Sites List in 5jso
Chlorine binding site 4 out of 5 in the Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl304

b:26.2
occ:1.00
 O B:HOH538 2.4 19.7 1.0
O B:HOH485 2.9 32.1 1.0
NH1 B:ARG38 3.0 17.6 1.0
NE B:ARG75 3.2 15.8 1.0
NH2 B:ARG38 3.4 20.7 1.0
NH2 B:ARG75 3.4 20.9 1.0
N B:ARG75 3.5 16.5 1.0
CZ B:ARG38 3.6 31.6 1.0
CZ B:ARG75 3.8 20.9 1.0
CB B:ARG75 3.9 10.7 1.0
CA B:LYS74 4.0 15.0 1.0
C B:LYS74 4.1 19.1 1.0
CG B:ARG75 4.2 12.4 1.0
CA B:ARG75 4.3 16.7 1.0
CD B:ARG75 4.3 15.2 1.0
CG2 B:ILE40 4.5 12.8 1.0
N B:THR76 4.7 18.9 1.0
NH1 B:ARG87 4.8 17.2 1.0
CB B:LYS74 4.8 11.0 1.0
O B:TRP73 4.9 8.1 1.0
NE B:ARG38 4.9 15.6 1.0
C B:ARG75 5.0 14.8 1.0

Chlorine binding site 5 out of 5 in 5jso

Go back to Chlorine Binding Sites List in 5jso
Chlorine binding site 5 out of 5 in the Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structures of Dddq From Ruegeria Lac. Reveal Key Residues For Metal Binding and Catalysis - Tris Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl305

b:32.8
occ:1.00
 O B:HOH489 2.6 24.1 1.0
O1 B:GOL306 3.1 31.7 1.0
NE1 B:TRP26 3.2 13.1 1.0
CD1 B:LEU30 3.8 13.3 1.0
CD B:ARG11 3.9 15.7 1.0
CD1 B:TRP26 4.1 12.8 1.0
CD2 B:LEU7 4.1 12.2 1.0
CE2 B:TRP26 4.2 15.7 1.0
CG B:LEU7 4.4 7.8 1.0
C1 B:GOL306 4.4 31.2 1.0
CZ2 B:TRP26 4.6 10.7 1.0
CG B:ARG11 4.6 13.7 1.0
O B:HOH478 4.8 12.4 1.0
CB B:ARG11 4.8 8.3 1.0
NE B:ARG11 4.8 20.2 1.0
OE1 B:GLU8 4.8 17.5 1.0
O B:HOH492 4.9 24.6 1.0
O2 B:GOL306 5.0 34.7 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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