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Iron 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
Chlorine (Cl) 5 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron 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 Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 5jsr

Go back to Iron Binding Sites List in 5jsr
Iron 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 Iron with other atoms in the Fe 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:Fe301

b:21.0
occ:1.00
 OE2 A:GLU129 2.0 17.5 1.0
OE1 A:GLU129 2.2 23.4 1.0
OH A:TYR131 2.2 26.5 1.0
NE2 A:HIS163 2.2 24.4 1.0
NE2 A:HIS125 2.3 17.7 1.0
OXT A:AKR302 2.3 30.8 1.0
CD A:GLU129 2.4 22.4 1.0
CE1 A:HIS163 3.0 20.6 1.0
CD2 A:HIS125 3.1 25.4 1.0
CZ A:TYR131 3.3 30.1 1.0
CE1 A:HIS125 3.3 18.2 1.0
CD2 A:HIS163 3.3 19.4 1.0
C A:AKR302 3.4 36.1 1.0
CE2 A:TYR131 3.7 32.9 1.0
CG A:GLU129 3.9 14.2 1.0
O A:AKR302 4.0 45.6 1.0
CD2 A:HIS123 4.0 22.6 1.0
NE2 A:HIS123 4.0 26.9 1.0
ND1 A:HIS163 4.1 19.7 1.0
CG A:HIS163 4.3 20.4 1.0
CG A:HIS125 4.3 21.0 1.0
CE1 A:TYR131 4.4 35.9 1.0
ND1 A:HIS125 4.4 17.7 1.0
CA A:AKR302 4.5 31.9 1.0
CB A:GLU129 4.6 17.8 1.0
NE1 A:TRP178 4.6 16.6 1.0
ND1 A:HIS157 4.7 21.9 1.0

Iron binding site 2 out of 2 in 5jsr

Go back to Iron Binding Sites List in 5jsr
Iron 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 Iron with other atoms in the Fe 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:Fe301

b:24.5
occ:1.00
 OE1 B:GLU129 2.1 18.0 1.0
OXT B:AKR302 2.2 27.9 1.0
OE2 B:GLU129 2.2 26.6 1.0
NE2 B:HIS125 2.3 19.8 1.0
NE2 B:HIS163 2.3 27.1 1.0
CD B:GLU129 2.5 23.1 1.0
OH B:TYR131 2.5 34.7 1.0
C B:AKR302 2.9 25.5 1.0
O B:AKR302 3.0 26.4 1.0
CE1 B:HIS163 3.2 24.8 1.0
CD2 B:HIS125 3.3 21.7 1.0
CE1 B:HIS125 3.3 18.6 1.0
CD2 B:HIS163 3.4 23.4 1.0
CZ B:TYR131 3.5 27.6 1.0
CE1 B:TYR131 3.6 22.0 1.0
NE2 B:HIS123 3.8 24.4 1.0
CD2 B:HIS123 3.9 21.4 1.0
CG B:GLU129 4.0 15.4 1.0
CA B:AKR302 4.3 23.3 1.0
ND1 B:HIS163 4.3 19.0 1.0
CG B:HIS125 4.4 16.4 1.0
ND1 B:HIS125 4.4 16.1 1.0
CG B:HIS163 4.4 25.0 1.0
CB B:GLU129 4.6 17.2 1.0
NE1 B:TRP178 4.6 13.3 1.0
ND1 B:HIS157 4.7 19.5 1.0
CE2 B:TYR131 4.8 30.1 1.0
CD1 B:TYR131 4.9 24.2 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: Tue Aug 6 02:54:40 2024

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