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Iron 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
Chlorine (Cl) 6 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 5jsp). 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: 5jsp:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 5jsp

Go back to Iron Binding Sites List in 5jsp
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:14.0
occ:1.00
 O1 A:DQY302 1.9 25.3 0.9
OE1 A:GLU129 2.1 16.1 1.0
NE2 A:HIS125 2.1 14.6 1.0
OE2 A:GLU129 2.3 19.0 1.0
NE2 A:HIS163 2.3 18.5 1.0
OH A:TYR131 2.3 28.6 1.0
CD A:GLU129 2.5 17.9 1.0
C1 A:DQY302 2.8 28.0 0.9
CE1 A:HIS163 3.1 16.4 1.0
CD2 A:HIS125 3.1 14.7 1.0
O2 A:DQY302 3.1 28.4 0.9
CE1 A:HIS125 3.1 15.9 1.0
CD2 A:HIS163 3.3 14.1 1.0
CZ A:TYR131 3.5 29.4 1.0
CE2 A:TYR131 3.8 33.3 1.0
CG A:GLU129 4.0 12.9 1.0
NE2 A:HIS123 4.0 15.7 1.0
CD2 A:HIS123 4.1 20.1 1.0
C2 A:DQY302 4.2 29.4 0.9
ND1 A:HIS163 4.2 17.8 1.0
ND1 A:HIS125 4.2 9.8 1.0
CG A:HIS125 4.2 13.7 1.0
CG A:HIS163 4.4 15.9 1.0
C3 A:DQY302 4.4 23.9 0.9
NE1 A:TRP178 4.6 14.3 1.0
CB A:GLU129 4.6 14.2 1.0
CE1 A:TYR131 4.6 27.2 1.0
ND1 A:HIS157 4.6 19.9 1.0

Iron binding site 2 out of 2 in 5jsp

Go back to Iron Binding Sites List in 5jsp
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:14.9
occ:1.00
 O1 B:DQY302 1.8 19.2 0.8
OE2 B:GLU129 2.1 17.9 1.0
NE2 B:HIS125 2.1 11.5 1.0
NE2 B:HIS163 2.2 19.9 1.0
OE1 B:GLU129 2.3 18.1 1.0
OH B:TYR131 2.4 31.3 1.0
CD B:GLU129 2.5 18.7 1.0
C1 B:DQY302 2.8 15.8 0.8
CE1 B:HIS125 3.1 13.9 1.0
O2 B:DQY302 3.1 24.9 0.8
CD2 B:HIS125 3.1 12.4 1.0
CD2 B:HIS163 3.1 16.9 1.0
CE1 B:HIS163 3.2 17.6 1.0
CZ B:TYR131 3.5 29.2 1.0
CE1 B:TYR131 3.8 31.2 1.0
NE2 B:HIS123 3.9 14.6 1.0
CG B:GLU129 4.0 15.5 1.0
C2 B:DQY302 4.1 26.8 0.8
CD2 B:HIS123 4.1 18.2 1.0
ND1 B:HIS125 4.2 14.6 1.0
CG B:HIS125 4.2 11.7 1.0
CG B:HIS163 4.3 17.8 1.0
ND1 B:HIS163 4.3 14.1 1.0
C3 B:DQY302 4.3 26.5 0.8
NE1 B:TRP178 4.5 13.5 1.0
CB B:GLU129 4.6 15.2 1.0
ND1 B:HIS157 4.6 18.9 1.0
CE2 B:TYR131 4.7 26.8 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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