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Iron 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:

Chlorine (Cl) 5 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 2 in 5jso

Go back to Iron Binding Sites List in 5jso
Iron binding site 1 out of 2 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 Iron with other atoms in the Fe 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:Fe301

b:13.8
occ:1.00
NE2 A:HIS125 2.1 14.0 1.0
OE1 A:GLU129 2.2 12.6 1.0
NE2 A:HIS163 2.2 17.8 1.0
OE2 A:GLU129 2.3 13.9 1.0
O1 A:TRS302 2.4 27.1 1.0
CD A:GLU129 2.6 15.1 1.0
C1 A:TRS302 2.7 24.5 1.0
CE1 A:HIS125 3.0 21.3 1.0
OH A:TYR131 3.1 17.5 0.3
CD2 A:HIS125 3.1 15.8 1.0
CE1 A:HIS163 3.1 14.7 1.0
CD2 A:HIS163 3.2 14.2 1.0
NE2 A:HIS123 3.8 18.0 1.0
CZ A:TYR131 3.9 15.8 0.3
CD2 A:HIS123 3.9 19.3 1.0
CG A:GLU129 4.1 11.8 1.0
ND1 A:HIS125 4.1 14.9 1.0
CE2 A:TYR131 4.2 12.9 0.3
CG A:HIS125 4.2 13.4 1.0
ND1 A:HIS163 4.2 20.1 1.0
CE1 A:TYR131 4.2 16.4 0.7
C A:TRS302 4.2 19.7 1.0
CG A:HIS163 4.3 15.6 1.0
ND1 A:HIS157 4.5 14.8 1.0
CB A:GLU129 4.6 11.5 1.0
NE1 A:TRP178 4.6 13.3 1.0
OH A:TYR131 4.8 13.1 0.7
C3 A:TRS302 4.9 21.4 1.0
CE1 A:TYR131 4.9 13.5 0.3
N A:TRS302 4.9 35.4 1.0

Iron binding site 2 out of 2 in 5jso

Go back to Iron Binding Sites List in 5jso
Iron binding site 2 out of 2 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 Iron with other atoms in the Fe 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
B:Fe301

b:14.4
occ:1.00
NE2 B:HIS125 2.1 13.3 1.0
OE1 B:GLU129 2.2 18.8 1.0
OE2 B:GLU129 2.2 15.6 1.0
O1 B:TRS302 2.3 27.6 1.0
NE2 B:HIS163 2.3 17.1 1.0
CD B:GLU129 2.5 17.1 1.0
C1 B:TRS302 2.7 29.2 1.0
CD2 B:HIS125 3.0 18.7 1.0
OH B:TYR131 3.1 18.6 0.3
CE1 B:HIS125 3.1 19.1 1.0
CE1 B:HIS163 3.2 17.3 1.0
CD2 B:HIS163 3.3 16.5 1.0
NE2 B:HIS123 3.7 20.2 1.0
CZ B:TYR131 3.9 16.4 0.3
CD2 B:HIS123 3.9 19.9 1.0
CG B:GLU129 4.0 15.2 1.0
CE2 B:TYR131 4.1 14.6 0.3
ND1 B:HIS125 4.2 17.9 1.0
CG B:HIS125 4.2 16.1 1.0
CE1 B:TYR131 4.2 16.1 0.7
C B:TRS302 4.2 19.0 1.0
ND1 B:HIS163 4.3 17.9 1.0
CG B:HIS163 4.4 19.9 1.0
NE1 B:TRP178 4.5 16.6 1.0
ND1 B:HIS157 4.5 17.7 1.0
CB B:GLU129 4.6 12.2 1.0
OH B:TYR131 4.7 13.5 0.7
N B:TRS302 4.8 38.8 1.0
CE1 B:TYR131 4.9 14.9 0.3
CZ B:TYR131 4.9 14.3 0.7
CE1 B:HIS123 4.9 19.6 1.0
C3 B:TRS302 5.0 21.4 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: Sun Dec 13 16:04:47 2020

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