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Iron in PDB 4x8b: Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form

Protein crystallography data

The structure of Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form, PDB code: 4x8b was solved by A.Vit, K.V.Goncharenko, W.Blankenfeldt, F.P.Seebeck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.75 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 134.780, 134.780, 141.204, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 15.7

Other elements in 4x8b:

The structure of Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form (pdb code 4x8b). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form, PDB code: 4x8b:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 4x8b

Go back to Iron Binding Sites List in 4x8b
Iron binding site 1 out of 2 in the Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe508

b:13.0
occ:1.00
NE2 A:HIS134 2.1 13.1 1.0
O A:HOH1272 2.1 19.8 1.0
NE2 A:HIS138 2.1 14.6 1.0
NE2 A:HIS51 2.1 12.3 1.0
O A:HOH1271 2.2 18.5 1.0
O A:HOH1270 2.2 20.4 1.0
CE1 A:HIS134 3.0 13.3 1.0
CD2 A:HIS134 3.1 14.2 1.0
CE1 A:HIS138 3.1 15.2 1.0
CD2 A:HIS138 3.1 14.8 1.0
CE1 A:HIS51 3.1 13.4 1.0
CD2 A:HIS51 3.1 12.4 1.0
HE1 A:HIS134 3.2 15.9 1.0
HD2 A:HIS134 3.2 17.1 1.0
HE1 A:HIS138 3.3 18.3 1.0
HE1 A:HIS51 3.3 16.1 1.0
HD2 A:HIS138 3.3 17.8 1.0
HD2 A:HIS51 3.3 14.9 1.0
HG3 A:GLN55 3.7 18.9 1.0
O A:HOH1269 4.1 35.0 1.0
ND1 A:HIS134 4.1 15.3 1.0
CG A:HIS134 4.2 13.2 1.0
ND1 A:HIS138 4.2 14.2 1.0
ND1 A:HIS51 4.2 13.6 1.0
CG A:HIS138 4.2 12.8 1.0
CG A:HIS51 4.3 14.0 1.0
OH A:TYR377 4.5 33.5 1.0
HE2 A:TYR377 4.6 33.4 1.0
CG A:GLN55 4.6 15.7 1.0
OE1 A:GLN55 4.6 23.2 1.0
CD A:GLN55 4.9 21.4 1.0
HD1 A:HIS134 4.9 18.4 1.0
HD1 A:HIS138 5.0 17.0 1.0

Iron binding site 2 out of 2 in 4x8b

Go back to Iron Binding Sites List in 4x8b
Iron binding site 2 out of 2 in the Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe508

b:21.5
occ:1.00
NE2 B:HIS51 2.1 21.5 1.0
NE2 B:HIS134 2.1 24.0 1.0
NE2 B:HIS138 2.1 22.8 1.0
O B:HOH1096 2.2 30.0 1.0
O B:HOH1097 2.2 29.2 1.0
O B:HOH1092 2.2 26.6 1.0
CE1 B:HIS51 3.0 23.0 1.0
CD2 B:HIS134 3.0 24.0 1.0
CE1 B:HIS138 3.0 22.0 1.0
CE1 B:HIS134 3.1 22.6 1.0
HE1 B:HIS51 3.1 27.6 1.0
CD2 B:HIS138 3.1 19.4 1.0
CD2 B:HIS51 3.1 20.8 1.0
HD2 B:HIS134 3.2 28.8 1.0
HE1 B:HIS138 3.2 26.4 1.0
HE1 B:HIS134 3.3 27.2 1.0
HD2 B:HIS138 3.3 23.3 1.0
HD2 B:HIS51 3.4 24.9 1.0
HG3 B:GLN55 3.6 30.5 1.0
ND1 B:HIS51 4.1 24.5 1.0
ND1 B:HIS138 4.2 20.8 1.0
CG B:HIS134 4.2 22.1 1.0
ND1 B:HIS134 4.2 23.8 1.0
O B:HOH930 4.2 40.9 1.0
CG B:HIS51 4.2 21.6 1.0
CG B:HIS138 4.2 18.7 1.0
CG B:GLN55 4.5 25.4 1.0
OE1 B:GLN55 4.6 33.7 1.0
HE2 B:TYR377 4.7 46.0 1.0
OH B:TYR377 4.7 44.5 1.0
CD B:GLN55 4.8 30.4 1.0
HD1 B:HIS51 4.9 29.4 1.0
HD1 B:HIS138 4.9 25.0 1.0
CL B:CL506 4.9 27.7 1.0
HD1 B:HIS134 5.0 28.6 1.0
HG2 B:GLN55 5.0 30.5 1.0

Reference:

K.V.Goncharenko, A.Vit, W.Blankenfeldt, F.P.Seebeck. Structure of the Sulfoxide Synthase Egtb From the Ergothioneine Biosynthetic Pathway. Angew.Chem.Int.Ed.Engl. 2015.
ISSN: ESSN 1521-3773
PubMed: 25597398
DOI: 10.1002/ANIE.201410045
Page generated: Sun Dec 13 15:51:38 2020

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