Iron in PDB 6on1: A Resting State Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus

The structure of A Resting State Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus, PDB code: 6on1 was solved by Y.Wang, I.Shin, Y.Fu, K.Colabroy, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.33 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	99.977, 45.215, 131.153, 90.00, 105.20, 90.00
R / Rfree (%)	20.7 / 25.6

The binding sites of Iron atom in the A Resting State Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus (pdb code 6on1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the A Resting State Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus, PDB code: 6on1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the A Resting State Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of A Resting State Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:31.4 occ:1.00 OE1 A:GLU154 2.0 32.8 1.0 NE2 A:HIS95 2.0 30.0 1.0 NE2 B:HIS19 2.2 30.9 1.0 CE1 B:HIS19 3.0 33.5 1.0 CD2 A:HIS95 3.0 31.6 1.0 CE1 A:HIS95 3.0 31.5 1.0 CD A:GLU154 3.0 36.7 1.0 CD2 B:HIS19 3.3 32.1 1.0 OE2 A:GLU154 3.4 34.4 1.0 O A:HOH385 3.8 44.1 1.0 ND1 B:HIS74 3.9 36.5 1.0 ND1 A:HIS95 4.1 32.3 1.0 CG A:HIS95 4.1 29.5 1.0 ND1 B:HIS19 4.2 33.4 1.0 CG B:HIS19 4.3 32.4 1.0 CG A:GLU154 4.4 32.7 1.0 OH A:TYR144 4.4 31.1 1.0 CB A:CYS97 4.5 32.8 1.0 CE1 B:HIS74 4.5 37.0 1.0 CB A:GLU154 4.6 33.2 1.0 CG B:HIS74 4.9 37.7 1.0 CE2 A:TYR144 4.9 33.9 1.0 O A:HOH338 5.0 36.0 1.0

Iron binding site 2 out of 6 in the A Resting State Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of A Resting State Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:29.2 occ:1.00 OE1 B:GLU154 2.0 33.9 1.0 NE2 B:HIS95 2.1 27.9 1.0 O A:HOH318 2.1 36.3 1.0 NE2 A:HIS19 2.1 31.6 1.0 O B:HOH313 2.3 35.2 1.0 O B:HOH347 2.3 33.2 1.0 CE1 B:HIS95 3.0 30.7 1.0 CE1 A:HIS19 3.0 28.1 1.0 CD B:GLU154 3.0 34.3 1.0 CD2 B:HIS95 3.1 32.1 1.0 CD2 A:HIS19 3.2 29.2 1.0 OE2 B:GLU154 3.3 33.2 1.0 ND1 A:HIS74 3.9 30.1 1.0 ND1 B:HIS95 4.1 31.4 1.0 ND1 A:HIS19 4.2 31.4 1.0 CG B:HIS95 4.2 29.5 1.0 CG A:HIS19 4.3 30.2 1.0 CG B:GLU154 4.4 35.9 1.0 OH B:TYR144 4.4 35.3 1.0 CB B:CYS97 4.5 30.2 1.0 CE1 A:HIS74 4.5 34.7 1.0 O B:HOH358 4.7 43.0 1.0 CB B:GLU154 4.7 35.5 1.0 CG A:HIS74 4.8 32.8 1.0 CE1 B:TYR144 4.9 30.7 1.0 O B:HOH312 5.0 34.0 1.0 SG B:CYS97 5.0 32.2 1.0

Iron binding site 3 out of 6 in the A Resting State Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of A Resting State Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:36.8 occ:1.00 OE1 C:GLU154 2.1 40.5 1.0 O D:HOH307 2.1 40.9 1.0 NE2 D:HIS19 2.1 39.8 1.0 NE2 C:HIS95 2.1 38.8 1.0 O C:HOH323 2.3 41.6 1.0 O C:HOH317 2.5 39.0 1.0 CE1 C:HIS95 2.9 39.0 1.0 CE1 D:HIS19 3.0 37.5 1.0 CD C:GLU154 3.1 40.9 1.0 CD2 D:HIS19 3.1 35.8 1.0 CD2 C:HIS95 3.2 38.7 1.0 OE2 C:GLU154 3.4 39.5 1.0 ND1 D:HIS74 4.0 37.1 1.0 ND1 C:HIS95 4.1 38.1 1.0 ND1 D:HIS19 4.2 35.6 1.0 O C:HOH338 4.2 48.0 1.0 CG C:HIS95 4.2 39.6 1.0 CG D:HIS19 4.2 39.2 1.0 OH C:TYR144 4.4 39.8 1.0 CG C:GLU154 4.5 38.9 1.0 CB C:CYS97 4.5 38.9 1.0 CE1 D:HIS74 4.6 38.2 1.0 CB C:GLU154 4.7 41.0 1.0 O C:HOH311 4.8 40.0 1.0 CG D:HIS74 4.9 35.7 1.0 CE2 C:TYR144 5.0 38.2 1.0

Iron binding site 4 out of 6 in the A Resting State Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of A Resting State Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:34.9 occ:1.00 O C:HOH308 2.0 42.8 1.0 OE1 D:GLU154 2.0 37.9 1.0 NE2 C:HIS19 2.1 35.4 1.0 NE2 D:HIS95 2.2 34.9 1.0 O D:HOH350 2.3 36.3 1.0 O D:HOH345 2.4 33.6 1.0 CE1 C:HIS19 2.9 34.7 1.0 CD D:GLU154 3.1 37.0 1.0 CE1 D:HIS95 3.1 37.6 1.0 CD2 C:HIS19 3.2 35.8 1.0 CD2 D:HIS95 3.2 37.1 1.0 OE2 D:GLU154 3.4 38.1 1.0 O D:HOH365 3.7 47.6 1.0 ND1 C:HIS74 4.0 34.4 1.0 ND1 C:HIS19 4.1 37.4 1.0 ND1 D:HIS95 4.2 37.0 1.0 CG C:HIS19 4.2 35.8 1.0 CG D:HIS95 4.3 34.2 1.0 OH D:TYR144 4.4 35.6 1.0 CB D:CYS97 4.4 36.8 1.0 CG D:GLU154 4.4 33.6 1.0 CE1 C:HIS74 4.6 37.8 1.0 CB D:GLU154 4.7 36.2 1.0 SG D:CYS97 4.9 37.2 1.0 CG C:HIS74 5.0 37.3 1.0

Iron binding site 5 out of 6 in the A Resting State Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of A Resting State Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe201 b:40.4 occ:1.00 O F:HOH318 2.0 44.3 1.0 OE1 E:GLU154 2.1 43.3 1.0 NE2 F:HIS19 2.1 43.1 1.0 NE2 E:HIS95 2.1 41.2 1.0 O E:HOH325 2.3 48.1 1.0 O E:HOH327 2.4 46.6 1.0 CE1 E:HIS95 3.0 41.4 1.0 CE1 F:HIS19 3.0 41.6 1.0 CD E:GLU154 3.0 45.8 1.0 CD2 F:HIS19 3.2 40.7 1.0 CD2 E:HIS95 3.2 37.1 1.0 OE2 E:GLU154 3.4 46.0 1.0 ND1 F:HIS74 4.0 39.7 1.0 ND1 E:HIS95 4.1 39.4 1.0 ND1 F:HIS19 4.2 44.4 1.0 CG E:HIS95 4.2 38.6 1.0 CG F:HIS19 4.3 40.9 1.0 CG E:GLU154 4.4 47.4 1.0 OH E:TYR144 4.4 42.6 1.0 CB E:CYS97 4.5 39.9 1.0 CE1 F:HIS74 4.6 42.5 1.0 CB E:GLU154 4.7 46.0 1.0 O F:HOH340 4.7 46.7 1.0 CG F:HIS74 4.9 39.9 1.0

Iron binding site 6 out of 6 in the A Resting State Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of A Resting State Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe201 b:37.3 occ:1.00 NE2 E:HIS19 2.1 41.5 1.0 O E:HOH308 2.1 47.0 1.0 OE1 F:GLU154 2.1 39.8 1.0 NE2 F:HIS95 2.1 40.9 1.0 O F:HOH331 2.4 39.4 1.0 O F:HOH339 2.5 42.6 1.0 CE1 E:HIS19 2.9 36.9 1.0 CE1 F:HIS95 3.0 42.8 1.0 CD F:GLU154 3.1 38.7 1.0 CD2 F:HIS95 3.1 41.1 1.0 CD2 E:HIS19 3.1 41.3 1.0 OE2 F:GLU154 3.4 39.1 1.0 ND1 E:HIS74 3.8 44.9 1.0 O F:HOH348 4.1 49.5 1.0 ND1 E:HIS19 4.1 41.4 1.0 ND1 F:HIS95 4.1 36.1 1.0 CG F:HIS95 4.2 40.0 1.0 CG E:HIS19 4.2 44.1 1.0 CE1 E:HIS74 4.4 45.2 1.0 OH F:TYR144 4.4 39.2 1.0 CB F:CYS97 4.4 39.7 1.0 CG F:GLU154 4.4 35.8 1.0 CB F:GLU154 4.6 38.9 1.0 CG E:HIS74 4.8 41.7 1.0

Y.Wang, I.Shin, Y.Fu, K.L.Colabroy, A.Liu. Crystal Structures of L-Dopa Dioxygenase From Streptomyces Sclerotialus. Biochemistry 2019.
ISSN: ISSN 0006-2960
PubMed: 31180203
DOI: 10.1021/ACS.BIOCHEM.9B00396