Iron in PDB 6on3: A Substrate Bound Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus

The structure of A Substrate Bound Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus, PDB code: 6on3 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)	44.01 / 2.31
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	99.830, 40.720, 128.430, 90.00, 105.11, 90.00
R / Rfree (%)	23.5 / 29.4

The binding sites of Iron atom in the A Substrate Bound Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus (pdb code 6on3). 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 Substrate Bound Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus, PDB code: 6on3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the A Substrate Bound 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 Substrate Bound Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:27.6 occ:1.00 OE1 B:GLU154 2.4 24.6 1.0 OZ A:DAH204 2.5 26.4 1.0 OE2 A:DAH204 2.5 25.6 1.0 NE2 B:HIS95 2.6 20.4 1.0 NE2 A:HIS19 2.6 23.3 1.0 CE2 A:DAH204 3.3 27.6 1.0 CZ A:DAH204 3.3 28.0 1.0 CD2 B:HIS95 3.3 21.1 1.0 CD B:GLU154 3.4 24.2 1.0 CE1 A:HIS19 3.4 24.5 1.0 CE1 B:HIS95 3.4 21.5 1.0 CD2 A:HIS19 3.6 23.6 1.0 OE2 B:GLU154 3.8 24.6 1.0 ND1 A:HIS74 4.1 24.3 1.0 OH B:TYR144 4.2 23.3 1.0 CG B:HIS95 4.4 20.8 1.0 ND1 B:HIS95 4.4 22.0 1.0 ND1 A:HIS19 4.6 24.9 1.0 CG B:GLU154 4.6 23.5 1.0 CE2 B:TYR144 4.6 23.4 1.0 CD2 A:DAH204 4.6 28.0 1.0 CB B:CYS97 4.6 22.7 1.0 CE1 A:DAH204 4.7 28.1 1.0 CB B:GLU154 4.7 22.7 1.0 CG A:HIS19 4.7 24.5 1.0 CE1 A:HIS74 4.8 24.8 1.0 CG A:HIS74 4.9 23.9 1.0 CZ B:TYR144 4.9 23.4 1.0

Iron binding site 2 out of 6 in the A Substrate Bound 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 Substrate Bound Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:26.6 occ:1.00 OZ B:DAH204 2.4 29.2 1.0 OE1 A:GLU154 2.5 27.4 1.0 NE2 B:HIS19 2.5 25.0 1.0 OE2 B:DAH204 2.5 29.4 1.0 NE2 A:HIS95 2.6 23.9 1.0 CD2 A:HIS95 3.2 23.8 1.0 CE1 B:HIS19 3.2 25.5 1.0 CE2 B:DAH204 3.2 30.6 1.0 CZ B:DAH204 3.3 30.8 1.0 CD A:GLU154 3.4 26.6 1.0 CD2 B:HIS19 3.7 25.6 1.0 CE1 A:HIS95 3.8 25.1 1.0 OE2 A:GLU154 3.9 26.9 1.0 OH A:TYR144 4.0 28.4 1.0 ND1 B:HIS74 4.0 26.4 1.0 ND1 B:HIS19 4.5 26.1 1.0 CG A:HIS95 4.5 24.7 1.0 CE1 A:TYR144 4.5 27.0 1.0 CD2 B:DAH204 4.6 29.9 1.0 CE1 B:DAH204 4.6 31.3 1.0 CG A:GLU154 4.6 25.4 1.0 CB A:CYS97 4.6 24.6 1.0 CB A:GLU154 4.7 24.4 1.0 CE1 B:HIS74 4.7 26.7 1.0 CG B:HIS19 4.7 26.5 1.0 ND1 A:HIS95 4.7 26.3 1.0 CZ A:TYR144 4.7 28.1 1.0 SG A:CYS97 4.9 23.9 1.0

Iron binding site 3 out of 6 in the A Substrate Bound 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 Substrate Bound Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:35.5 occ:1.00 OZ C:DAH202 2.5 31.9 1.0 NE2 D:HIS95 2.5 26.0 1.0 OE2 C:DAH202 2.5 27.8 1.0 NE2 C:HIS19 2.5 27.2 1.0 OE1 D:GLU154 2.6 28.9 1.0 CE1 D:HIS95 3.2 26.4 1.0 CE2 C:DAH202 3.3 30.2 1.0 CZ C:DAH202 3.3 31.3 1.0 CD2 D:HIS95 3.4 26.8 1.0 CE1 C:HIS19 3.5 28.1 1.0 CD2 C:HIS19 3.5 26.9 1.0 CD D:GLU154 3.5 27.6 1.0 OH D:TYR144 3.9 28.7 1.0 OE2 D:GLU154 4.0 27.8 1.0 ND1 C:HIS74 4.1 27.9 1.0 ND1 D:HIS95 4.3 27.0 1.0 CG D:HIS95 4.4 26.4 1.0 CE1 D:TYR144 4.5 27.0 1.0 ND1 C:HIS19 4.6 28.5 1.0 CG D:GLU154 4.6 26.2 1.0 CD2 C:DAH202 4.6 30.0 1.0 CG C:HIS19 4.7 28.0 1.0 CZ D:TYR144 4.7 27.6 1.0 CE1 C:DAH202 4.7 30.9 1.0 CE1 C:HIS74 4.7 28.3 1.0 CB D:GLU154 4.7 26.1 1.0 CB D:CYS97 4.8 26.3 1.0

Iron binding site 4 out of 6 in the A Substrate Bound 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 Substrate Bound Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:33.0 occ:1.00 OZ D:DAH202 2.4 31.2 1.0 OE2 D:DAH202 2.5 32.1 1.0 NE2 C:HIS95 2.5 28.0 1.0 OE1 C:GLU154 2.6 33.0 1.0 NE2 D:HIS19 2.7 28.0 1.0 CE2 D:DAH202 3.2 33.1 1.0 CZ D:DAH202 3.3 33.1 1.0 CD2 C:HIS95 3.3 28.5 1.0 CE1 C:HIS95 3.4 28.6 1.0 CD C:GLU154 3.5 32.8 1.0 CD2 D:HIS19 3.6 28.8 1.0 CE1 D:HIS19 3.6 28.4 1.0 OE2 C:GLU154 3.8 33.1 1.0 ND1 D:HIS74 4.0 28.2 1.0 OH C:TYR144 4.2 32.3 1.0 ND1 C:HIS95 4.4 30.1 1.0 CG C:HIS95 4.4 29.2 1.0 CE1 C:TYR144 4.4 32.2 1.0 CD2 D:DAH202 4.6 33.4 1.0 CE1 D:DAH202 4.6 33.6 1.0 CG C:GLU154 4.6 31.8 1.0 CB C:GLU154 4.7 31.4 1.0 CB C:CYS97 4.7 29.4 1.0 ND1 D:HIS19 4.7 28.0 1.0 CG D:HIS19 4.8 29.0 1.0 CE1 D:HIS74 4.8 28.5 1.0 CZ C:TYR144 4.8 32.1 1.0 CG D:HIS74 4.9 27.5 1.0

Iron binding site 5 out of 6 in the A Substrate Bound 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 Substrate Bound Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe201 b:37.3 occ:1.00 OZ E:DAH202 2.3 33.2 1.0 NE2 E:HIS19 2.5 32.1 1.0 NE2 F:HIS95 2.5 29.5 1.0 OE2 E:DAH202 2.7 32.9 1.0 OE1 F:GLU154 2.9 30.8 1.0 CZ E:DAH202 3.1 35.8 1.0 CE2 E:DAH202 3.2 34.4 1.0 CE1 F:HIS95 3.2 28.9 1.0 CE1 E:HIS19 3.4 31.7 1.0 ND1 E:HIS74 3.4 33.6 1.0 CD2 E:HIS19 3.4 32.7 1.0 CD2 F:HIS95 3.7 29.0 1.0 CD F:GLU154 3.9 30.1 1.0 OE2 F:GLU154 4.1 29.6 1.0 CE1 E:HIS74 4.2 35.0 1.0 CE1 E:DAH202 4.3 37.2 1.0 CG E:HIS74 4.4 33.9 1.0 ND1 F:HIS95 4.4 29.3 1.0 ND1 E:HIS19 4.4 32.4 1.0 CD2 E:DAH202 4.5 34.6 1.0 OH F:TYR144 4.5 30.5 1.0 CG E:HIS19 4.5 33.0 1.0 CB E:HIS74 4.5 32.4 1.0 CG F:HIS95 4.7 28.6 1.0 CB F:CYS97 5.0 30.8 1.0

Iron binding site 6 out of 6 in the A Substrate Bound 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 Substrate Bound Structure of L-Dopa Dioxygenase From Streptomyces Sclerotialus within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe201 b:38.9 occ:1.00 OZ F:DAH203 2.5 35.9 1.0 OE2 F:DAH203 2.5 34.3 1.0 OE1 E:GLU154 2.5 35.1 1.0 NE2 E:HIS95 2.6 29.2 1.0 NE2 F:HIS19 2.6 33.9 1.0 CD2 E:HIS95 3.0 30.0 1.0 CE2 F:DAH203 3.3 36.3 1.0 CZ F:DAH203 3.3 37.4 1.0 CE1 F:HIS19 3.4 34.4 1.0 CD E:GLU154 3.5 35.4 1.0 CE1 E:HIS95 3.5 29.1 1.0 CD2 F:HIS19 3.7 33.5 1.0 OE2 E:GLU154 3.9 36.8 1.0 CG E:HIS95 4.1 29.9 1.0 OH E:TYR144 4.2 32.3 1.0 ND1 E:HIS95 4.3 29.4 1.0 ND1 F:HIS74 4.3 33.9 1.0 CB E:CYS97 4.4 33.8 1.0 CD2 F:DAH203 4.6 36.3 1.0 ND1 F:HIS19 4.6 35.9 1.0 CB E:GLU154 4.6 33.2 1.0 CE1 E:TYR144 4.7 33.0 1.0 CG E:GLU154 4.7 34.4 1.0 CE1 F:DAH203 4.7 38.0 1.0 CG F:HIS19 4.8 34.1 1.0 SG E:CYS97 4.8 34.5 1.0 CZ E:TYR144 4.9 32.6 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