Iron in PDB 7wzx: The Structure of A Twitch Radical Sam Dehydrogenase Spey

The structure of The Structure of A Twitch Radical Sam Dehydrogenase Spey, PDB code: 7wzx was solved by X.L.Hou, J.H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.22 / 1.98
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.93, 93.93, 143.42, 90, 90, 120
R / Rfree (%)	20.9 / 23.4

The binding sites of Iron atom in the The Structure of A Twitch Radical Sam Dehydrogenase Spey (pdb code 7wzx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the The Structure of A Twitch Radical Sam Dehydrogenase Spey, PDB code: 7wzx:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the The Structure of A Twitch Radical Sam Dehydrogenase Spey


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Structure of A Twitch Radical Sam Dehydrogenase Spey within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:43.3 occ:1.00 FE1 A:SF4401 0.0 43.3 1.0 S2 A:SF4401 2.3 47.3 1.0 S4 A:SF4401 2.3 42.0 1.0 S3 A:SF4401 2.3 44.8 1.0 O A:SAM403 2.4 45.9 1.0 FE4 A:SF4401 2.7 42.7 1.0 FE3 A:SF4401 2.7 42.0 1.0 FE2 A:SF4401 2.7 40.0 1.0 N A:SAM403 2.8 47.3 1.0 C A:SAM403 3.2 42.3 1.0 CA A:SAM403 3.5 46.4 1.0 SD A:SAM403 3.5 73.9 1.0 CG A:SAM403 3.6 76.0 1.0 OH A:TYR121 3.9 42.0 1.0 S1 A:SF4401 4.0 41.8 1.0 CB A:SAM403 4.1 57.7 1.0 CE A:SAM403 4.3 75.0 1.0 O A:GLY69 4.4 42.2 1.0 OXT A:SAM403 4.4 50.1 1.0 CZ A:TYR121 4.6 44.4 1.0 CE2 A:TYR121 4.7 45.5 1.0 SG A:CYS24 4.7 44.4 1.0 C A:GLY69 5.0 47.3 1.0 SG A:CYS31 5.0 40.5 1.0

Iron binding site 2 out of 8 in the The Structure of A Twitch Radical Sam Dehydrogenase Spey


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Structure of A Twitch Radical Sam Dehydrogenase Spey within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:40.0 occ:1.00 FE2 A:SF4401 0.0 40.0 1.0 S1 A:SF4401 2.2 41.8 1.0 S3 A:SF4401 2.3 44.8 1.0 S4 A:SF4401 2.3 42.0 1.0 SG A:CYS31 2.5 40.5 1.0 FE4 A:SF4401 2.5 42.7 1.0 FE3 A:SF4401 2.6 42.0 1.0 FE1 A:SF4401 2.7 43.3 1.0 CB A:CYS31 3.3 42.9 1.0 S2 A:SF4401 3.8 47.3 1.0 CB A:SER35 4.2 40.0 1.0 OG A:SER35 4.3 42.9 1.0 CA A:CYS31 4.3 45.0 1.0 CE A:SAM403 4.4 75.0 1.0 CB A:CYS28 4.6 43.4 1.0 CD A:PRO36 4.7 40.3 1.0 SD A:SAM403 4.7 73.9 1.0 SG A:CYS28 4.8 44.6 1.0 SG A:CYS24 4.9 44.4 1.0 O A:SAM403 4.9 45.9 1.0

Iron binding site 3 out of 8 in the The Structure of A Twitch Radical Sam Dehydrogenase Spey


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Structure of A Twitch Radical Sam Dehydrogenase Spey within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:42.0 occ:1.00 FE3 A:SF4401 0.0 42.0 1.0 S4 A:SF4401 2.2 42.0 1.0 S2 A:SF4401 2.3 47.3 1.0 S1 A:SF4401 2.3 41.8 1.0 SG A:CYS28 2.5 44.6 1.0 FE2 A:SF4401 2.6 40.0 1.0 FE4 A:SF4401 2.6 42.7 1.0 FE1 A:SF4401 2.7 43.3 1.0 CB A:CYS28 3.2 43.4 1.0 S3 A:SF4401 3.8 44.8 1.0 N A:CYS28 4.2 48.5 1.0 CA A:CYS28 4.3 47.3 1.0 CE2 A:TYR121 4.4 45.5 1.0 O A:SAM403 4.5 45.9 1.0 CB A:MET26 4.5 51.4 1.0 OH A:TYR121 4.5 42.0 1.0 CZ A:TYR121 4.5 44.4 1.0 CE A:MET26 4.7 49.5 1.0 CB A:CYS31 4.7 42.9 1.0 SG A:CYS31 4.7 40.5 1.0 SG A:CYS24 4.9 44.4 1.0 CE2 A:PHE153 5.0 40.6 1.0 SD A:MET26 5.0 50.8 1.0

Iron binding site 4 out of 8 in the The Structure of A Twitch Radical Sam Dehydrogenase Spey


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Structure of A Twitch Radical Sam Dehydrogenase Spey within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:42.7 occ:1.00 FE4 A:SF4401 0.0 42.7 1.0 S3 A:SF4401 2.2 44.8 1.0 S1 A:SF4401 2.3 41.8 1.0 S2 A:SF4401 2.3 47.3 1.0 SG A:CYS24 2.5 44.4 1.0 FE2 A:SF4401 2.5 40.0 1.0 FE3 A:SF4401 2.6 42.0 1.0 FE1 A:SF4401 2.7 43.3 1.0 CB A:CYS24 3.3 48.9 1.0 S4 A:SF4401 3.8 42.0 1.0 O A:MET26 4.3 49.8 1.0 N A:SAM403 4.3 47.3 1.0 CB A:MET26 4.4 51.4 1.0 CB A:SER35 4.5 40.0 1.0 C A:GLY69 4.6 47.3 1.0 CA A:GLY69 4.6 46.4 1.0 C A:MET26 4.7 48.0 1.0 N A:MET26 4.7 48.9 1.0 O A:GLY69 4.7 42.2 1.0 ND2 A:ASN98 4.8 47.8 1.0 CA A:CYS24 4.8 44.6 1.0 SG A:CYS31 4.8 40.5 1.0 SG A:CYS28 4.8 44.6 1.0 CA A:MET26 4.8 49.0 1.0 OG A:SER35 4.9 42.9 1.0 O A:SAM403 5.0 45.9 1.0

Iron binding site 5 out of 8 in the The Structure of A Twitch Radical Sam Dehydrogenase Spey


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Structure of A Twitch Radical Sam Dehydrogenase Spey within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:32.4 occ:1.00 FE1 A:SF4402 0.0 32.4 1.0 S2 A:SF4402 2.2 33.3 1.0 S4 A:SF4402 2.3 29.3 1.0 S3 A:SF4402 2.3 30.1 1.0 SG A:CYS175 2.4 33.9 1.0 FE2 A:SF4402 2.6 30.5 1.0 FE4 A:SF4402 2.6 31.4 1.0 FE3 A:SF4402 2.7 32.5 1.0 CB A:CYS175 3.2 30.3 1.0 S1 A:SF4402 3.8 31.5 1.0 CA A:GLY246 4.3 32.3 1.0 CB A:ALA178 4.5 33.5 1.0 N A:ALA178 4.7 28.9 1.0 CA A:CYS175 4.7 29.8 1.0 CB A:LEU177 4.7 29.4 1.0 SG A:CYS244 4.8 34.5 1.0 SG A:CYS194 4.8 31.0 1.0 SG A:CYS241 4.9 33.5 1.0 CB A:CYS194 5.0 27.5 1.0 CD1 A:LEU177 5.0 31.0 1.0

Iron binding site 6 out of 8 in the The Structure of A Twitch Radical Sam Dehydrogenase Spey


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Structure of A Twitch Radical Sam Dehydrogenase Spey within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:30.5 occ:1.00 FE2 A:SF4402 0.0 30.5 1.0 S1 A:SF4402 2.2 31.5 1.0 S3 A:SF4402 2.3 30.1 1.0 S4 A:SF4402 2.3 29.3 1.0 SG A:CYS194 2.5 31.0 1.0 FE1 A:SF4402 2.6 32.4 1.0 FE4 A:SF4402 2.7 31.4 1.0 FE3 A:SF4402 2.7 32.5 1.0 CB A:CYS194 3.3 27.5 1.0 S2 A:SF4402 3.8 33.3 1.0 CD1 A:LEU238 4.1 35.6 1.0 CB A:GLN196 4.3 33.8 1.0 N A:SER197 4.5 31.7 1.0 CB A:SER197 4.6 30.4 1.0 SG A:CYS175 4.7 33.9 1.0 OE1 A:GLN196 4.7 33.0 1.0 CA A:CYS194 4.8 34.3 1.0 SG A:CYS244 4.9 34.5 1.0 SG A:CYS241 4.9 33.5 1.0

Iron binding site 7 out of 8 in the The Structure of A Twitch Radical Sam Dehydrogenase Spey


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Structure of A Twitch Radical Sam Dehydrogenase Spey within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:32.5 occ:1.00 FE3 A:SF4402 0.0 32.5 1.0 S4 A:SF4402 2.2 29.3 1.0 S2 A:SF4402 2.3 33.3 1.0 S1 A:SF4402 2.3 31.5 1.0 SG A:CYS241 2.5 33.5 1.0 FE4 A:SF4402 2.6 31.4 1.0 FE2 A:SF4402 2.7 30.5 1.0 FE1 A:SF4402 2.7 32.4 1.0 CB A:CYS241 3.6 30.9 1.0 CA A:CYS241 3.8 37.7 1.0 S3 A:SF4402 3.8 30.1 1.0 N A:CYS241 4.1 35.9 1.0 CD1 A:LEU238 4.3 35.6 1.0 CD1 A:PHE172 4.3 39.8 1.0 CG A:LEU238 4.6 37.5 1.0 CB A:CYS244 4.7 37.6 1.0 SG A:CYS244 4.8 34.5 1.0 C A:ALA240 4.8 35.2 1.0 CB A:LEU238 4.8 33.2 1.0 SG A:CYS194 4.9 31.0 1.0 CB A:PHE172 5.0 37.1 1.0

Iron binding site 8 out of 8 in the The Structure of A Twitch Radical Sam Dehydrogenase Spey


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Structure of A Twitch Radical Sam Dehydrogenase Spey within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:31.4 occ:1.00 FE4 A:SF4402 0.0 31.4 1.0 S3 A:SF4402 2.2 30.1 1.0 S1 A:SF4402 2.3 31.5 1.0 S2 A:SF4402 2.3 33.3 1.0 SG A:CYS244 2.4 34.5 1.0 FE3 A:SF4402 2.6 32.5 1.0 FE1 A:SF4402 2.6 32.4 1.0 FE2 A:SF4402 2.7 30.5 1.0 CB A:CYS244 3.1 37.6 1.0 S4 A:SF4402 3.8 29.3 1.0 CB A:GLN196 4.1 33.8 1.0 N A:GLY246 4.2 32.5 1.0 CA A:GLY246 4.2 32.3 1.0 CG A:GLN196 4.5 33.4 1.0 CA A:CYS244 4.6 36.7 1.0 CD A:GLN196 4.7 34.8 1.0 CA A:CYS241 4.7 37.7 1.0 SG A:CYS175 4.7 33.9 1.0 SG A:CYS241 4.8 33.5 1.0 O A:HOH548 4.8 35.7 1.0 SG A:CYS194 4.8 31.0 1.0

J.Zhang, X.Hou, Z.Chen, Y.Ko, M.W.Ruszczycky, Y.Chen, J.Zhou, H.W.Liu. Dioxane Bridge Formation During the Biosynthesis of Spectinomycin Involves A Twitch Radical S -Adenosyl Methionine Dehydrogenase That May Have Evolved From An Epimerase. J.Am.Chem.Soc. V. 144 9910 2022.
ISSN: ESSN 1520-5126
PubMed: 35622017
DOI: 10.1021/JACS.2C02676