Iron in PDB 7x0b: The Structure of A Twitch Radical Sam Dehydrogenase Spey

The structure of The Structure of A Twitch Radical Sam Dehydrogenase Spey, PDB code: 7x0b 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)	35.93 / 2.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.932, 94.196, 107.577, 90, 90, 90
R / Rfree (%)	21.8 / 24.7

The structure of The Structure of A Twitch Radical Sam Dehydrogenase Spey also contains other interesting chemical elements:

Chlorine	(Cl)	6 atoms
Sodium	(Na)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the The Structure of A Twitch Radical Sam Dehydrogenase Spey (pdb code 7x0b). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the The Structure of A Twitch Radical Sam Dehydrogenase Spey, PDB code: 7x0b:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 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:19.4 occ:1.00 FE1 A:SF4401 0.0 19.4 1.0 S3 A:SF4401 2.1 20.1 1.0 S2 A:SF4401 2.1 20.5 1.0 S4 A:SF4401 2.1 21.5 1.0 SG A:CYS28 2.6 26.3 1.0 FE3 A:SF4401 2.9 15.7 1.0 FE2 A:SF4401 2.9 18.0 1.0 FE4 A:SF4401 3.0 20.2 1.0 CB A:CYS28 3.1 17.6 1.0 S1 A:SF4401 3.7 22.9 1.0 CB A:MET26 4.1 15.9 1.0 N A:CYS28 4.1 16.0 1.0 CA A:CYS28 4.2 17.0 1.0 CE2 A:TYR121 4.4 23.4 1.0 OH A:TYR121 4.4 29.3 1.0 SD A:MET26 4.5 28.2 1.0 CZ A:TYR121 4.5 23.9 1.0 CE A:MET26 4.7 21.4 1.0 NE2 A:HIS254 4.8 18.1 1.0 CE2 A:PHE153 4.8 19.9 1.0 CB A:CYS31 4.9 16.8 1.0 CG A:MET26 4.9 24.0 1.0

Iron binding site 2 out of 16 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:18.0 occ:1.00 FE2 A:SF4401 0.0 18.0 1.0 S4 A:SF4401 2.1 21.5 1.0 S1 A:SF4401 2.1 22.9 1.0 S3 A:SF4401 2.1 20.1 1.0 SG A:CYS31 2.6 17.0 1.0 FE3 A:SF4401 2.9 15.7 1.0 FE1 A:SF4401 2.9 19.4 1.0 FE4 A:SF4401 3.0 20.2 1.0 CB A:CYS31 3.0 16.8 1.0 S2 A:SF4401 3.7 20.5 1.0 CA A:CYS31 4.0 14.8 1.0 OG A:SER35 4.0 15.4 1.0 CB A:SER35 4.1 17.5 1.0 CD A:PRO36 4.4 19.5 1.0 CE A:SAM403 4.7 55.4 1.0 CB A:CYS28 4.7 17.6 1.0 C A:CYS31 4.8 16.7 1.0 N A:SER35 4.8 20.7 1.0 N A:ALA32 5.0 13.7 1.0

Iron binding site 3 out of 16 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:15.7 occ:1.00 FE3 A:SF4401 0.0 15.7 1.0 S4 A:SF4401 2.1 21.5 1.0 S2 A:SF4401 2.1 20.5 1.0 S1 A:SF4401 2.1 22.9 1.0 SG A:CYS24 2.5 19.8 1.0 FE1 A:SF4401 2.9 19.4 1.0 FE2 A:SF4401 2.9 18.0 1.0 FE4 A:SF4401 3.0 20.2 1.0 CB A:CYS24 3.1 22.6 1.0 S3 A:SF4401 3.7 20.1 1.0 CB A:MET26 3.9 15.9 1.0 N A:SAM403 4.0 27.5 1.0 O A:MET26 4.5 21.4 1.0 CA A:GLY69 4.5 19.5 1.0 C A:GLY69 4.5 18.6 1.0 ND2 A:ASN98 4.5 15.8 1.0 N A:MET26 4.6 18.5 1.0 CB A:SER35 4.6 17.5 1.0 CA A:CYS24 4.6 14.7 1.0 CA A:MET26 4.6 16.4 1.0 C A:MET26 4.7 18.2 1.0 O A:GLY69 4.7 15.5 1.0 CG A:MET26 4.7 24.0 1.0 OG A:SER35 4.9 15.4 1.0 N A:GLU70 5.0 17.2 1.0 SD A:MET26 5.0 28.2 1.0

Iron binding site 4 out of 16 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:20.2 occ:1.00 FE4 A:SF4401 0.0 20.2 1.0 S2 A:SF4401 2.1 20.5 1.0 S3 A:SF4401 2.1 20.1 1.0 S1 A:SF4401 2.1 22.9 1.0 O A:SAM403 2.5 17.0 1.0 FE2 A:SF4401 3.0 18.0 1.0 FE1 A:SF4401 3.0 19.4 1.0 FE3 A:SF4401 3.0 15.7 1.0 C A:SAM403 3.1 13.0 1.0 N A:SAM403 3.2 27.5 1.0 CA A:SAM403 3.6 45.2 1.0 SD A:SAM403 3.6 57.5 1.0 S4 A:SF4401 3.7 21.5 1.0 OH A:TYR121 3.8 29.3 1.0 OXT A:SAM403 3.9 38.5 1.0 CB A:SAM403 3.9 48.1 1.0 CE A:SAM403 4.1 55.4 1.0 CG A:SAM403 4.3 52.9 1.0 CZ A:TYR121 4.6 23.9 1.0 C2' A:SAM403 4.6 45.1 1.0 CE2 A:TYR121 4.7 23.4 1.0 C3' A:SAM403 4.7 43.6 1.0 O A:GLY69 4.7 15.5 1.0

Iron binding site 5 out of 16 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:20.9 occ:1.00 FE1 A:SF4402 0.0 20.9 1.0 S3 A:SF4402 2.1 23.6 1.0 S2 A:SF4402 2.1 23.4 1.0 S4 A:SF4402 2.1 25.2 1.0 SG A:CYS175 2.5 22.1 1.0 FE4 A:SF4402 2.9 17.6 1.0 FE3 A:SF4402 2.9 20.5 1.0 FE2 A:SF4402 2.9 22.9 1.0 CB A:CYS175 3.0 19.2 1.0 S1 A:SF4402 3.7 24.7 1.0 CA A:GLY246 4.2 17.3 1.0 CB A:ALA178 4.4 15.9 1.0 CA A:CYS175 4.5 17.6 1.0 N A:ALA178 4.6 24.0 1.0 CB A:LEU177 4.8 16.6 1.0 CD1 A:LEU177 5.0 25.9 1.0

Iron binding site 6 out of 16 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:22.9 occ:1.00 FE2 A:SF4402 0.0 22.9 1.0 S1 A:SF4402 2.1 24.7 1.0 S3 A:SF4402 2.1 23.6 1.0 S4 A:SF4402 2.1 25.2 1.0 SG A:CYS241 2.6 26.7 1.0 FE3 A:SF4402 2.9 20.5 1.0 FE4 A:SF4402 2.9 17.6 1.0 FE1 A:SF4402 2.9 20.9 1.0 CB A:CYS241 3.5 24.4 1.0 CA A:CYS241 3.6 22.8 1.0 S2 A:SF4402 3.7 23.4 1.0 N A:CYS241 3.9 29.9 1.0 CD1 A:LEU238 4.2 20.1 1.0 CD1 A:PHE172 4.4 24.8 1.0 CG A:LEU238 4.5 24.5 1.0 CB A:LEU238 4.7 27.4 1.0 C A:ALA240 4.8 24.3 1.0 CB A:CYS244 4.8 23.0 1.0 N A:LEU238 4.9 20.9 1.0 C A:CYS241 4.9 19.3 1.0

Iron binding site 7 out of 16 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:20.5 occ:1.00 FE3 A:SF4402 0.0 20.5 1.0 S2 A:SF4402 2.1 23.4 1.0 S1 A:SF4402 2.1 24.7 1.0 S4 A:SF4402 2.1 25.2 1.0 SG A:CYS244 2.6 22.1 1.0 FE2 A:SF4402 2.9 22.9 1.0 FE4 A:SF4402 2.9 17.6 1.0 FE1 A:SF4402 2.9 20.9 1.0 CB A:CYS244 3.0 23.0 1.0 S3 A:SF4402 3.7 23.6 1.0 CB A:GLN196 4.0 24.1 1.0 N A:GLY246 4.1 18.0 1.0 CA A:GLY246 4.1 17.3 1.0 CG A:GLN196 4.4 21.9 1.0 CA A:CYS244 4.5 21.5 1.0 CD A:GLN196 4.6 16.6 1.0 O A:HOH589 4.7 18.0 1.0 CA A:CYS241 4.8 22.8 1.0 C A:CYS244 4.8 19.9 1.0 NE2 A:GLN196 5.0 13.9 1.0 SG A:CYS175 5.0 22.1 1.0 SG A:CYS194 5.0 18.7 1.0

Iron binding site 8 out of 16 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:17.6 occ:1.00 FE4 A:SF4402 0.0 17.6 1.0 S2 A:SF4402 2.1 23.4 1.0 S1 A:SF4402 2.1 24.7 1.0 S3 A:SF4402 2.1 23.6 1.0 SG A:CYS194 2.5 18.7 1.0 FE1 A:SF4402 2.9 20.9 1.0 FE3 A:SF4402 2.9 20.5 1.0 FE2 A:SF4402 2.9 22.9 1.0 CB A:CYS194 3.3 14.2 1.0 S4 A:SF4402 3.7 25.2 1.0 CD1 A:LEU238 3.9 20.1 1.0 CB A:GLN196 4.4 24.1 1.0 N A:SER197 4.4 17.9 1.0 CB A:SER197 4.5 26.0 1.0 CA A:CYS194 4.7 18.7 1.0 OG A:SER197 4.7 22.3 1.0 OE1 A:GLN196 4.8 16.6 1.0 SG A:CYS175 4.9 22.1 1.0 CA A:SER197 4.9 20.6 1.0

Iron binding site 9 out of 16 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 9 of The Structure of A Twitch Radical Sam Dehydrogenase Spey within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:22.0 occ:1.00 FE1 B:SF4401 0.0 22.0 1.0 S3 B:SF4401 2.1 25.6 1.0 S4 B:SF4401 2.1 26.8 1.0 S2 B:SF4401 2.1 29.0 1.0 SG B:CYS24 2.6 26.1 1.0 FE3 B:SF4401 2.9 24.1 1.0 FE4 B:SF4401 2.9 23.4 1.0 FE2 B:SF4401 3.0 25.7 1.0 CB B:CYS24 3.1 22.6 1.0 S1 B:SF4401 3.6 28.6 1.0 CB B:MET26 4.1 20.8 1.0 N B:SAM403 4.2 35.6 1.0 O B:MET26 4.4 26.0 1.0 CA B:GLY69 4.4 31.4 1.0 C B:GLY69 4.5 24.8 1.0 CA B:CYS24 4.6 21.3 1.0 CB B:SER35 4.6 25.2 1.0 O B:GLY69 4.7 17.3 1.0 N B:MET26 4.7 23.4 1.0 C B:MET26 4.7 28.1 1.0 CA B:MET26 4.7 22.3 1.0 N B:GLU70 4.9 26.1 1.0

Iron binding site 10 out of 16 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 10 of The Structure of A Twitch Radical Sam Dehydrogenase Spey within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:25.7 occ:1.00 FE2 B:SF4401 0.0 25.7 1.0 S1 B:SF4401 2.1 28.6 1.0 S4 B:SF4401 2.1 26.8 1.0 S3 B:SF4401 2.1 25.6 1.0 OXT B:SAM403 2.6 24.1 1.0 FE1 B:SF4401 3.0 22.0 1.0 FE4 B:SF4401 3.0 23.4 1.0 FE3 B:SF4401 3.0 24.1 1.0 N B:SAM403 3.1 35.6 1.0 SD B:SAM403 3.2 61.5 1.0 C B:SAM403 3.4 26.1 1.0 CA B:SAM403 3.6 36.8 1.0 OH B:TYR121 3.7 26.6 1.0 CE B:SAM403 3.7 61.3 1.0 S2 B:SF4401 3.8 29.0 1.0 CB B:SAM403 3.9 48.4 1.0 CG B:SAM403 4.1 58.5 1.0 C3' B:SAM403 4.5 46.7 1.0 CZ B:TYR121 4.5 27.6 1.0 O B:SAM403 4.5 38.2 1.0 CE2 B:TYR121 4.6 17.9 1.0 C2' B:SAM403 4.6 42.1 1.0 O B:GLY69 4.6 17.3 1.0 C5' B:SAM403 4.9 53.3 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