Iron in PDB 5ul4: Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin and S-Adenosylmethionine Bound

The structure of Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin and S-Adenosylmethionine Bound, PDB code: 5ul4 was solved by J.Bridwell-Rabb, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.84 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.360, 99.600, 121.440, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 23.1

The structure of Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin and S-Adenosylmethionine Bound also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Iron atom in the Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin and S-Adenosylmethionine Bound (pdb code 5ul4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin and S-Adenosylmethionine Bound, PDB code: 5ul4:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin and S-Adenosylmethionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin and S-Adenosylmethionine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:33.9 occ:1.00 FE1 A:SF4801 0.0 33.9 1.0 O A:SAM803 2.2 35.7 0.5 O A:SAM803 2.2 36.6 0.5 N A:SAM803 2.2 42.4 0.5 N A:SAM803 2.3 27.3 0.5 S3 A:SF4801 2.3 36.7 1.0 S4 A:SF4801 2.3 33.6 1.0 S2 A:SF4801 2.3 30.5 1.0 FE2 A:SF4801 2.7 31.3 1.0 FE4 A:SF4801 2.8 29.6 1.0 FE3 A:SF4801 2.8 28.8 1.0 SD A:SAM803 2.9 46.2 0.5 C A:SAM803 3.0 33.2 0.5 C A:SAM803 3.0 35.7 0.5 CA A:SAM803 3.1 31.9 0.5 CA A:SAM803 3.2 41.0 0.5 CE A:SAM803 3.5 38.7 0.5 O A:HOH924 3.5 37.5 0.5 CG A:SAM803 3.8 38.6 0.5 CB A:SAM803 3.8 36.5 0.5 S1 A:SF4801 4.0 30.9 1.0 O A:HOH1241 4.0 31.3 0.5 O A:HOH906 4.1 40.7 0.5 OXT A:SAM803 4.1 32.7 0.5 OXT A:SAM803 4.2 38.4 0.5 CB A:SAM803 4.2 44.6 0.5 C5' A:SAM803 4.6 42.4 0.5 O A:GLU363 4.6 29.6 1.0 SG A:CYS313 4.6 30.1 1.0 SG A:CYS318 4.8 31.8 1.0 SG A:CYS321 4.8 29.5 1.0 NZ A:LYS448 4.9 38.7 1.0 CG A:ARG399 4.9 36.9 1.0

Iron binding site 2 out of 4 in the Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin and S-Adenosylmethionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin and S-Adenosylmethionine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:31.3 occ:1.00 FE2 A:SF4801 0.0 31.3 1.0 S4 A:SF4801 2.3 33.6 1.0 S3 A:SF4801 2.3 36.7 1.0 SG A:CYS318 2.3 31.8 1.0 S1 A:SF4801 2.3 30.9 1.0 FE3 A:SF4801 2.7 28.8 1.0 FE4 A:SF4801 2.7 29.6 1.0 FE1 A:SF4801 2.7 33.9 1.0 CB A:CYS318 3.1 35.6 1.0 O A:SAM803 3.5 35.7 0.5 S2 A:SF4801 3.9 30.5 1.0 NZ A:LYS448 4.1 38.7 1.0 N A:CYS318 4.2 37.2 1.0 CA A:CYS318 4.3 37.8 1.0 O A:HOH924 4.3 37.5 0.5 CD2 A:TYR315 4.4 36.0 1.0 CB A:CYS321 4.5 30.9 1.0 O A:SAM803 4.5 36.6 0.5 SG A:CYS321 4.6 29.5 1.0 C A:SAM803 4.6 33.2 0.5 N A:SAM803 4.7 27.3 0.5 N A:SAM803 4.7 42.4 0.5 SG A:CYS313 4.8 30.1 1.0 CE2 A:TYR315 4.9 32.9 1.0

Iron binding site 3 out of 4 in the Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin and S-Adenosylmethionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin and S-Adenosylmethionine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:28.8 occ:1.00 FE3 A:SF4801 0.0 28.8 1.0 SG A:CYS321 2.2 29.5 1.0 S2 A:SF4801 2.3 30.5 1.0 S1 A:SF4801 2.3 30.9 1.0 S4 A:SF4801 2.3 33.6 1.0 FE2 A:SF4801 2.7 31.3 1.0 FE4 A:SF4801 2.7 29.6 1.0 FE1 A:SF4801 2.8 33.9 1.0 CB A:CYS321 3.1 30.9 1.0 N A:SAM803 3.7 42.4 0.5 NH2 A:ARG323 3.8 28.9 1.0 S3 A:SF4801 3.9 36.7 1.0 N29 A:B12802 4.1 35.4 1.0 SD A:SAM803 4.5 46.2 0.5 CA A:CYS321 4.6 32.1 1.0 CZ A:ARG323 4.6 32.8 1.0 CB A:CYS318 4.6 35.6 1.0 CD A:ARG323 4.6 28.0 1.0 SG A:CYS318 4.7 31.8 1.0 O A:SAM803 4.7 35.7 0.5 CE A:SAM803 4.8 38.7 0.5 SG A:CYS313 4.8 30.1 1.0 N A:SAM803 4.8 27.3 0.5 NE A:ARG323 4.9 31.1 1.0 OE2 A:GLU363 4.9 33.1 1.0 O A:SAM803 4.9 36.6 0.5

Iron binding site 4 out of 4 in the Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin and S-Adenosylmethionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin and S-Adenosylmethionine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:29.6 occ:1.00 FE4 A:SF4801 0.0 29.6 1.0 SG A:CYS313 2.3 30.1 1.0 S3 A:SF4801 2.3 36.7 1.0 S1 A:SF4801 2.3 30.9 1.0 S2 A:SF4801 2.3 30.5 1.0 FE3 A:SF4801 2.7 28.8 1.0 FE2 A:SF4801 2.7 31.3 1.0 FE1 A:SF4801 2.8 33.9 1.0 CB A:CYS313 3.3 27.1 1.0 S4 A:SF4801 3.9 33.6 1.0 N A:SAM803 3.9 27.3 0.5 N A:SER316 3.9 29.8 1.0 CA A:SER316 4.3 31.5 1.0 N A:SAM803 4.4 42.4 0.5 O A:SAM803 4.5 35.7 0.5 CA A:CYS313 4.7 28.7 1.0 O A:SAM803 4.7 36.6 0.5 CB A:TYR315 4.7 27.4 1.0 SG A:CYS321 4.7 29.5 1.0 NH2 A:ARG323 4.8 28.9 1.0 SG A:CYS318 4.8 31.8 1.0 CD2 A:TYR315 4.8 36.0 1.0 CZ A:ARG323 4.9 32.8 1.0 O A:HOH1241 5.0 31.3 0.5

J.Bridwell-Rabb, A.Zhong, H.G.Sun, C.L.Drennan, H.W.Liu. A B12-Dependent Radical Sam Enzyme Involved in Oxetanocin A Biosynthesis. Nature V. 544 322 2017.
ISSN: ESSN 1476-4687
PubMed: 28346939
DOI: 10.1038/NATURE21689