Iron in PDB 5ul3: Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin Bound

The structure of Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin Bound, PDB code: 5ul3 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)	49.80 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.357, 99.595, 121.439, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.2

The structure of Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin 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 Bound (pdb code 5ul3). 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 Bound, PDB code: 5ul3:
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 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 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:25.1 occ:1.00 FE1 A:SF4801 0.0 25.1 1.0 SG A:CYS318 2.2 24.6 1.0 S3 A:SF4801 2.2 29.8 1.0 S4 A:SF4801 2.3 27.3 1.0 S2 A:SF4801 2.3 24.2 1.0 FE3 A:SF4801 2.7 24.4 1.0 FE2 A:SF4801 2.7 28.0 1.0 FE4 A:SF4801 2.7 25.1 1.0 CB A:CYS318 3.0 24.7 1.0 NZ A:LYS448 3.8 32.0 0.5 S1 A:SF4801 3.9 26.0 1.0 N A:CYS318 4.1 28.1 1.0 CA A:CYS318 4.2 26.3 1.0 NZ A:LYS448 4.2 29.8 0.5 CD2 A:TYR315 4.3 27.6 1.0 CB A:CYS321 4.5 22.0 1.0 SG A:CYS321 4.6 24.2 1.0 S1 A:DTT803 4.6 34.5 1.0 CE A:LYS448 4.7 34.9 0.5 CE2 A:TYR315 4.8 23.4 1.0 SG A:CYS313 4.8 25.9 1.0 O A:HOH1031 4.9 38.0 1.0

Iron binding site 2 out of 4 in the Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin 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 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:28.0 occ:1.00 FE2 A:SF4801 0.0 28.0 1.0 S4 A:SF4801 2.3 27.3 1.0 S3 A:SF4801 2.3 29.8 1.0 S1 A:SF4801 2.3 26.0 1.0 S1 A:DTT803 2.4 34.5 1.0 FE1 A:SF4801 2.7 25.1 1.0 FE4 A:SF4801 2.8 25.1 1.0 FE3 A:SF4801 2.8 24.4 1.0 O2 A:DTT803 3.1 52.4 1.0 C1 A:DTT803 3.4 30.2 1.0 C2 A:DTT803 3.7 45.3 1.0 S2 A:SF4801 4.0 24.2 1.0 C3 A:DTT803 4.2 54.1 1.0 O A:HOH1031 4.2 38.0 1.0 NZ A:LYS448 4.2 32.0 0.5 O A:HOH1227 4.3 32.5 1.0 O A:HOH1064 4.6 38.0 1.0 SG A:CYS318 4.7 24.6 1.0 SG A:CYS313 4.7 25.9 1.0 NZ A:LYS448 4.8 29.8 0.5 SG A:CYS321 4.9 24.2 1.0 O A:HOH1097 4.9 35.6 1.0 O A:GLU363 4.9 24.4 1.0 CG A:ARG399 5.0 32.8 1.0

Iron binding site 3 out of 4 in the Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin 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 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:24.4 occ:1.00 FE3 A:SF4801 0.0 24.4 1.0 SG A:CYS321 2.3 24.2 1.0 S1 A:SF4801 2.3 26.0 1.0 S2 A:SF4801 2.3 24.2 1.0 S4 A:SF4801 2.3 27.3 1.0 FE1 A:SF4801 2.7 25.1 1.0 FE4 A:SF4801 2.7 25.1 1.0 FE2 A:SF4801 2.8 28.0 1.0 CB A:CYS321 3.1 22.0 1.0 S3 A:SF4801 3.9 29.8 1.0 NH2 A:ARG323 3.9 24.2 1.0 O A:HOH1064 4.2 38.0 1.0 N29 A:B12802 4.2 24.0 1.0 CA A:CYS321 4.6 24.2 1.0 CB A:CYS318 4.6 24.7 1.0 CZ A:ARG323 4.6 25.2 1.0 CD A:ARG323 4.7 23.4 1.0 SG A:CYS318 4.7 24.6 1.0 O2 A:DTT803 4.7 52.4 1.0 SG A:CYS313 4.9 25.9 1.0 OE2 A:GLU363 4.9 26.2 1.0 NE A:ARG323 5.0 25.4 1.0

Iron binding site 4 out of 4 in the Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin 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 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:25.1 occ:1.00 FE4 A:SF4801 0.0 25.1 1.0 S2 A:SF4801 2.3 24.2 1.0 S3 A:SF4801 2.3 29.8 1.0 SG A:CYS313 2.3 25.9 1.0 S1 A:SF4801 2.3 26.0 1.0 FE3 A:SF4801 2.7 24.4 1.0 FE1 A:SF4801 2.7 25.1 1.0 FE2 A:SF4801 2.8 28.0 1.0 CB A:CYS313 3.3 23.7 1.0 S4 A:SF4801 3.9 27.3 1.0 N A:SER316 4.0 26.2 1.0 O A:HOH1097 4.1 35.6 1.0 CA A:SER316 4.4 25.0 1.0 CB A:TYR315 4.6 22.0 1.0 CA A:CYS313 4.7 22.7 1.0 SG A:CYS318 4.8 24.6 1.0 S1 A:DTT803 4.8 34.5 1.0 CD2 A:TYR315 4.8 27.6 1.0 SG A:CYS321 4.8 24.2 1.0 NH2 A:ARG323 4.8 24.2 1.0 CZ A:ARG323 4.9 25.2 1.0

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