Iron in PDB 4pkf: Benzylsuccinate Synthase Alpha-Beta-Gamma Complex

All present enzymatic activity of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex:
4.1.99.11;

The structure of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex, PDB code: 4pkf was solved by M.A.Funk, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.53 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	113.424, 120.421, 136.048, 90.00, 90.00, 90.00
R / Rfree (%)	12.9 / 17.7

The structure of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the Benzylsuccinate Synthase Alpha-Beta-Gamma Complex (pdb code 4pkf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Benzylsuccinate Synthase Alpha-Beta-Gamma Complex, PDB code: 4pkf:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Benzylsuccinate Synthase Alpha-Beta-Gamma Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:31.0 occ:1.00 FE1 B:SF4101 0.0 31.0 1.0 S3 B:SF4101 2.2 31.4 1.0 SG B:CYS29 2.3 31.8 1.0 S4 B:SF4101 2.3 29.1 1.0 S2 B:SF4101 2.3 31.2 1.0 FE2 B:SF4101 2.7 28.3 1.0 FE4 B:SF4101 2.7 31.4 1.0 FE3 B:SF4101 2.8 30.1 1.0 CB B:CYS29 3.1 31.0 1.0 S1 B:SF4101 3.9 29.2 1.0 CB B:TRP31 4.1 25.0 1.0 CA B:HIS70 4.2 38.6 1.0 CD1 B:TRP31 4.4 30.5 1.0 N B:HIS70 4.6 39.1 1.0 CA B:CYS29 4.6 34.7 1.0 CG B:TRP31 4.7 32.9 1.0 CD2 B:HIS70 4.7 37.8 1.0 CB B:HIS70 4.7 41.7 1.0 SG B:CYS67 4.7 35.3 1.0 SG B:CYS44 4.8 27.0 1.0 SG B:CYS26 4.8 33.2 1.0 CA B:CYS26 4.8 34.7 1.0 N B:GLN32 4.9 23.7 1.0 N B:TRP31 4.9 27.7 1.0 C B:ARG69 4.9 39.3 1.0 CA B:TRP31 4.9 28.8 1.0 CG B:HIS70 5.0 41.0 1.0 O B:ARG69 5.0 42.3 1.0

Iron binding site 2 out of 4 in the Benzylsuccinate Synthase Alpha-Beta-Gamma Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:28.3 occ:1.00 FE2 B:SF4101 0.0 28.3 1.0 S4 B:SF4101 2.2 29.1 1.0 S3 B:SF4101 2.3 31.4 1.0 S1 B:SF4101 2.3 29.2 1.0 SG B:CYS44 2.3 27.0 1.0 FE3 B:SF4101 2.7 30.1 1.0 FE1 B:SF4101 2.7 31.0 1.0 FE4 B:SF4101 2.7 31.4 1.0 CB B:CYS44 3.1 24.4 1.0 S2 B:SF4101 3.9 31.2 1.0 CA B:CYS44 4.1 26.7 1.0 NH2 B:ARG69 4.2 41.5 1.0 CB B:ALA46 4.4 29.2 1.0 CB B:TRP31 4.5 25.0 1.0 SG B:CYS67 4.6 35.3 1.0 SG B:CYS26 4.7 33.2 1.0 SG B:CYS29 4.7 31.8 1.0 C B:CYS44 4.9 23.2 1.0

Iron binding site 3 out of 4 in the Benzylsuccinate Synthase Alpha-Beta-Gamma Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:30.1 occ:1.00 FE3 B:SF4101 0.0 30.1 1.0 S1 B:SF4101 2.2 29.2 1.0 SG B:CYS26 2.3 33.2 1.0 S2 B:SF4101 2.3 31.2 1.0 S4 B:SF4101 2.3 29.1 1.0 FE2 B:SF4101 2.7 28.3 1.0 FE4 B:SF4101 2.7 31.4 1.0 FE1 B:SF4101 2.8 31.0 1.0 CB B:CYS26 3.3 28.9 1.0 CA B:CYS26 3.7 34.7 1.0 S3 B:SF4101 3.9 31.4 1.0 N B:CYS26 4.4 38.0 1.0 CD1 B:LEU59 4.5 25.7 1.0 CA B:THR66 4.5 40.1 1.0 N B:CYS67 4.6 42.6 1.0 C B:THR66 4.6 41.0 1.0 CD2 B:LEU59 4.7 28.8 1.0 CB B:CYS29 4.7 31.0 1.0 SG B:CYS29 4.8 31.8 1.0 SG B:CYS44 4.8 27.0 1.0 SG B:CYS67 4.9 35.3 1.0 N B:THR66 4.9 42.5 1.0 C B:CYS26 4.9 35.1 1.0 CB B:CYS44 4.9 24.4 1.0

Iron binding site 4 out of 4 in the Benzylsuccinate Synthase Alpha-Beta-Gamma Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:31.4 occ:1.00 FE4 B:SF4101 0.0 31.4 1.0 S2 B:SF4101 2.2 31.2 1.0 S3 B:SF4101 2.3 31.4 1.0 SG B:CYS67 2.3 35.3 1.0 S1 B:SF4101 2.3 29.2 1.0 FE3 B:SF4101 2.7 30.1 1.0 FE1 B:SF4101 2.7 31.0 1.0 FE2 B:SF4101 2.7 28.3 1.0 CB B:CYS67 3.2 41.1 1.0 N B:CYS67 3.5 42.6 1.0 CA B:CYS67 3.8 36.6 1.0 S4 B:SF4101 3.9 29.1 1.0 NH2 B:ARG69 4.1 41.5 1.0 C B:THR66 4.2 41.0 1.0 N B:HIS70 4.3 39.1 1.0 C B:CYS67 4.3 37.8 1.0 O B:CYS67 4.4 35.3 1.0 NE B:ARG69 4.6 58.2 1.0 CA B:HIS70 4.6 38.6 1.0 C B:ARG69 4.7 39.3 1.0 SG B:CYS44 4.7 27.0 1.0 SG B:CYS26 4.7 33.2 1.0 N B:ARG69 4.8 37.9 1.0 CB B:ARG69 4.8 41.1 1.0 CZ B:ARG69 4.8 55.5 1.0 SG B:CYS29 4.8 31.8 1.0 O B:THR66 4.8 44.0 1.0 CA B:THR66 4.8 40.1 1.0 CB B:HIS70 4.9 41.7 1.0 CA B:ARG69 5.0 39.7 1.0

M.A.Funk, E.T.Judd, E.N.Marsh, S.J.Elliott, C.L.Drennan. Structures of Benzylsuccinate Synthase Elucidate Roles of Accessory Subunits in Glycyl Radical Enzyme Activation and Activity. Proc.Natl.Acad.Sci.Usa V. 111 10161 2014.
ISSN: ESSN 1091-6490
PubMed: 24982148
DOI: 10.1073/PNAS.1405983111