Iron in PDB 3c8f: 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme with Partially Disordered Adomet

All present enzymatic activity of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme with Partially Disordered Adomet:
1.97.1.4;

The structure of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme with Partially Disordered Adomet, PDB code: 3c8f was solved by J.L.Vey, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.90 / 2.25
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	58.051, 58.051, 117.466, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 29.8

The binding sites of Iron atom in the 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme with Partially Disordered Adomet (pdb code 3c8f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme with Partially Disordered Adomet, PDB code: 3c8f:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme with Partially Disordered Adomet


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme with Partially Disordered Adomet within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:45.8 occ:1.00 FE1 A:SF4500 0.0 45.8 1.0 S2 A:SF4500 2.3 46.0 1.0 S3 A:SF4500 2.3 44.5 1.0 S4 A:SF4500 2.3 48.7 1.0 SG A:CYS33 2.3 48.1 1.0 FE3 A:SF4500 2.6 46.5 1.0 FE4 A:SF4500 2.6 42.0 1.0 FE2 A:SF4500 2.7 46.9 1.0 CB A:CYS33 3.2 46.0 1.0 S1 A:SF4500 3.8 46.2 1.0 NZ A:LYS131 3.8 42.9 1.0 N A:CYS33 4.0 45.0 1.0 CA A:CYS33 4.2 46.5 1.0 CE A:LYS131 4.2 39.9 1.0 CB A:MET31 4.3 47.2 1.0 SG A:CYS36 4.5 47.8 1.0 SG A:CYS29 4.7 44.3 1.0 CB A:CYS36 4.7 51.7 1.0 CA A:MT2501 4.9 54.9 1.0 C A:MET31 5.0 45.5 1.0 CA A:CYS36 5.0 55.7 1.0

Iron binding site 2 out of 4 in the 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme with Partially Disordered Adomet


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme with Partially Disordered Adomet within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:46.9 occ:1.00 FE2 A:SF4500 0.0 46.9 1.0 S4 A:SF4500 2.3 48.7 1.0 S1 A:SF4500 2.3 46.2 1.0 S3 A:SF4500 2.3 44.5 1.0 CA A:MT2501 2.4 54.9 1.0 FE3 A:SF4500 2.7 46.5 1.0 FE1 A:SF4500 2.7 45.8 1.0 FE4 A:SF4500 2.8 42.0 1.0 O A:MT2501 2.9 52.9 1.0 C A:MT2501 3.1 53.4 1.0 N A:MT2501 3.3 52.6 1.0 CB A:MT2501 3.4 59.7 1.0 S2 A:SF4500 4.0 46.0 1.0 ND2 A:ASN106 4.1 54.0 1.0 OD1 A:ASN106 4.2 49.5 1.0 OXT A:MT2501 4.2 54.4 1.0 NZ A:LYS131 4.3 42.9 1.0 O A:GLY78 4.5 44.9 1.0 CG A:ASN106 4.6 49.0 1.0 SG A:CYS29 4.8 44.3 1.0 SG A:CYS36 4.8 47.8 1.0 CG A:MT2501 4.8 65.6 1.0 SG A:CYS33 4.8 48.1 1.0 O A:GLY77 5.0 46.4 1.0

Iron binding site 3 out of 4 in the 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme with Partially Disordered Adomet


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme with Partially Disordered Adomet within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:46.5 occ:1.00 FE3 A:SF4500 0.0 46.5 1.0 S1 A:SF4500 2.3 46.2 1.0 S4 A:SF4500 2.3 48.7 1.0 SG A:CYS36 2.3 47.8 1.0 S2 A:SF4500 2.3 46.0 1.0 FE1 A:SF4500 2.6 45.8 1.0 FE2 A:SF4500 2.7 46.9 1.0 FE4 A:SF4500 2.7 42.0 1.0 CB A:CYS36 3.3 51.7 1.0 S3 A:SF4500 3.8 44.5 1.0 NE1 A:TRP42 3.9 47.5 1.0 CA A:CYS36 3.9 55.7 1.0 CD1 A:TRP42 4.6 45.0 1.0 N A:HIS37 4.6 61.4 1.0 SG A:CYS33 4.6 48.1 1.0 C A:CYS36 4.7 58.6 1.0 O A:ASN38 4.7 57.5 1.0 CB A:CYS33 4.8 46.0 1.0 SG A:CYS29 4.9 44.3 1.0 OG1 A:THR41 4.9 45.0 1.0 CA A:MT2501 5.0 54.9 1.0 O A:MT2501 5.0 52.9 1.0 N A:CYS36 5.0 55.0 1.0

Iron binding site 4 out of 4 in the 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme with Partially Disordered Adomet


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme with Partially Disordered Adomet within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:42.0 occ:1.00 FE4 A:SF4500 0.0 42.0 1.0 S3 A:SF4500 2.3 44.5 1.0 S2 A:SF4500 2.3 46.0 1.0 SG A:CYS29 2.3 44.3 1.0 S1 A:SF4500 2.3 46.2 1.0 FE1 A:SF4500 2.6 45.8 1.0 FE3 A:SF4500 2.7 46.5 1.0 FE2 A:SF4500 2.8 46.9 1.0 CB A:CYS29 3.4 39.9 1.0 S4 A:SF4500 3.9 48.7 1.0 CB A:MET31 4.1 47.2 1.0 ND2 A:ASN106 4.2 54.0 1.0 O A:MET31 4.4 45.2 1.0 NE1 A:TRP42 4.5 47.5 1.0 O A:MT2501 4.5 52.9 1.0 CA A:GLY78 4.6 47.6 1.0 C A:MET31 4.6 45.5 1.0 CD1 A:TRP42 4.7 45.0 1.0 SG A:CYS33 4.7 48.1 1.0 C A:GLY78 4.7 45.6 1.0 N A:MET31 4.7 46.5 1.0 CA A:MET31 4.8 46.5 1.0 O A:GLY78 4.8 44.9 1.0 CA A:CYS29 4.8 41.4 1.0 SG A:CYS36 4.8 47.8 1.0 CA A:MT2501 5.0 54.9 1.0

J.L.Vey, J.Yang, M.Li, W.E.Broderick, J.B.Broderick, C.L.Drennan. Structural Basis For Glycyl Radical Formation By Pyruvate Formate-Lyase Activating Enzyme. Proc.Natl.Acad.Sci.Usa V. 105 16137 2008.
ISSN: ISSN 0027-8424
PubMed: 18852451
DOI: 10.1073/PNAS.0806640105