Iron in PDB 3utd: EC_ISPH in Complex with 4-Oxopentyl Diphosphate

All present enzymatic activity of EC_ISPH in Complex with 4-Oxopentyl Diphosphate:
1.17.1.2;

The structure of EC_ISPH in Complex with 4-Oxopentyl Diphosphate, PDB code: 3utd was solved by I.Span, K.Wang, W.Wang, Y.Zhang, A.Bacher, W.Eisenreich, C.Schulz, E.Oldfield, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.73 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.110, 80.390, 111.240, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 20.6

The binding sites of Iron atom in the EC_ISPH in Complex with 4-Oxopentyl Diphosphate (pdb code 3utd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the EC_ISPH in Complex with 4-Oxopentyl Diphosphate, PDB code: 3utd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the EC_ISPH in Complex with 4-Oxopentyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of EC_ISPH in Complex with 4-Oxopentyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe317 b:12.9 occ:1.00 FE1 A:F3S317 0.0 12.9 1.0 S1 A:F3S317 2.2 13.9 1.0 S2 A:F3S317 2.2 15.8 1.0 S3 A:F3S317 2.3 13.2 1.0 SG A:CYS12 2.3 13.6 1.0 FE4 A:F3S317 2.6 14.4 1.0 FE3 A:F3S317 2.7 13.7 1.0 CB A:CYS12 3.3 14.2 1.0 S4 A:F3S317 3.9 14.7 1.0 N A:GLY14 4.2 14.3 1.0 CA A:GLY14 4.3 13.5 1.0 N A:VAL15 4.3 12.5 1.0 C30 A:0CJ318 4.4 16.3 1.0 CB A:ALA268 4.4 16.5 1.0 CG2 A:VAL15 4.4 14.0 1.0 C28 A:0CJ318 4.5 13.8 1.0 C27 A:0CJ318 4.6 16.0 1.0 CB A:ALA199 4.6 13.4 1.0 SG A:CYS197 4.7 13.9 1.0 CA A:CYS12 4.7 13.2 1.0 SG A:CYS96 4.7 13.5 1.0 C A:GLY14 4.7 13.0 1.0 C A:CYS12 4.9 13.6 1.0 N A:ALA13 5.0 14.3 1.0

Iron binding site 2 out of 6 in the EC_ISPH in Complex with 4-Oxopentyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of EC_ISPH in Complex with 4-Oxopentyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe317 b:13.7 occ:1.00 FE3 A:F3S317 0.0 13.7 1.0 S4 A:F3S317 2.3 14.7 1.0 S1 A:F3S317 2.3 13.9 1.0 SG A:CYS96 2.3 13.5 1.0 S3 A:F3S317 2.3 13.2 1.0 FE4 A:F3S317 2.7 14.4 1.0 FE1 A:F3S317 2.7 12.9 1.0 CB A:CYS96 3.1 13.6 1.0 S2 A:F3S317 4.0 15.8 1.0 CA A:GLY14 4.0 13.5 1.0 CB A:LEU98 4.4 13.9 1.0 N A:GLY14 4.4 14.3 1.0 C22 A:0CJ318 4.5 8.6 1.0 CD1 A:LEU98 4.5 15.3 1.0 CA A:CYS96 4.6 13.9 1.0 SG A:CYS12 4.6 13.6 1.0 CG A:LEU98 4.7 14.8 1.0 SG A:CYS197 4.8 13.9 1.0 C30 A:0CJ318 4.9 16.3 1.0

Iron binding site 3 out of 6 in the EC_ISPH in Complex with 4-Oxopentyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of EC_ISPH in Complex with 4-Oxopentyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe317 b:14.4 occ:1.00 FE4 A:F3S317 0.0 14.4 1.0 S2 A:F3S317 2.2 15.8 1.0 S4 A:F3S317 2.3 14.7 1.0 SG A:CYS197 2.3 13.9 1.0 S3 A:F3S317 2.4 13.2 1.0 FE1 A:F3S317 2.6 12.9 1.0 FE3 A:F3S317 2.7 13.7 1.0 CB A:CYS197 3.2 12.3 1.0 S1 A:F3S317 3.8 13.9 1.0 CB A:ALA199 4.3 13.4 1.0 OG1 A:THR200 4.5 13.8 1.0 OG1 A:THR167 4.6 13.6 1.0 CB A:THR167 4.7 11.8 1.0 CA A:CYS197 4.7 11.9 1.0 SG A:CYS12 4.7 13.6 1.0 CD1 A:LEU98 4.7 15.3 1.0 C30 A:0CJ318 4.8 16.3 1.0 O A:HOH325 4.8 14.0 1.0 SG A:CYS96 4.8 13.5 1.0 CG2 A:THR168 4.9 13.9 1.0 N A:ALA199 5.0 13.1 1.0

Iron binding site 4 out of 6 in the EC_ISPH in Complex with 4-Oxopentyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of EC_ISPH in Complex with 4-Oxopentyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe317 b:14.0 occ:1.00 FE1 B:F3S317 0.0 14.0 1.0 S1 B:F3S317 2.2 14.3 1.0 S2 B:F3S317 2.2 15.8 1.0 SG B:CYS12 2.3 13.4 1.0 S3 B:F3S317 2.3 14.0 1.0 FE4 B:F3S317 2.6 14.9 1.0 FE3 B:F3S317 2.7 13.8 1.0 CB B:CYS12 3.3 13.0 1.0 S4 B:F3S317 3.9 15.4 1.0 N B:GLY14 4.2 13.4 1.0 CA B:GLY14 4.3 12.6 1.0 CG2 B:VAL15 4.3 12.6 1.0 N B:VAL15 4.4 13.1 1.0 CB B:ALA268 4.4 12.6 1.0 C30 B:0CJ318 4.4 15.5 1.0 C28 B:0CJ318 4.5 14.7 1.0 CB B:ALA199 4.6 14.1 1.0 C27 B:0CJ318 4.6 17.1 1.0 SG B:CYS197 4.7 14.7 1.0 CA B:CYS12 4.7 12.0 1.0 SG B:CYS96 4.7 13.4 1.0 C B:GLY14 4.8 12.3 1.0 C B:CYS12 4.9 12.1 1.0

Iron binding site 5 out of 6 in the EC_ISPH in Complex with 4-Oxopentyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of EC_ISPH in Complex with 4-Oxopentyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe317 b:13.8 occ:1.00 FE3 B:F3S317 0.0 13.8 1.0 S4 B:F3S317 2.2 15.4 1.0 SG B:CYS96 2.3 13.4 1.0 S1 B:F3S317 2.3 14.3 1.0 S3 B:F3S317 2.3 14.0 1.0 FE1 B:F3S317 2.7 14.0 1.0 FE4 B:F3S317 2.7 14.9 1.0 CB B:CYS96 3.1 12.5 1.0 S2 B:F3S317 4.0 15.8 1.0 CA B:GLY14 4.0 12.6 1.0 C22 B:0CJ318 4.3 9.8 1.0 N B:GLY14 4.4 13.4 1.0 CD1 B:LEU98 4.5 15.3 1.0 CB B:LEU98 4.5 13.9 1.0 CA B:CYS96 4.6 12.7 1.0 SG B:CYS12 4.6 13.4 1.0 CG B:LEU98 4.7 13.9 1.0 SG B:CYS197 4.8 14.7 1.0

Iron binding site 6 out of 6 in the EC_ISPH in Complex with 4-Oxopentyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of EC_ISPH in Complex with 4-Oxopentyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe317 b:14.9 occ:1.00 FE4 B:F3S317 0.0 14.9 1.0 S2 B:F3S317 2.3 15.8 1.0 S4 B:F3S317 2.3 15.4 1.0 SG B:CYS197 2.3 14.7 1.0 S3 B:F3S317 2.4 14.0 1.0 FE1 B:F3S317 2.6 14.0 1.0 FE3 B:F3S317 2.7 13.8 1.0 CB B:CYS197 3.2 14.6 1.0 S1 B:F3S317 3.8 14.3 1.0 CB B:ALA199 4.2 14.1 1.0 OG1 B:THR200 4.5 14.6 1.0 OG1 B:THR167 4.7 12.8 1.0 O B:HOH327 4.7 13.8 1.0 CB B:THR167 4.7 13.3 1.0 CA B:CYS197 4.7 12.7 1.0 SG B:CYS12 4.7 13.4 1.0 CD1 B:LEU98 4.8 15.3 1.0 C30 B:0CJ318 4.8 15.5 1.0 SG B:CYS96 4.9 13.4 1.0 CG2 B:THR168 5.0 11.1 1.0 N B:ALA199 5.0 15.0 1.0 CB B:CYS12 5.0 13.0 1.0

I.Span, K.Wang, W.Wang, Y.Zhang, A.Bacher, W.Eisenreich, K.Li, C.Schulz, E.Oldfield, M.Groll. Discovery of Acetylene Hydratase Activity of the Iron-Sulphur Protein Isph. Nat Commun V. 3 1042 2012.
ISSN: ESSN 2041-1723
PubMed: 22948824
DOI: 10.1038/NCOMMS2052