Iron in PDB 4mv0: Isph in Complex with Pyridin-2-Ylmethyl Diphosphate

All present enzymatic activity of Isph in Complex with Pyridin-2-Ylmethyl Diphosphate:
1.17.1.2;

The structure of Isph in Complex with Pyridin-2-Ylmethyl Diphosphate, PDB code: 4mv0 was solved by I.Span, K.Wang, Y.Song, W.Eisenreich, A.Bacher, E.Oldfield, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.97 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.470, 80.800, 111.490, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 25.6

The binding sites of Iron atom in the Isph in Complex with Pyridin-2-Ylmethyl Diphosphate (pdb code 4mv0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Isph in Complex with Pyridin-2-Ylmethyl Diphosphate, PDB code: 4mv0:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Isph in Complex with Pyridin-2-Ylmethyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Isph in Complex with Pyridin-2-Ylmethyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:21.4 occ:1.00 FE1 A:F3S401 0.0 21.4 1.0 S1 A:F3S401 2.3 22.1 1.0 SG A:CYS197 2.3 19.9 1.0 S2 A:F3S401 2.3 21.5 1.0 S3 A:F3S401 2.3 21.0 1.0 FE4 A:F3S401 2.7 20.9 1.0 FE3 A:F3S401 2.7 21.0 1.0 CB A:CYS197 3.1 20.3 1.0 S4 A:F3S401 3.8 22.6 1.0 CB A:ALA199 4.2 21.2 1.0 N4 A:2E6402 4.3 21.9 1.0 C3 A:2E6402 4.3 21.8 1.0 OG1 A:THR200 4.5 20.8 1.0 CA A:CYS197 4.6 20.5 1.0 CB A:THR167 4.7 21.5 1.0 OG1 A:THR167 4.7 21.9 1.0 CD1 A:LEU98 4.7 24.7 1.0 SG A:CYS12 4.8 21.1 1.0 SG A:CYS96 4.8 20.0 1.0 O A:HOH511 4.8 21.0 1.0

Iron binding site 2 out of 6 in the Isph in Complex with Pyridin-2-Ylmethyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Isph in Complex with Pyridin-2-Ylmethyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:21.0 occ:1.00 FE3 A:F3S401 0.0 21.0 1.0 SG A:CYS96 2.2 20.0 1.0 S1 A:F3S401 2.3 22.1 1.0 S4 A:F3S401 2.3 22.6 1.0 S3 A:F3S401 2.3 21.0 1.0 FE4 A:F3S401 2.7 20.9 1.0 FE1 A:F3S401 2.7 21.4 1.0 CB A:CYS96 3.2 20.2 1.0 S2 A:F3S401 4.0 21.5 1.0 CA A:GLY14 4.1 22.3 1.0 CB A:LEU98 4.4 24.2 1.0 C3 A:2E6402 4.4 21.8 1.0 N A:GLY14 4.4 22.2 1.0 CD1 A:LEU98 4.5 24.7 1.0 N4 A:2E6402 4.5 21.9 1.0 CA A:CYS96 4.6 20.4 1.0 SG A:CYS12 4.7 21.1 1.0 C2 A:2E6402 4.7 20.4 1.0 CG A:LEU98 4.7 24.5 1.0 SG A:CYS197 4.9 19.9 1.0 N A:LEU98 5.0 23.1 1.0

Iron binding site 3 out of 6 in the Isph in Complex with Pyridin-2-Ylmethyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Isph in Complex with Pyridin-2-Ylmethyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:20.9 occ:1.00 FE4 A:F3S401 0.0 20.9 1.0 S4 A:F3S401 2.2 22.6 1.0 SG A:CYS12 2.3 21.1 1.0 S2 A:F3S401 2.3 21.5 1.0 S3 A:F3S401 2.3 21.0 1.0 FE1 A:F3S401 2.7 21.4 1.0 FE3 A:F3S401 2.7 21.0 1.0 CB A:CYS12 3.3 21.1 1.0 S1 A:F3S401 3.9 22.1 1.0 N4 A:2E6402 3.9 21.9 1.0 N A:GLY14 4.2 22.2 1.0 C5 A:2E6402 4.2 21.0 1.0 C7 A:2E6402 4.2 22.5 1.0 CA A:GLY14 4.3 22.3 1.0 N A:VAL15 4.3 22.4 1.0 CG2 A:VAL15 4.4 22.7 1.0 CB A:ALA268 4.5 24.4 1.0 C3 A:2E6402 4.6 21.8 1.0 CB A:ALA199 4.6 21.2 1.0 CA A:CYS12 4.6 21.0 1.0 SG A:CYS96 4.7 20.0 1.0 SG A:CYS197 4.7 19.9 1.0 C A:GLY14 4.7 22.2 1.0 N A:ALA13 4.9 21.8 1.0 C A:CYS12 4.9 21.2 1.0

Iron binding site 4 out of 6 in the Isph in Complex with Pyridin-2-Ylmethyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Isph in Complex with Pyridin-2-Ylmethyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:20.6 occ:1.00 FE1 B:F3S401 0.0 20.6 1.0 S1 B:F3S401 2.3 20.5 1.0 SG B:CYS197 2.3 20.7 1.0 S2 B:F3S401 2.3 20.6 1.0 S3 B:F3S401 2.3 20.4 1.0 FE4 B:F3S401 2.6 20.7 1.0 FE3 B:F3S401 2.8 20.6 1.0 CB B:CYS197 3.2 21.0 1.0 S4 B:F3S401 3.8 20.7 1.0 CB B:ALA199 4.2 21.0 1.0 C3 B:2E6402 4.3 20.8 1.0 N4 B:2E6402 4.3 22.1 1.0 OG1 B:THR200 4.5 20.3 1.0 CB B:THR167 4.6 22.8 1.0 OG1 B:THR167 4.6 22.9 1.0 SG B:CYS12 4.7 20.2 1.0 CA B:CYS197 4.7 20.8 1.0 O B:HOH506 4.7 25.1 1.0 CD1 B:LEU98 4.7 25.4 1.0 SG B:CYS96 4.8 24.4 1.0 CB B:CYS12 5.0 20.7 1.0 N B:ALA199 5.0 20.5 1.0

Iron binding site 5 out of 6 in the Isph in Complex with Pyridin-2-Ylmethyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Isph in Complex with Pyridin-2-Ylmethyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:20.6 occ:1.00 FE3 B:F3S401 0.0 20.6 1.0 SG B:CYS96 2.2 24.4 1.0 S3 B:F3S401 2.3 20.4 1.0 S1 B:F3S401 2.3 20.5 1.0 S4 B:F3S401 2.3 20.7 1.0 FE4 B:F3S401 2.7 20.7 1.0 FE1 B:F3S401 2.8 20.6 1.0 CB B:CYS96 3.0 23.9 1.0 CA B:GLY14 4.0 22.1 1.0 S2 B:F3S401 4.1 20.6 1.0 CB B:LEU98 4.3 25.2 1.0 N B:GLY14 4.4 22.0 1.0 C3 B:2E6402 4.5 20.8 1.0 CD1 B:LEU98 4.5 25.4 1.0 CA B:CYS96 4.5 23.9 1.0 SG B:CYS12 4.6 20.2 1.0 N4 B:2E6402 4.7 22.1 1.0 C2 B:2E6402 4.7 20.9 1.0 CG B:LEU98 4.7 25.4 1.0 SG B:CYS197 4.9 20.7 1.0

Iron binding site 6 out of 6 in the Isph in Complex with Pyridin-2-Ylmethyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Isph in Complex with Pyridin-2-Ylmethyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:20.7 occ:1.00 FE4 B:F3S401 0.0 20.7 1.0 SG B:CYS12 2.2 20.2 1.0 S4 B:F3S401 2.2 20.7 1.0 S3 B:F3S401 2.3 20.4 1.0 S2 B:F3S401 2.3 20.6 1.0 FE1 B:F3S401 2.6 20.6 1.0 FE3 B:F3S401 2.7 20.6 1.0 CB B:CYS12 3.3 20.7 1.0 S1 B:F3S401 3.9 20.5 1.0 N4 B:2E6402 4.0 22.1 1.0 N B:GLY14 4.2 22.0 1.0 C5 B:2E6402 4.2 21.0 1.0 CA B:GLY14 4.3 22.1 1.0 C7 B:2E6402 4.3 21.6 1.0 N B:VAL15 4.3 21.9 1.0 CG2 B:VAL15 4.4 21.5 1.0 CB B:ALA268 4.4 22.2 1.0 CB B:ALA199 4.6 21.0 1.0 C3 B:2E6402 4.6 20.8 1.0 CA B:CYS12 4.6 21.1 1.0 SG B:CYS96 4.7 24.4 1.0 SG B:CYS197 4.7 20.7 1.0 C B:GLY14 4.8 22.0 1.0 C B:CYS12 4.9 21.3 1.0

I.Span, K.Wang, W.Eisenreich, A.Bacher, Y.Zhang, E.Oldfield, M.Groll. Insights Into the Binding of Pyridines to the Iron-Sulfur Enzyme Isph. J.Am.Chem.Soc. V. 136 7926 2014.
ISSN: ISSN 0002-7863
PubMed: 24813236
DOI: 10.1021/JA501127J