Iron in PDB 4s3d: Ispg in Complex with Ppi

All present enzymatic activity of Ispg in Complex with Ppi:
1.17.7.1;

The structure of Ispg in Complex with Ppi, PDB code: 4s3d was solved by F.Quitterer, A.Frank, K.Wang, G.Rao, B.O'dowd, J.Li, F.Guerra, S.Abdel-Azeim, A.Bacher, J.Eppinger, E.Oldfield, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.020, 63.260, 86.530, 90.00, 127.30, 90.00
R / Rfree (%)	14.1 / 19.2

The binding sites of Iron atom in the Ispg in Complex with Ppi (pdb code 4s3d). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Ispg in Complex with Ppi, PDB code: 4s3d:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Ispg in Complex with Ppi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ispg in Complex with Ppi within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe901 b:32.8 occ:1.00 FE1 A:F3S901 0.0 32.8 1.0 S1 A:F3S901 2.2 34.9 1.0 S3 A:F3S901 2.2 38.0 1.0 S2 A:F3S901 2.3 35.5 1.0 SG A:CYS300 2.4 32.5 1.0 FE3 A:F3S901 2.7 31.9 1.0 FE4 A:F3S901 2.8 74.6 1.0 CB A:CYS300 3.4 28.9 1.0 N A:CYS300 3.5 30.1 1.0 CA A:CYS300 4.0 28.8 1.0 C A:GLY299 4.2 30.4 1.0 S4 A:F3S901 4.2 41.6 1.0 CA A:GLY299 4.4 31.0 1.0 CB A:ARG302 4.5 34.0 1.0 SG A:CYS343 4.5 33.3 1.0 CD A:ARG302 4.7 31.9 1.0 C A:CYS300 4.7 30.7 1.0 CG A:ARG302 4.7 33.5 1.0 N A:GLY299 4.8 29.2 1.0 O A:GLY299 5.0 31.2 1.0 SG A:CYS297 5.0 38.2 1.0

Iron binding site 2 out of 3 in the Ispg in Complex with Ppi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ispg in Complex with Ppi within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe901 b:31.9 occ:1.00 FE3 A:F3S901 0.0 31.9 1.0 S3 A:F3S901 2.2 38.0 1.0 S1 A:F3S901 2.2 34.9 1.0 S4 A:F3S901 2.2 41.6 1.0 SG A:CYS343 2.3 33.3 1.0 FE4 A:F3S901 2.7 74.6 1.0 FE1 A:F3S901 2.7 32.8 1.0 CB A:CYS343 3.4 40.0 1.0 N A:CYS343 3.6 34.0 1.0 CA A:CYS343 3.9 31.9 1.0 S2 A:F3S901 4.2 35.5 1.0 CB A:VAL345 4.2 29.8 1.0 C A:GLY342 4.2 33.4 1.0 C A:CYS343 4.3 31.8 1.0 O A:CYS343 4.4 33.9 1.0 N A:VAL345 4.6 32.8 1.0 CA A:GLY342 4.6 28.5 1.0 CG2 A:VAL345 4.6 31.5 1.0 CB A:ARG302 4.7 34.0 1.0 CD A:ARG302 4.7 31.9 1.0 SG A:CYS300 4.7 32.5 1.0 N A:ASN346 4.8 27.7 1.0 SG A:CYS297 4.8 38.2 1.0 NE A:ARG302 4.9 30.9 1.0 N A:GLY342 4.9 30.2 1.0 CA A:VAL345 4.9 30.3 1.0 O A:GLY342 5.0 29.2 1.0

Iron binding site 3 out of 3 in the Ispg in Complex with Ppi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ispg in Complex with Ppi within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe901 b:74.6 occ:1.00 FE4 A:F3S901 0.0 74.6 1.0 S4 A:F3S901 2.3 41.6 1.0 S3 A:F3S901 2.3 38.0 1.0 S2 A:F3S901 2.3 35.5 1.0 SG A:CYS297 2.5 38.2 1.0 FE3 A:F3S901 2.7 31.9 1.0 FE1 A:F3S901 2.8 32.8 1.0 CB A:CYS297 3.2 36.4 1.0 S1 A:F3S901 3.5 34.9 1.0 N A:GLY299 4.0 29.2 1.0 CA A:GLY299 4.1 31.0 1.0 N A:GLY342 4.4 30.2 1.0 CA A:GLY342 4.5 28.5 1.0 CA A:CYS297 4.6 30.1 1.0 CD A:PRO298 4.6 28.7 1.0 N A:CYS343 4.7 34.0 1.0 C A:GLY299 4.8 30.4 1.0 N A:CYS300 4.8 30.1 1.0 N A:PRO298 4.8 29.1 1.0 C A:CYS297 4.8 28.9 1.0 SG A:CYS343 4.9 33.3 1.0 C A:GLY342 5.0 33.4 1.0

F.Quitterer, A.Frank, K.Wang, G.Rao, B.O'dowd, J.Li, F.Guerra, S.Abdel-Azeim, A.Bacher, J.Eppinger, E.Oldfield, M.Groll. Atomic Resolution Structures of Discrete Stages on the Reaction Coordinate of the [FE4S4] Enzyme Ispg (Gcpe). J.Mol.Biol. 2015.
ISSN: ESSN 1089-8638
PubMed: 25868383
DOI: 10.1016/J.JMB.2015.04.002