Iron in PDB 4s3c: Ispg in Complex with Epoxide Intermediate

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

The structure of Ispg in Complex with Epoxide Intermediate, PDB code: 4s3c 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)	10.00 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	110.930, 62.840, 86.200, 90.00, 127.02, 90.00
R / Rfree (%)	12.3 / 16.1

The binding sites of Iron atom in the Ispg in Complex with Epoxide Intermediate (pdb code 4s3c). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Ispg in Complex with Epoxide Intermediate, PDB code: 4s3c:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Ispg in Complex with Epoxide Intermediate


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 Epoxide Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe902 b:22.9 occ:1.00 FE1 A:SF4902 0.0 22.9 1.0 S3 A:SF4902 2.2 22.3 1.0 S4 A:SF4902 2.3 22.9 1.0 S2 A:SF4902 2.3 22.5 1.0 SG A:CYS300 2.3 22.2 1.0 FE2 A:SF4902 2.6 28.4 1.0 FE3 A:SF4902 2.6 22.9 1.0 FE4 A:SF4902 2.7 24.0 1.0 CB A:CYS300 3.4 20.5 1.0 N A:CYS300 3.6 22.7 1.0 S1 A:SF4902 3.9 23.4 1.0 CA A:CYS300 4.0 20.8 1.0 C A:GLY299 4.1 19.4 1.0 C2 A:43Q901 4.1 23.6 1.0 O1 A:43Q901 4.3 29.8 1.0 C1 A:43Q901 4.4 25.4 1.0 CB A:ARG302 4.4 22.5 1.0 SG A:CYS343 4.4 21.8 1.0 CA A:GLY299 4.5 19.7 1.0 CD A:ARG302 4.6 26.1 1.0 C A:CYS300 4.7 22.4 1.0 CG A:ARG302 4.8 24.5 1.0 O A:GLY299 4.8 23.0 1.0 C3 A:43Q901 4.8 33.3 1.0 O A:HOH1041 4.9 20.4 1.0 SG A:CYS297 4.9 20.2 1.0 N A:GLY299 4.9 17.7 1.0 N A:ARG302 5.0 20.9 1.0

Iron binding site 2 out of 4 in the Ispg in Complex with Epoxide Intermediate


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 Epoxide Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe902 b:28.4 occ:1.00 FE2 A:SF4902 0.0 28.4 1.0 O1 A:43Q901 1.9 29.8 1.0 S4 A:SF4902 2.1 22.9 1.0 S1 A:SF4902 2.3 23.4 1.0 S3 A:SF4902 2.3 22.3 1.0 FE4 A:SF4902 2.5 24.0 1.0 FE1 A:SF4902 2.6 22.9 1.0 FE3 A:SF4902 2.6 22.9 1.0 C3 A:43Q901 2.9 33.3 1.0 C1 A:43Q901 3.1 25.4 1.0 S2 A:SF4902 3.7 22.5 1.0 C2 A:43Q901 3.7 23.6 1.0 C4 A:43Q901 3.8 25.3 1.0 C A:43Q901 3.8 33.5 1.0 CB A:CYS297 4.3 19.6 1.0 OD1 A:ASN346 4.3 24.2 1.0 SG A:CYS297 4.4 20.2 1.0 O A:43Q901 4.6 35.6 1.0 SG A:CYS300 4.7 22.2 1.0 SG A:CYS343 4.7 21.8 1.0 CB A:ASN346 4.9 18.2 1.0 CB A:VAL345 4.9 18.3 1.0 O2 A:43Q901 4.9 17.5 1.0

Iron binding site 3 out of 4 in the Ispg in Complex with Epoxide Intermediate


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 Epoxide Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe902 b:22.9 occ:1.00 FE3 A:SF4902 0.0 22.9 1.0 S1 A:SF4902 2.2 23.4 1.0 S4 A:SF4902 2.2 22.9 1.0 SG A:CYS343 2.3 21.8 1.0 S2 A:SF4902 2.3 22.5 1.0 FE2 A:SF4902 2.6 28.4 1.0 FE1 A:SF4902 2.6 22.9 1.0 FE4 A:SF4902 2.6 24.0 1.0 CB A:CYS343 3.3 22.1 1.0 N A:CYS343 3.6 21.3 1.0 CA A:CYS343 3.9 22.3 1.0 S3 A:SF4902 3.9 22.3 1.0 C A:CYS343 4.2 21.1 1.0 O A:CYS343 4.3 20.5 1.0 CB A:VAL345 4.3 18.3 1.0 C A:GLY342 4.3 20.1 1.0 O1 A:43Q901 4.4 29.8 1.0 CD A:ARG302 4.5 26.1 1.0 SG A:CYS300 4.6 22.2 1.0 CB A:ARG302 4.6 22.5 1.0 CG2 A:VAL345 4.6 23.5 1.0 N A:VAL345 4.6 21.0 1.0 CA A:GLY342 4.8 20.5 1.0 NE A:ARG302 4.8 27.2 1.0 SG A:CYS297 4.8 20.2 1.0 O A:GLY342 4.9 20.5 1.0 N A:ASN346 4.9 18.2 1.0 N A:VAL344 5.0 20.5 1.0

Iron binding site 4 out of 4 in the Ispg in Complex with Epoxide Intermediate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ispg in Complex with Epoxide Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe902 b:24.0 occ:1.00 FE4 A:SF4902 0.0 24.0 1.0 S2 A:SF4902 2.2 22.5 1.0 S1 A:SF4902 2.3 23.4 1.0 S3 A:SF4902 2.3 22.3 1.0 SG A:CYS297 2.3 20.2 1.0 FE2 A:SF4902 2.5 28.4 1.0 FE3 A:SF4902 2.6 22.9 1.0 FE1 A:SF4902 2.7 22.9 1.0 CB A:CYS297 3.2 19.6 1.0 S4 A:SF4902 3.7 22.9 1.0 N A:GLY342 4.0 19.4 1.0 O1 A:43Q901 4.0 29.8 1.0 CA A:GLY299 4.0 19.7 1.0 CA A:GLY342 4.0 20.5 1.0 N A:GLY299 4.1 17.7 1.0 N A:CYS343 4.3 21.3 1.0 C A:GLY342 4.5 20.1 1.0 CA A:CYS297 4.6 16.4 1.0 C A:GLY299 4.6 19.4 1.0 N A:CYS300 4.7 22.7 1.0 SG A:CYS343 4.8 21.8 1.0 C A:CYS297 4.9 16.4 1.0 N A:PRO298 4.9 14.9 1.0 SG A:CYS300 5.0 22.2 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