Iron in PDB 7e1r: Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp

The structure of Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp, PDB code: 7e1r was solved by J.S.Zhou, L.Zhang, L.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.74 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.793, 104.443, 99.576, 90, 99.52, 90
R / Rfree (%)	20.6 / 24.3

The binding sites of Iron atom in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp (pdb code 7e1r). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp, PDB code: 7e1r:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:23.4 occ:1.00 FE1 A:SF41002 0.0 23.4 1.0 S4 A:SF41002 2.3 27.7 1.0 S2 A:SF41002 2.3 26.1 1.0 S3 A:SF41002 2.3 31.3 1.0 SG A:CYS300 2.6 41.4 1.0 FE4 A:SF41002 2.7 24.2 1.0 FE2 A:SF41002 2.7 21.9 1.0 FE3 A:SF41002 2.7 20.0 1.0 CB A:CYS300 3.4 34.7 1.0 N A:ASN303 3.7 29.4 1.0 CA A:ASN303 3.7 34.5 1.0 CA A:CYS300 3.9 32.4 1.0 S1 A:SF41002 3.9 24.5 1.0 N A:CYS304 4.2 29.0 1.0 N A:GLY311 4.3 42.2 1.0 C A:ASN303 4.4 27.6 1.0 C A:ARG310 4.5 40.0 1.0 C A:CYS300 4.6 29.8 1.0 CA A:ARG310 4.6 36.0 1.0 CA A:GLY311 4.7 40.3 1.0 OD1 A:ASN303 4.7 37.0 1.0 N A:VAL301 4.8 34.0 1.0 CB A:ASN303 4.8 34.5 1.0 C A:SER302 4.9 34.2 1.0 O A:ARG310 4.9 39.9 1.0 SG A:CYS308 4.9 35.0 1.0 N A:SER302 5.0 34.5 1.0 SG A:CYS320 5.0 35.0 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:21.9 occ:1.00 FE2 A:SF41002 0.0 21.9 1.0 S1 A:SF41002 2.3 24.5 1.0 S4 A:SF41002 2.3 27.7 1.0 S3 A:SF41002 2.3 31.3 1.0 SG A:CYS308 2.6 35.0 1.0 FE3 A:SF41002 2.7 20.0 1.0 FE4 A:SF41002 2.7 24.2 1.0 FE1 A:SF41002 2.7 23.4 1.0 CB A:CYS308 3.3 29.1 1.0 S2 A:SF41002 3.9 26.1 1.0 CB A:ALA314 3.9 36.8 1.0 N A:GLY311 3.9 42.2 1.0 CA A:GLY311 4.1 40.3 1.0 CB A:PRO274 4.4 29.3 1.0 CA A:CYS308 4.8 35.2 1.0 C A:ARG310 4.8 40.0 1.0 N A:ALA314 4.9 42.4 1.0 CG A:PRO274 4.9 31.9 1.0 SG A:CYS300 4.9 41.4 1.0 CA A:ALA314 5.0 43.2 1.0 SG A:CYS304 5.0 21.6 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:20.0 occ:1.00 FE3 A:SF41002 0.0 20.0 1.0 S1 A:SF41002 2.3 24.5 1.0 S4 A:SF41002 2.3 27.7 1.0 S2 A:SF41002 2.3 26.1 1.0 SG A:CYS320 2.5 35.0 1.0 FE4 A:SF41002 2.7 24.2 1.0 FE2 A:SF41002 2.7 21.9 1.0 FE1 A:SF41002 2.7 23.4 1.0 CB A:CYS320 3.3 26.1 1.0 CA A:CYS320 3.8 29.8 1.0 S3 A:SF41002 3.9 31.3 1.0 N A:ILE321 4.2 26.0 1.0 C A:CYS320 4.3 34.2 1.0 N A:ALA322 4.5 24.1 1.0 CB A:ALA322 4.5 27.9 1.0 CB A:ALA314 4.5 36.8 1.0 SG A:CYS304 4.9 21.6 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:24.2 occ:1.00 FE4 A:SF41002 0.0 24.2 1.0 S2 A:SF41002 2.3 26.1 1.0 S3 A:SF41002 2.3 31.3 1.0 S1 A:SF41002 2.3 24.5 1.0 SG A:CYS304 2.6 21.6 1.0 FE3 A:SF41002 2.7 20.0 1.0 FE2 A:SF41002 2.7 21.9 1.0 FE1 A:SF41002 2.7 23.4 1.0 N A:CYS304 3.2 29.0 1.0 CB A:CYS304 3.5 21.5 1.0 S4 A:SF41002 3.8 27.7 1.0 CA A:CYS304 3.8 21.2 1.0 N A:VAL305 4.0 23.4 1.0 C A:ASN303 4.2 27.6 1.0 CB A:ALA322 4.3 27.9 1.0 CA A:ASN303 4.4 34.5 1.0 N A:ASN303 4.4 29.4 1.0 C A:CYS304 4.4 21.8 1.0 CG2 A:VAL305 4.6 27.6 1.0 SG A:CYS320 4.7 35.0 1.0 N A:ALA322 4.7 24.1 1.0 CG2 A:ILE321 4.7 20.7 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1002 b:25.5 occ:1.00 FE1 C:SF41002 0.0 25.5 1.0 S2 C:SF41002 2.3 27.6 1.0 S4 C:SF41002 2.3 32.5 1.0 S3 C:SF41002 2.3 39.8 1.0 SG C:CYS300 2.7 41.0 1.0 FE3 C:SF41002 2.7 22.6 1.0 FE4 C:SF41002 2.7 31.7 1.0 FE2 C:SF41002 2.7 21.6 1.0 N C:ASN303 3.4 40.6 1.0 CA C:ASN303 3.5 37.6 1.0 CB C:CYS300 3.5 38.5 1.0 CA C:CYS300 3.9 34.6 1.0 S1 C:SF41002 3.9 27.2 1.0 N C:CYS304 3.9 37.8 1.0 C C:ASN303 4.2 35.5 1.0 C C:ARG310 4.5 46.0 1.0 C C:CYS300 4.6 36.2 1.0 CA C:ARG310 4.6 41.2 1.0 C C:SER302 4.6 41.7 1.0 N C:GLY311 4.7 47.0 1.0 CB C:ASN303 4.7 38.3 1.0 OD1 C:ASN303 4.7 31.5 1.0 O C:ARG310 4.7 49.2 1.0 N C:VAL301 4.7 42.1 1.0 N C:SER302 4.8 38.7 1.0 SG C:CYS320 4.9 30.6 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1002 b:21.6 occ:1.00 FE2 C:SF41002 0.0 21.6 1.0 S4 C:SF41002 2.3 32.5 1.0 S1 C:SF41002 2.3 27.2 1.0 S3 C:SF41002 2.3 39.8 1.0 SG C:CYS308 2.7 48.0 1.0 FE3 C:SF41002 2.7 22.6 1.0 FE4 C:SF41002 2.7 31.7 1.0 FE1 C:SF41002 2.7 25.5 1.0 CB C:CYS308 3.3 38.3 1.0 N C:GLY311 3.9 47.0 1.0 S2 C:SF41002 3.9 27.6 1.0 CB C:ALA314 4.1 37.6 1.0 CA C:GLY311 4.2 41.8 1.0 C C:ARG310 4.5 46.0 1.0 CA C:ARG310 4.7 41.2 1.0 CA C:CYS308 4.7 37.7 1.0 CB C:PRO274 4.8 35.8 1.0 CG2 C:VAL305 4.8 33.5 1.0 N C:ARG310 4.9 44.3 1.0 SG C:CYS300 4.9 41.0 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1002 b:22.6 occ:1.00 FE3 C:SF41002 0.0 22.6 1.0 S1 C:SF41002 2.3 27.2 1.0 S2 C:SF41002 2.3 27.6 1.0 S4 C:SF41002 2.3 32.5 1.0 SG C:CYS320 2.6 30.6 1.0 FE4 C:SF41002 2.7 31.7 1.0 FE2 C:SF41002 2.7 21.6 1.0 FE1 C:SF41002 2.7 25.5 1.0 CB C:CYS320 3.4 27.5 1.0 S3 C:SF41002 3.9 39.8 1.0 CA C:CYS320 3.9 29.7 1.0 N C:ILE321 4.2 28.3 1.0 C C:CYS320 4.3 32.2 1.0 N C:ALA322 4.4 26.3 1.0 CB C:ALA322 4.4 23.5 1.0 SG C:CYS304 4.7 31.9 1.0 CB C:ALA314 4.7 37.6 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Holo-Acp within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1002 b:31.7 occ:1.00 FE4 C:SF41002 0.0 31.7 1.0 S1 C:SF41002 2.3 27.2 1.0 S3 C:SF41002 2.3 39.8 1.0 S2 C:SF41002 2.3 27.6 1.0 SG C:CYS304 2.6 31.9 1.0 FE3 C:SF41002 2.7 22.6 1.0 FE2 C:SF41002 2.7 21.6 1.0 FE1 C:SF41002 2.7 25.5 1.0 N C:CYS304 3.1 37.8 1.0 CB C:CYS304 3.5 30.0 1.0 CA C:CYS304 3.7 32.2 1.0 N C:VAL305 3.8 24.9 1.0 S4 C:SF41002 3.9 32.5 1.0 CG2 C:VAL305 4.0 33.5 1.0 C C:ASN303 4.1 35.5 1.0 C C:CYS304 4.2 27.3 1.0 CB C:ALA322 4.3 23.5 1.0 CA C:ASN303 4.3 37.6 1.0 N C:ASN303 4.5 40.6 1.0 N C:ALA322 4.7 26.3 1.0 CG2 C:ILE321 4.9 22.5 1.0 SG C:CYS320 4.9 30.6 1.0 O C:VAL305 4.9 39.4 1.0 CA C:VAL305 4.9 24.6 1.0 CB C:VAL305 5.0 28.2 1.0

L.Yu, Y.Duan, S.Shen, J.Hu, P.Zhang, W.Song, X.Ruan, J.Jiang, Y.Zhang, L.Zhou, J.Jia, X.Hang, C.Tian, H.Lin, H.Z.Chen, J.E.Cronan, H.Bi, L.Zhang. Helicobacter Pylori Fabx Contains A [4FE-4S] Cluster Essential For Unsaturated Fatty Acid Synthesis Nat Commun 2021.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-021-27148-0