Iron in PDB 7e1s: Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Octanoyl-Acp

The structure of Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Octanoyl-Acp, PDB code: 7e1s 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)	72.62 / 2.31
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.894, 100.133, 105.479, 90, 90, 90
R / Rfree (%)	23.3 / 28.6

The binding sites of Iron atom in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Octanoyl-Acp (pdb code 7e1s). 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 Octanoyl-Acp, PDB code: 7e1s:
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 Octanoyl-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 Octanoyl-Acp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:41.3 occ:1.00 FE1 A:SF41002 0.0 41.3 1.0 S2 A:SF41002 2.3 39.2 1.0 S4 A:SF41002 2.3 48.8 1.0 S3 A:SF41002 2.3 47.6 1.0 SG A:CYS300 2.3 44.8 1.0 FE2 A:SF41002 2.7 42.8 1.0 FE3 A:SF41002 2.7 41.7 1.0 FE4 A:SF41002 2.8 43.9 1.0 O A:HOH1101 2.9 47.0 1.0 CB A:CYS300 3.3 43.6 1.0 N A:ASN303 3.6 48.0 1.0 CA A:ASN303 3.6 46.9 1.0 CA A:CYS300 3.8 41.8 1.0 S1 A:SF41002 3.9 43.9 1.0 N A:CYS304 4.2 46.8 1.0 C A:ASN303 4.5 45.9 1.0 C A:CYS300 4.5 44.4 1.0 CA A:ARG310 4.6 56.1 1.0 SG A:CYS320 4.6 39.6 1.0 N A:VAL301 4.6 40.0 1.0 N A:GLY311 4.7 45.5 1.0 SG A:CYS308 4.7 42.7 1.0 CB A:ASN303 4.7 45.8 1.0 C A:ARG310 4.7 46.9 1.0 OD1 A:ASN303 4.8 44.9 1.0 C A:SER302 4.8 47.9 1.0 N A:SER302 4.9 51.0 1.0 N A:CYS300 5.0 47.8 1.0 SG A:CYS304 5.0 39.2 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Octanoyl-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 Octanoyl-Acp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:42.8 occ:1.00 FE2 A:SF41002 0.0 42.8 1.0 SG A:CYS308 2.3 42.7 1.0 S1 A:SF41002 2.3 43.9 1.0 S4 A:SF41002 2.3 48.8 1.0 S3 A:SF41002 2.3 47.6 1.0 FE1 A:SF41002 2.7 41.3 1.0 FE3 A:SF41002 2.7 41.7 1.0 FE4 A:SF41002 2.8 43.9 1.0 CB A:CYS308 3.1 42.1 1.0 S2 A:SF41002 3.9 39.2 1.0 CB A:ALA314 3.9 38.5 1.0 N A:GLY311 4.0 45.5 1.0 SG A:CYS300 4.4 44.8 1.0 CA A:GLY311 4.6 44.0 1.0 CA A:CYS308 4.6 41.9 1.0 CB A:PRO274 4.6 35.6 1.0 C A:ARG310 4.7 46.9 1.0 CA A:ARG310 4.7 56.1 1.0 SG A:CYS304 4.8 39.2 1.0 SG A:CYS320 4.9 39.6 1.0 N A:ALA314 5.0 35.6 1.0 N A:ARG310 5.0 50.2 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Octanoyl-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 Octanoyl-Acp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:41.7 occ:1.00 FE3 A:SF41002 0.0 41.7 1.0 S2 A:SF41002 2.3 39.2 1.0 SG A:CYS320 2.3 39.6 1.0 S1 A:SF41002 2.3 43.9 1.0 S4 A:SF41002 2.3 48.8 1.0 FE4 A:SF41002 2.7 43.9 1.0 FE1 A:SF41002 2.7 41.3 1.0 FE2 A:SF41002 2.7 42.8 1.0 CB A:CYS320 3.3 36.3 1.0 CA A:CYS320 3.6 35.7 1.0 S3 A:SF41002 3.9 47.6 1.0 N A:ILE321 4.1 40.1 1.0 C A:CYS320 4.2 41.2 1.0 N A:ALA322 4.4 37.2 1.0 CB A:ALA322 4.5 40.1 1.0 SG A:CYS304 4.5 39.2 1.0 CB A:ALA314 4.6 38.5 1.0 SG A:CYS308 4.8 42.7 1.0 SG A:CYS300 4.9 44.8 1.0 N A:CYS320 5.0 38.3 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Octanoyl-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 Octanoyl-Acp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:43.9 occ:1.00 FE4 A:SF41002 0.0 43.9 1.0 S2 A:SF41002 2.3 39.2 1.0 S1 A:SF41002 2.3 43.9 1.0 S3 A:SF41002 2.3 47.6 1.0 SG A:CYS304 2.3 39.2 1.0 FE3 A:SF41002 2.7 41.7 1.0 FE2 A:SF41002 2.8 42.8 1.0 FE1 A:SF41002 2.8 41.3 1.0 N A:CYS304 3.2 46.8 1.0 CB A:CYS304 3.4 41.5 1.0 CA A:CYS304 3.8 45.1 1.0 N A:VAL305 3.9 38.5 1.0 S4 A:SF41002 3.9 48.8 1.0 C A:ASN303 4.2 45.9 1.0 CB A:ALA322 4.3 40.1 1.0 CG2 A:VAL305 4.3 40.3 1.0 CA A:ASN303 4.3 46.9 1.0 C A:CYS304 4.4 40.4 1.0 N A:ASN303 4.5 48.0 1.0 SG A:CYS320 4.5 39.6 1.0 N A:ALA322 4.7 37.2 1.0 CB A:CYS308 4.7 42.1 1.0 SG A:CYS308 4.7 42.7 1.0 CG2 A:ILE321 4.8 39.9 1.0 SG A:CYS300 4.9 44.8 1.0 O A:VAL305 4.9 43.1 1.0 O A:HOH1101 5.0 47.0 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Octanoyl-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 Octanoyl-Acp within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1002 b:33.0 occ:1.00 FE1 C:SF41002 0.0 33.0 1.0 SG C:CYS300 2.3 41.4 1.0 S2 C:SF41002 2.3 30.7 1.0 S3 C:SF41002 2.3 39.7 1.0 S4 C:SF41002 2.3 38.7 1.0 O C:HOH1101 2.6 41.7 1.0 FE2 C:SF41002 2.7 35.1 1.0 FE3 C:SF41002 2.8 35.9 1.0 FE4 C:SF41002 2.8 37.8 1.0 CB C:CYS300 3.3 37.6 1.0 CA C:ASN303 3.7 35.0 1.0 N C:ASN303 3.8 35.9 1.0 CA C:CYS300 3.8 36.1 1.0 S1 C:SF41002 3.9 37.3 1.0 N C:CYS304 4.2 32.6 1.0 C C:ASN303 4.5 31.6 1.0 CA C:ARG310 4.6 39.5 1.0 N C:GLY311 4.6 40.8 1.0 C C:CYS300 4.6 35.6 1.0 C C:ARG310 4.6 42.7 1.0 SG C:CYS320 4.6 34.1 1.0 OD1 C:ASN303 4.7 27.3 1.0 SG C:CYS308 4.7 32.9 1.0 N C:VAL301 4.7 35.0 1.0 CB C:ASN303 4.8 30.6 1.0 C C:SER302 4.9 33.2 1.0 SG C:CYS304 5.0 38.2 1.0 N C:SER302 5.0 37.2 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Octanoyl-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 Octanoyl-Acp within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1002 b:35.1 occ:1.00 FE2 C:SF41002 0.0 35.1 1.0 SG C:CYS308 2.3 32.9 1.0 S1 C:SF41002 2.3 37.3 1.0 S3 C:SF41002 2.3 39.7 1.0 S4 C:SF41002 2.3 38.7 1.0 FE1 C:SF41002 2.7 33.0 1.0 FE4 C:SF41002 2.8 37.8 1.0 FE3 C:SF41002 2.8 35.9 1.0 CB C:CYS308 3.2 37.1 1.0 S2 C:SF41002 3.9 30.7 1.0 N C:GLY311 4.0 40.8 1.0 CB C:ALA314 4.0 28.8 1.0 CA C:GLY311 4.3 38.7 1.0 CB C:PRO274 4.5 34.8 1.0 SG C:CYS300 4.6 41.4 1.0 CA C:CYS308 4.6 33.7 1.0 C C:ARG310 4.7 42.7 1.0 SG C:CYS304 4.9 38.2 1.0 CA C:ARG310 4.9 39.5 1.0 SG C:CYS320 4.9 34.1 1.0 N C:ALA314 4.9 28.5 1.0 N C:ARG310 4.9 42.9 1.0 CG C:PRO274 4.9 35.9 1.0 CG2 C:VAL305 4.9 29.5 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Octanoyl-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 Octanoyl-Acp within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1002 b:35.9 occ:1.00 FE3 C:SF41002 0.0 35.9 1.0 SG C:CYS320 2.2 34.1 1.0 S4 C:SF41002 2.3 38.7 1.0 S2 C:SF41002 2.3 30.7 1.0 S1 C:SF41002 2.3 37.3 1.0 FE4 C:SF41002 2.7 37.8 1.0 FE1 C:SF41002 2.8 33.0 1.0 FE2 C:SF41002 2.8 35.1 1.0 CB C:CYS320 3.2 30.2 1.0 CA C:CYS320 3.7 30.7 1.0 S3 C:SF41002 3.9 39.7 1.0 O C:HOH1101 4.1 41.7 1.0 C C:CYS320 4.2 33.4 1.0 N C:ILE321 4.2 32.2 1.0 O C:HOH1137 4.3 31.3 1.0 N C:ALA322 4.4 35.5 1.0 CB C:ALA322 4.5 35.3 1.0 CB C:ALA314 4.6 28.8 1.0 SG C:CYS304 4.6 38.2 1.0 SG C:CYS300 4.8 41.4 1.0 SG C:CYS308 4.9 32.9 1.0 N C:CYS320 5.0 36.1 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Dehydrogenase/Isomerase Fabx From Helicobacter Pylori in Complex with Octanoyl-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 Octanoyl-Acp within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1002 b:37.8 occ:1.00 FE4 C:SF41002 0.0 37.8 1.0 S2 C:SF41002 2.3 30.7 1.0 S1 C:SF41002 2.3 37.3 1.0 S3 C:SF41002 2.3 39.7 1.0 SG C:CYS304 2.3 38.2 1.0 FE3 C:SF41002 2.7 35.9 1.0 FE2 C:SF41002 2.8 35.1 1.0 FE1 C:SF41002 2.8 33.0 1.0 N C:CYS304 3.3 32.6 1.0 CB C:CYS304 3.4 36.7 1.0 CA C:CYS304 3.8 36.4 1.0 S4 C:SF41002 3.9 38.7 1.0 N C:VAL305 3.9 34.8 1.0 O C:HOH1101 4.0 41.7 1.0 CB C:ALA322 4.2 35.3 1.0 CG2 C:VAL305 4.3 29.5 1.0 C C:ASN303 4.3 31.6 1.0 C C:CYS304 4.4 33.0 1.0 SG C:CYS320 4.5 34.1 1.0 CA C:ASN303 4.5 35.0 1.0 N C:ALA322 4.7 35.5 1.0 N C:ASN303 4.7 35.9 1.0 CG2 C:ILE321 4.7 28.8 1.0 SG C:CYS308 4.8 32.9 1.0 CB C:CYS308 4.9 37.1 1.0 SG C:CYS300 4.9 41.4 1.0 O C:VAL305 4.9 32.0 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