Iron in PDB 5exk: Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate

All present enzymatic activity of Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate:
2.8.1.8;

The structure of Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate, PDB code: 5exk was solved by M.I.Mclaughlin, N.D.Lanz, P.J.Goldman, K.-H.Lee, S.J.Booker, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.03 / 1.86
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.773, 95.971, 114.328, 90.00, 90.46, 90.00
R / Rfree (%)	16 / 20.1

The structure of Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 42;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate (pdb code 5exk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 42 binding sites of Iron where determined in the Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate, PDB code: 5exk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 42 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate


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 M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:12.3 occ:1.00 FE1 A:F3S401 0.0 12.3 1.0 S2 A:F3S401 2.3 11.5 1.0 S3 A:F3S401 2.3 10.6 1.0 S1 A:F3S401 2.3 11.7 1.0 SG A:CYS66 2.4 12.7 1.0 FE4 A:F3S401 2.6 11.1 1.0 FE3 A:F3S401 2.7 11.9 1.0 CB A:CYS66 3.2 8.0 1.0 S6 B:XOK602 4.1 11.5 1.0 CB A:ASN62 4.2 11.5 1.0 O A:HOH515 4.3 18.9 1.0 CD1 A:TYR293 4.7 14.9 1.0 O A:ASN62 4.7 12.3 1.0 CA A:CYS66 4.7 12.9 1.0 SG A:CYS55 4.8 11.7 1.0 SG A:CYS60 4.8 12.2 1.0 CA A:TYR293 4.8 9.8 1.0 ND2 A:ASN62 4.9 10.1 1.0 C A:ASN62 4.9 13.4 1.0 C7 B:XOK602 4.9 9.8 1.0

Iron binding site 2 out of 42 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate


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 M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:11.9 occ:1.00 FE3 A:F3S401 0.0 11.9 1.0 S1 A:F3S401 2.2 11.7 1.0 S3 A:F3S401 2.3 10.6 1.0 S6 B:XOK602 2.4 11.5 1.0 SG A:CYS55 2.4 11.7 1.0 FE1 A:F3S401 2.7 12.3 1.0 FE4 A:F3S401 2.7 11.1 1.0 CB A:CYS55 3.3 10.1 1.0 CA A:CYS55 3.8 9.4 1.0 C6 B:XOK602 3.8 11.7 1.0 S2 A:F3S401 3.8 11.5 1.0 C7 B:XOK602 3.9 9.8 1.0 N A:CYS55 4.2 7.7 1.0 OG1 A:THR73 4.3 9.4 1.0 N A:THR73 4.3 11.0 1.0 CB A:THR73 4.4 9.9 1.0 NE1 A:TRP67 4.7 15.5 1.0 CG1 A:VAL54 4.8 7.6 1.0 CA A:ALA72 4.8 10.2 1.0 SG A:CYS60 4.8 12.2 1.0 CB A:CYS60 4.8 10.2 1.0 SG A:CYS66 4.9 12.7 1.0 CB A:CYS66 4.9 8.0 1.0 C5 B:XOK602 5.0 6.7 1.0 C A:ALA72 5.0 11.4 1.0 CA A:THR73 5.0 11.8 1.0

Iron binding site 3 out of 42 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate


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 M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:11.1 occ:1.00 FE4 A:F3S401 0.0 11.1 1.0 S2 A:F3S401 2.2 11.5 1.0 S6 B:XOK602 2.3 11.5 1.0 S3 A:F3S401 2.3 10.6 1.0 SG A:CYS60 2.4 12.2 1.0 FE1 A:F3S401 2.6 12.3 1.0 FE3 A:F3S401 2.7 11.9 1.0 CB A:CYS60 3.2 10.2 1.0 C6 B:XOK602 3.5 11.7 1.0 C5 B:XOK602 3.7 6.7 1.0 S1 A:F3S401 3.9 11.7 1.0 C7 B:XOK602 4.0 9.8 1.0 CB A:ASN62 4.1 11.5 1.0 ND2 A:ASN62 4.2 10.1 1.0 C4 B:XOK602 4.3 6.3 1.0 CG A:ARG290 4.5 9.3 1.0 CB A:ARG290 4.6 11.1 1.0 CA A:CYS60 4.6 9.6 1.0 CG A:ASN62 4.6 18.2 1.0 SG A:CYS66 4.7 12.7 1.0 C3 B:XOK602 4.8 10.8 1.0 N A:ASN62 4.8 12.2 1.0 CA A:ASN62 4.8 12.3 1.0 SG A:CYS55 4.8 11.7 1.0 CA A:CYS55 4.9 9.4 1.0 CB A:CYS55 4.9 10.1 1.0 C A:ASN62 4.9 13.4 1.0 N A:ILE63 5.0 12.2 1.0

Iron binding site 4 out of 42 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate


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 M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:10.2 occ:1.00 FE1 A:SF4402 0.0 10.2 1.0 S2 A:SF4402 2.3 10.0 1.0 S3 A:SF4402 2.3 10.8 1.0 S4 A:SF4402 2.3 10.5 1.0 SG A:CYS88 2.4 9.8 1.0 FE4 A:SF4402 2.7 11.1 1.0 FE2 A:SF4402 2.7 10.8 1.0 FE3 A:SF4402 2.8 9.1 1.0 CB A:CYS88 3.2 7.3 1.0 O A:HOH835 3.8 15.8 1.0 S1 A:SF4402 3.9 11.4 1.0 SD A:MET404 4.3 9.7 1.0 CB A:ILE90 4.4 11.6 1.0 CD1 A:ILE90 4.5 15.3 1.0 CA A:CYS88 4.7 12.1 1.0 SG A:CYS85 4.7 12.4 1.0 CE A:MET404 4.8 7.1 1.0 CG1 A:ILE90 4.8 11.7 1.0 CB A:CYS85 4.8 11.4 1.0 O A:MET404 4.9 11.3 1.0 SG A:CYS81 4.9 11.8 1.0 N A:MET404 4.9 8.8 1.0 O A:HOH552 5.0 14.3 1.0

Iron binding site 5 out of 42 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate


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 M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:10.8 occ:1.00 FE2 A:SF4402 0.0 10.8 1.0 S1 A:SF4402 2.3 11.4 1.0 S4 A:SF4402 2.3 10.5 1.0 S3 A:SF4402 2.3 10.8 1.0 SG A:CYS85 2.4 12.4 1.0 FE4 A:SF4402 2.7 11.1 1.0 FE1 A:SF4402 2.7 10.2 1.0 FE3 A:SF4402 2.8 9.1 1.0 CB A:CYS85 3.3 11.4 1.0 NH2 A:ARG192 3.8 8.8 1.0 S2 A:SF4402 3.9 10.0 1.0 O A:MET404 3.9 11.3 1.0 N A:CYS85 4.0 8.7 1.0 CA A:CYS85 4.3 10.8 1.0 CE2 A:PHE195 4.5 7.4 1.0 CB A:CYS88 4.5 7.3 1.0 CB A:ARG83 4.6 10.2 1.0 SG A:CYS88 4.7 9.8 1.0 C A:ARG84 4.7 11.7 1.0 N A:MET404 4.9 8.8 1.0 SG A:CYS81 4.9 11.8 1.0 N A:ARG84 4.9 8.3 1.0 C A:ARG83 4.9 12.8 1.0 C A:MET404 4.9 10.7 1.0 O A:HOH741 4.9 12.1 1.0 CZ A:PHE195 4.9 7.2 1.0 CZ A:ARG192 5.0 8.8 1.0

Iron binding site 6 out of 42 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate


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 M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:9.1 occ:1.00 FE3 A:SF4402 0.0 9.1 1.0 O A:MET404 2.3 11.3 1.0 S4 A:SF4402 2.3 10.5 1.0 S1 A:SF4402 2.4 11.4 1.0 S2 A:SF4402 2.4 10.0 1.0 N A:MET404 2.4 8.8 1.0 SD A:MET404 2.7 9.7 1.0 FE2 A:SF4402 2.8 10.8 1.0 FE1 A:SF4402 2.8 10.2 1.0 FE4 A:SF4402 2.8 11.1 1.0 C A:MET404 3.1 10.7 1.0 CA A:MET404 3.2 8.5 1.0 CE A:MET404 3.7 7.1 1.0 CG A:MET404 3.7 10.6 1.0 CB A:MET404 3.9 6.0 1.0 S3 A:SF4402 4.0 10.8 1.0 OXT A:MET404 4.2 10.2 1.0 NH2 A:ARG192 4.3 8.8 1.0 O A:HOH578 4.6 13.4 1.0 O A:HOH835 4.6 15.8 1.0 SG A:CYS81 4.8 11.8 1.0 O A:GLY122 4.9 10.2 1.0 SG A:CYS85 4.9 12.4 1.0 SG A:CYS88 5.0 9.8 1.0

Iron binding site 7 out of 42 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate


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 M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:11.1 occ:1.00 FE4 A:SF4402 0.0 11.1 1.0 S3 A:SF4402 2.3 10.8 1.0 S1 A:SF4402 2.3 11.4 1.0 S2 A:SF4402 2.3 10.0 1.0 SG A:CYS81 2.4 11.8 1.0 FE1 A:SF4402 2.7 10.2 1.0 FE2 A:SF4402 2.7 10.8 1.0 FE3 A:SF4402 2.8 9.1 1.0 CB A:CYS81 3.3 13.0 1.0 S4 A:SF4402 3.9 10.5 1.0 O A:ARG83 4.0 11.5 1.0 N A:MET404 4.0 8.8 1.0 CB A:ARG83 4.3 10.2 1.0 C A:ARG83 4.3 12.8 1.0 N A:ALA124 4.5 9.6 1.0 CA A:ARG83 4.7 10.3 1.0 O A:HOH552 4.7 14.3 1.0 N A:ARG83 4.7 9.4 1.0 CA A:CYS81 4.7 11.7 1.0 O A:MET404 4.8 11.3 1.0 CB A:ALA124 4.9 8.2 1.0 SG A:CYS85 4.9 12.4 1.0 SG A:CYS88 4.9 9.8 1.0

Iron binding site 8 out of 42 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate


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 M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:11.0 occ:1.00 FE1 C:F3S401 0.0 11.0 1.0 S2 C:F3S401 2.2 10.5 1.0 S1 C:F3S401 2.3 10.6 1.0 S3 C:F3S401 2.3 11.0 1.0 SG C:CYS66 2.4 12.5 1.0 FE3 C:F3S401 2.6 9.6 1.0 FE4 C:F3S401 2.7 10.9 1.0 CB C:CYS66 3.3 10.1 1.0 S6 D:XOK602 4.1 10.3 1.0 CB C:ASN62 4.2 8.9 1.0 O C:HOH518 4.3 12.0 1.0 O C:ASN62 4.7 11.8 1.0 CA C:CYS66 4.7 7.8 1.0 CD1 C:TYR293 4.8 8.2 1.0 SG C:CYS60 4.8 10.5 1.0 SG C:CYS55 4.8 9.7 1.0 CA C:TYR293 4.8 8.2 1.0 C C:ASN62 4.9 10.4 1.0 ND2 C:ASN62 4.9 11.7 1.0 C7 D:XOK602 4.9 9.6 1.0

Iron binding site 9 out of 42 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:9.6 occ:1.00 FE3 C:F3S401 0.0 9.6 1.0 S1 C:F3S401 2.2 10.6 1.0 S3 C:F3S401 2.3 11.0 1.0 S6 D:XOK602 2.3 10.3 1.0 SG C:CYS55 2.4 9.7 1.0 FE1 C:F3S401 2.6 11.0 1.0 FE4 C:F3S401 2.7 10.9 1.0 CB C:CYS55 3.3 10.8 1.0 C6 D:XOK602 3.8 7.7 1.0 CA C:CYS55 3.8 10.1 1.0 S2 C:F3S401 3.8 10.5 1.0 C7 D:XOK602 4.0 9.6 1.0 OG1 C:THR73 4.2 10.3 1.0 N C:CYS55 4.2 9.7 1.0 N C:THR73 4.3 9.2 1.0 CB C:THR73 4.4 9.4 1.0 CG1 C:VAL54 4.7 7.9 1.0 NE1 C:TRP67 4.8 9.7 1.0 CB C:CYS60 4.8 9.2 1.0 CA C:ALA72 4.8 10.9 1.0 SG C:CYS60 4.8 10.5 1.0 SG C:CYS66 4.8 12.5 1.0 C5 D:XOK602 4.9 7.5 1.0 CB C:CYS66 4.9 10.1 1.0 C C:ALA72 5.0 9.6 1.0

Iron binding site 10 out of 42 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of M. Tuberculosis Lipoyl Synthase with 6- Thiooctanoyl Peptide Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:10.9 occ:1.00 FE4 C:F3S401 0.0 10.9 1.0 S2 C:F3S401 2.2 10.5 1.0 S3 C:F3S401 2.3 11.0 1.0 S6 D:XOK602 2.3 10.3 1.0 SG C:CYS60 2.4 10.5 1.0 FE1 C:F3S401 2.7 11.0 1.0 FE3 C:F3S401 2.7 9.6 1.0 CB C:CYS60 3.1 9.2 1.0 C6 D:XOK602 3.4 7.7 1.0 C5 D:XOK602 3.6 7.5 1.0 S1 C:F3S401 4.0 10.6 1.0 C7 D:XOK602 4.0 9.6 1.0 CB C:ASN62 4.0 8.9 1.0 C4 D:XOK602 4.3 7.1 1.0 ND2 C:ASN62 4.3 11.7 1.0 CG C:ARG290 4.5 7.1 1.0 CA C:CYS60 4.6 9.7 1.0 CB C:ARG290 4.6 6.0 1.0 CG C:ASN62 4.7 12.9 1.0 SG C:CYS66 4.7 12.5 1.0 C3 D:XOK602 4.8 6.1 1.0 N C:ASN62 4.8 7.0 1.0 CA C:ASN62 4.8 9.2 1.0 SG C:CYS55 4.9 9.7 1.0 C C:ASN62 4.9 10.4 1.0 CA C:CYS55 4.9 10.1 1.0 CB C:CYS55 4.9 10.8 1.0

M.I.Mclaughlin, N.D.Lanz, P.J.Goldman, K.H.Lee, S.J.Booker, C.L.Drennan. Crystallographic Snapshots of Sulfur Insertion By Lipoyl Synthase. Proc.Natl.Acad.Sci.Usa V. 113 9446 2016.
ISSN: ESSN 1091-6490
PubMed: 27506792
DOI: 10.1073/PNAS.1602486113