Iron in PDB 5why: Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides

The structure of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides, PDB code: 5why was solved by T.L.Grove, P.Himes, A.Bowers, J.B.Bonanno, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.68 / 2.69
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.929, 59.357, 81.363, 83.09, 73.31, 66.63
R / Rfree (%)	22.5 / 28.1

The structure of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides (pdb code 5why). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides, PDB code: 5why:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:69.9 occ:1.00 FE1 A:SF4501 0.0 69.9 1.0 S2 A:SF4501 2.2 69.7 1.0 S3 A:SF4501 2.2 70.5 1.0 S4 A:SF4501 2.2 70.7 1.0 SG A:CYS344 2.6 75.0 1.0 FE4 A:SF4501 3.0 70.4 1.0 FE2 A:SF4501 3.0 70.7 1.0 FE3 A:SF4501 3.1 70.6 1.0 CB A:CYS344 3.7 75.0 1.0 S1 A:SF4501 3.7 70.4 1.0 CB A:SER346 3.8 69.3 1.0 OG A:SER346 4.0 71.1 1.0 N A:SER346 4.8 70.0 1.0 CA A:SER346 4.9 69.7 1.0 N A:ALA414 4.9 74.4 1.0 CA A:CYS344 5.0 74.7 1.0

Iron binding site 2 out of 24 in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:70.7 occ:1.00 FE2 A:SF4501 0.0 70.7 1.0 S1 A:SF4501 2.2 70.4 1.0 S4 A:SF4501 2.2 70.7 1.0 S3 A:SF4501 2.2 70.5 1.0 SG A:CYS413 2.6 72.0 1.0 FE1 A:SF4501 3.0 69.9 1.0 FE4 A:SF4501 3.0 70.4 1.0 FE3 A:SF4501 3.1 70.6 1.0 CB A:CYS413 3.2 71.6 1.0 CA A:CYS413 3.6 73.9 1.0 S2 A:SF4501 3.8 69.7 1.0 N A:ALA414 4.0 74.4 1.0 N A:ALA415 4.0 77.3 1.0 C A:CYS413 4.1 76.1 1.0 CB A:ALA415 4.1 75.5 1.0 CG1 A:VAL284 4.5 72.7 1.0 CA A:ALA415 4.7 76.3 1.0 N A:CYS413 4.9 73.8 1.0 O A:CYS413 5.0 75.2 1.0

Iron binding site 3 out of 24 in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:70.6 occ:1.00 FE3 A:SF4501 0.0 70.6 1.0 S4 A:SF4501 2.2 70.7 1.0 S1 A:SF4501 2.2 70.4 1.0 S2 A:SF4501 2.2 69.7 1.0 FE1 A:SF4501 3.1 69.9 1.0 FE2 A:SF4501 3.1 70.7 1.0 FE4 A:SF4501 3.1 70.4 1.0 S3 A:SF4501 3.9 70.5 1.0 CE1 A:HIS363 4.3 66.8 1.0 NE2 A:HIS363 5.0 67.0 1.0

Iron binding site 4 out of 24 in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:70.4 occ:1.00 FE4 A:SF4501 0.0 70.4 1.0 S2 A:SF4501 2.2 69.7 1.0 S3 A:SF4501 2.2 70.5 1.0 S1 A:SF4501 2.2 70.4 1.0 SG A:CYS362 2.6 69.1 1.0 FE1 A:SF4501 3.0 69.9 1.0 FE2 A:SF4501 3.0 70.7 1.0 FE3 A:SF4501 3.1 70.6 1.0 CB A:CYS362 3.3 67.8 1.0 S4 A:SF4501 3.8 70.7 1.0 CB A:SER346 4.3 69.3 1.0 CB A:GLN364 4.4 69.7 1.0 OG A:SER346 4.4 71.1 1.0 CE1 A:HIS363 4.5 66.8 1.0 CB A:ALA415 4.5 75.5 1.0 CA A:CYS362 4.7 67.3 1.0 ND1 A:HIS363 4.8 65.8 1.0 N A:GLN364 4.9 67.2 1.0 NE2 A:HIS363 5.0 67.0 1.0

Iron binding site 5 out of 24 in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:60.4 occ:1.00 FE1 A:SF4502 0.0 60.4 1.0 S4 A:SF4502 2.2 61.3 1.0 S3 A:SF4502 2.2 59.2 1.0 S2 A:SF4502 2.2 59.3 1.0 SG A:CYS104 2.6 65.9 1.0 FE2 A:SF4502 2.9 60.0 1.0 FE3 A:SF4502 3.0 60.0 1.0 FE4 A:SF4502 3.1 58.2 1.0 CB A:CYS104 3.4 65.5 1.0 S1 A:SF4502 3.7 59.2 1.0 O A:LEU106 3.9 64.6 1.0 CB A:LEU106 4.0 65.1 1.0 C A:LEU106 4.2 64.8 1.0 CA A:LEU106 4.4 65.1 1.0 N A:LEU106 4.5 65.3 1.0 N A:SAM504 4.5 60.4 1.0 CA A:CYS104 4.8 66.0 1.0 C A:GLY154 4.9 62.9 1.0 ND2 A:ASN188 4.9 61.5 1.0 O A:GLY154 4.9 62.4 1.0

Iron binding site 6 out of 24 in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:60.0 occ:1.00 FE2 A:SF4502 0.0 60.0 1.0 S3 A:SF4502 2.2 59.2 1.0 S4 A:SF4502 2.2 61.3 1.0 S1 A:SF4502 2.2 59.2 1.0 SG A:CYS108 2.6 68.0 1.0 FE1 A:SF4502 2.9 60.4 1.0 FE4 A:SF4502 3.0 58.2 1.0 FE3 A:SF4502 3.1 60.0 1.0 CB A:CYS108 3.3 66.7 1.0 S2 A:SF4502 3.7 59.3 1.0 NH1 A:ARG222 3.8 66.4 1.0 CB A:LEU106 4.0 65.1 1.0 N A:CYS108 4.2 67.7 1.0 CA A:CYS108 4.3 67.1 1.0 CZ A:ARG222 4.4 67.9 1.0 O A:SAM504 4.5 61.2 1.0 CD1 A:LEU106 4.5 65.2 1.0 CB A:CYS111 4.7 73.1 1.0 NH2 A:ARG222 4.7 68.1 1.0 CG A:LEU106 4.9 65.2 1.0 C A:LEU106 5.0 64.8 1.0

Iron binding site 7 out of 24 in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:60.0 occ:1.00 FE3 A:SF4502 0.0 60.0 1.0 S2 A:SF4502 2.2 59.3 1.0 S4 A:SF4502 2.2 61.3 1.0 S1 A:SF4502 2.2 59.2 1.0 SG A:CYS111 2.5 73.0 1.0 FE1 A:SF4502 3.0 60.4 1.0 FE4 A:SF4502 3.1 58.2 1.0 FE2 A:SF4502 3.1 60.0 1.0 CB A:CYS111 3.2 73.1 1.0 S3 A:SF4502 3.8 59.2 1.0 CE A:SAM504 4.2 64.3 1.0 CB A:ALA113 4.3 81.6 1.0 SD A:SAM504 4.4 62.4 1.0 CA A:CYS111 4.6 71.7 1.0 C8 A:SAM504 4.8 66.5 1.0 CB A:CYS108 4.8 66.7 1.0 N A:ALA113 5.0 79.7 1.0

Iron binding site 8 out of 24 in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:58.2 occ:1.00 FE4 A:SF4502 0.0 58.2 1.0 S1 A:SF4502 2.2 59.2 1.0 S3 A:SF4502 2.2 59.2 1.0 S2 A:SF4502 2.2 59.3 1.0 O A:SAM504 2.5 61.2 1.0 N A:SAM504 2.5 60.4 1.0 FE2 A:SF4502 3.0 60.0 1.0 SD A:SAM504 3.0 62.4 1.0 FE3 A:SF4502 3.1 60.0 1.0 FE1 A:SF4502 3.1 60.4 1.0 C A:SAM504 3.2 60.4 1.0 CA A:SAM504 3.2 60.6 1.0 CG A:SAM504 3.4 61.0 1.0 CB A:SAM504 3.8 60.1 1.0 S4 A:SF4502 3.9 61.3 1.0 O A:GLY154 4.2 62.4 1.0 CE A:SAM504 4.2 64.3 1.0 OXT A:SAM504 4.4 61.2 1.0 NH1 A:ARG222 4.4 66.4 1.0 C5' A:SAM504 4.5 62.2 1.0 C3' A:SAM504 4.6 63.9 1.0 SG A:CYS104 4.8 65.9 1.0 OE1 A:GLU155 4.9 60.1 1.0 CB A:ASN188 4.9 61.9 1.0 C A:GLY154 4.9 62.9 1.0

Iron binding site 9 out of 24 in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:83.5 occ:1.00 FE1 A:SF4503 0.0 83.5 1.0 S3 A:SF4503 2.2 86.0 1.0 S2 A:SF4503 2.2 82.2 1.0 S4 A:SF4503 2.2 82.8 1.0 SG A:CYS400 2.7 90.5 1.0 CB A:CYS400 2.9 91.8 1.0 FE3 A:SF4503 3.0 84.5 1.0 FE4 A:SF4503 3.1 84.4 1.0 FE2 A:SF4503 3.1 86.1 1.0 CA A:CYS400 3.5 91.7 1.0 S1 A:SF4503 3.7 85.1 1.0 N A:CYS400 4.4 92.4 1.0 CG2 A:VAL427 4.6 86.4 1.0 C A:CYS400 4.7 91.8 1.0 CG1 A:VAL394 4.8 88.2 1.0 O A:CYS400 4.8 90.5 1.0 CB A:VAL394 5.0 90.5 1.0

Iron binding site 10 out of 24 in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:86.1 occ:1.00 FE2 A:SF4503 0.0 86.1 1.0 S3 A:SF4503 2.2 86.0 1.0 S4 A:SF4503 2.2 82.8 1.0 S1 A:SF4503 2.2 85.1 1.0 SG A:CYS409 2.7 85.5 1.0 CB A:CYS409 2.8 86.1 1.0 FE1 A:SF4503 3.1 83.5 1.0 FE4 A:SF4503 3.1 84.4 1.0 FE3 A:SF4503 3.1 84.5 1.0 S2 A:SF4503 3.8 82.2 1.0 O A:ALA405 4.2 81.4 1.0 CA A:CYS409 4.4 84.0 1.0 N A:GLY411 4.4 77.7 1.0 CA A:GLY411 4.4 80.6 1.0 C A:GLY411 4.5 81.5 1.0 N A:GLY412 4.6 77.9 1.0 CA A:LYS406 4.7 84.2 1.0 CG1 A:VAL394 4.7 88.2 1.0 C A:ALA405 4.8 82.6 1.0 O A:GLY411 5.0 83.9 1.0

T.L.Grove, P.M.Himes, S.Hwang, H.Yumerefendi, J.B.Bonanno, B.Kuhlman, S.C.Almo, A.A.Bowers. Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides. J. Am. Chem. Soc. V. 139 11734 2017.
ISSN: ESSN 1520-5126
PubMed: 28704043
DOI: 10.1021/JACS.7B01283