Iron in PDB 6djt: Structure of TYW1 with A Lysine-Pyruvate Adduct Bound

All present enzymatic activity of Structure of TYW1 with A Lysine-Pyruvate Adduct Bound:
4.1.3.44;

The structure of Structure of TYW1 with A Lysine-Pyruvate Adduct Bound, PDB code: 6djt was solved by T.A.J.Grell, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.31 / 1.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.260, 80.109, 86.456, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 19.5

The binding sites of Iron atom in the Structure of TYW1 with A Lysine-Pyruvate Adduct Bound (pdb code 6djt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Structure of TYW1 with A Lysine-Pyruvate Adduct Bound, PDB code: 6djt:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Structure of TYW1 with A Lysine-Pyruvate Adduct Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of TYW1 with A Lysine-Pyruvate Adduct Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:28.3 occ:0.58 FE1 A:SF4401 0.0 28.3 0.6 S3 A:SF4401 2.3 30.4 0.6 S4 A:SF4401 2.3 32.4 0.6 S2 A:SF4401 2.3 29.7 0.6 SG A:CYS39 2.3 24.6 0.8 FE3 A:SF4401 2.7 30.2 0.6 FE4 A:SF4401 2.7 33.4 0.6 FE2 A:SF4401 3.0 36.1 0.6 CB A:CYS39 3.4 22.6 0.8 S1 A:SF4401 3.9 34.1 0.6 CB A:KPI41 3.9 32.5 0.6 CB A:KPI41 3.9 33.0 0.4 CD A:KPI41 4.1 48.9 0.4 CD A:KPI41 4.1 48.7 0.6 CG A:KPI41 4.6 41.4 0.4 CG A:KPI41 4.6 41.9 0.6 SG A:CYS52 4.6 24.7 0.2 NZ A:KPI41 4.7 58.1 0.6 CG2 A:THR49 4.7 27.0 1.0 NZ A:KPI41 4.8 58.0 0.4 SG A:CYS26 4.8 45.7 1.0 N A:KPI41 4.8 24.3 0.6 N A:KPI41 4.8 25.1 0.4 SG A:CYS52 4.8 29.4 0.6 CA A:CYS39 4.8 21.4 0.8 CE A:KPI41 4.9 54.3 0.6 CE A:KPI41 4.9 54.0 0.4 CA A:KPI41 4.9 28.3 0.6 CA A:KPI41 4.9 28.2 0.4 OG1 A:THR49 4.9 27.7 1.0

Iron binding site 2 out of 6 in the Structure of TYW1 with A Lysine-Pyruvate Adduct Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of TYW1 with A Lysine-Pyruvate Adduct Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:36.1 occ:0.58 FE2 A:SF4401 0.0 36.1 0.6 S1 A:SF4401 2.2 34.1 0.6 S3 A:SF4401 2.3 30.4 0.6 NZ A:KPI41 2.4 58.1 0.6 O2 A:KPI41 2.4 62.1 0.6 S4 A:SF4401 2.5 32.4 0.6 NZ A:KPI41 2.5 58.0 0.4 FE4 A:SF4401 2.8 33.4 0.6 FE3 A:SF4401 2.8 30.2 0.6 CX1 A:KPI41 3.0 60.6 0.4 FE1 A:SF4401 3.0 28.3 0.6 CX1 A:KPI41 3.1 60.1 0.6 CX2 A:KPI41 3.1 61.4 0.6 C1 A:KPI41 3.2 61.0 0.4 CE A:KPI41 3.3 54.0 0.4 CE A:KPI41 3.3 54.3 0.6 CD A:KPI41 3.4 48.7 0.6 CD A:KPI41 3.5 48.9 0.4 CX2 A:KPI41 4.0 59.6 0.4 S2 A:SF4401 4.0 29.7 0.6 O1 A:KPI41 4.0 56.8 0.4 O1 A:KPI41 4.3 59.6 0.6 C1 A:KPI41 4.6 59.6 0.6 CG A:KPI41 4.6 41.4 0.4 CG A:KPI41 4.6 41.9 0.6 O A:HOH503 4.7 52.4 1.0 CB A:ALA132 4.8 25.2 1.0 SG A:CYS26 4.8 45.7 1.0 SG A:CYS52 4.8 29.4 0.6 CB A:KPI41 4.9 32.5 0.6 CB A:KPI41 4.9 33.0 0.4

Iron binding site 3 out of 6 in the Structure of TYW1 with A Lysine-Pyruvate Adduct Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of TYW1 with A Lysine-Pyruvate Adduct Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:30.2 occ:0.58 FE3 A:SF4401 0.0 30.2 0.6 S4 A:SF4401 2.2 32.4 0.6 S1 A:SF4401 2.3 34.1 0.6 S2 A:SF4401 2.3 29.7 0.6 SG A:CYS52 2.3 29.4 0.6 FE4 A:SF4401 2.7 33.4 0.6 FE1 A:SF4401 2.7 28.3 0.6 FE2 A:SF4401 2.8 36.1 0.6 SG A:CYS52 2.9 17.9 0.2 CB A:CYS52 3.3 24.9 0.2 CB A:CYS52 3.3 26.5 0.6 CB A:CYS52 3.4 24.8 0.2 SG A:CYS52 3.6 24.7 0.2 S3 A:SF4401 3.8 30.4 0.6 CB A:ALA132 4.5 25.2 1.0 CA A:CYS52 4.7 23.7 0.6 CB A:CYS26 4.7 38.0 1.0 SG A:CYS26 4.7 45.7 1.0 ND1 A:HIS130 4.7 25.4 0.2 CA A:CYS52 4.7 23.5 0.2 CA A:CYS52 4.7 23.3 0.2 CD2 A:HIS130 4.7 25.4 0.2 NZ A:KPI41 4.8 58.1 0.6 SG A:CYS39 4.9 24.6 0.8 C A:CYS52 4.9 24.1 0.2 O A:CYS52 4.9 23.7 0.2 C A:CYS52 5.0 25.0 0.6 O2 A:KPI41 5.0 62.1 0.6

Iron binding site 4 out of 6 in the Structure of TYW1 with A Lysine-Pyruvate Adduct Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of TYW1 with A Lysine-Pyruvate Adduct Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:33.4 occ:0.58 FE4 A:SF4401 0.0 33.4 0.6 S1 A:SF4401 2.3 34.1 0.6 S3 A:SF4401 2.3 30.4 0.6 S2 A:SF4401 2.3 29.7 0.6 SG A:CYS26 2.3 45.7 1.0 FE3 A:SF4401 2.7 30.2 0.6 FE1 A:SF4401 2.7 28.3 0.6 FE2 A:SF4401 2.8 36.1 0.6 CB A:CYS26 3.1 38.0 1.0 S4 A:SF4401 3.8 32.4 0.6 O2 A:KPI41 4.2 62.1 0.6 CB A:TRP28 4.5 29.0 1.0 CA A:CYS26 4.6 40.0 1.0 CD1 A:TRP28 4.6 34.8 1.0 SG A:CYS52 4.7 29.4 0.6 SG A:CYS39 4.7 24.6 0.8 CB A:CYS39 4.9 22.6 0.8 CG A:TRP28 5.0 30.7 1.0

Iron binding site 5 out of 6 in the Structure of TYW1 with A Lysine-Pyruvate Adduct Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of TYW1 with A Lysine-Pyruvate Adduct Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe412 b:32.1 occ:0.84 FE1 A:FS0412 0.0 32.1 0.8 S2 A:FS0412 2.3 29.9 0.8 S1 A:FS0412 2.3 33.4 0.8 SG A:CYS69 2.3 39.2 0.9 SG A:CYS66 2.4 35.6 0.9 FE2 A:FS0412 2.7 31.0 0.8 CB A:CYS66 3.1 36.2 0.9 CB A:CYS69 3.4 45.0 0.9 N A:CYS66 3.6 35.5 0.9 CA A:CYS66 4.0 35.2 0.9 S5 A:FS0412 4.2 32.4 0.8 CB A:GLN64 4.4 30.9 1.0 OE1 A:GLN64 4.4 35.1 1.0 CE1 A:PHE68 4.7 59.9 1.0 O A:HOH674 4.7 70.2 1.0 N A:ASN65 4.8 28.6 1.0 SG A:CYS62 4.8 26.8 0.9 CA A:CYS69 4.8 50.5 0.9 C A:ASN65 4.8 32.6 1.0 O A:HOH538 4.8 42.5 1.0 C A:GLN64 4.9 32.3 1.0 C A:CYS66 5.0 37.4 0.9

Iron binding site 6 out of 6 in the Structure of TYW1 with A Lysine-Pyruvate Adduct Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of TYW1 with A Lysine-Pyruvate Adduct Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe412 b:31.0 occ:0.84 FE2 A:FS0412 0.0 31.0 0.8 S1 A:FS0412 2.3 33.4 0.8 S2 A:FS0412 2.3 29.9 0.8 SG A:CYS62 2.3 26.8 0.9 S5 A:FS0412 2.3 32.4 0.8 FE1 A:FS0412 2.7 32.1 0.8 CB A:CYS62 3.3 28.0 0.9 O A:HOH535 4.1 33.6 1.0 CB A:GLN64 4.3 30.9 1.0 SG A:CYS69 4.4 39.2 0.9 O2 A:GOL405 4.4 48.9 0.9 O A:GLN64 4.5 34.2 1.0 O A:HOH662 4.5 56.0 1.0 C A:GLN64 4.6 32.3 1.0 N A:GLN64 4.7 26.6 1.0 SG A:CYS66 4.7 35.6 0.9 CA A:GLN64 4.7 26.9 1.0 OE1 A:GLN64 4.8 35.1 1.0 CA A:CYS62 4.8 22.0 0.9 CB A:CYS69 5.0 45.0 0.9

T.A.J.Grell, A.P.Young, C.L.Drennan, V.Bandarian. Biochemical and Structural Characterization of A Schiff Base in the Radical-Mediated Biosynthesis of 4-Demethylwyosine By TYW1. J. Am. Chem. Soc. V. 140 6842 2018.
ISSN: ESSN 1520-5126
PubMed: 29792696
DOI: 10.1021/JACS.8B01493