Iron in PDB 6z93: [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)

The structure of [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ), PDB code: 6z93 was solved by L.Pecqueur, J.Zhou, M.Fontecave, B.Golinelli-Pimpaneau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.03 / 1.51
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.381, 85.812, 39.512, 90.00, 93.92, 90.00
R / Rfree (%)	16.8 / 19.4

The structure of [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) (pdb code 6z93). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ), PDB code: 6z93:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:18.9 occ:0.90 FE1 A:SF4301 0.0 18.9 0.9 O2 A:EDO302 2.3 24.7 1.0 S3 A:SF4301 2.3 18.3 0.9 S2 A:SF4301 2.3 17.4 0.9 S4 A:SF4301 2.3 18.0 0.9 O1 A:EDO302 2.5 24.3 1.0 FE3 A:SF4301 2.7 16.4 0.9 FE4 A:SF4301 2.8 16.5 0.9 FE2 A:SF4301 2.8 16.6 0.9 C1 A:EDO302 3.2 25.4 1.0 C2 A:EDO302 3.2 25.9 1.0 S1 A:SF4301 3.9 17.1 0.9 NH2 A:ARG54 3.9 19.3 1.0 OG A:SER101 4.1 19.9 1.0 OE2 A:GLU45 4.1 18.9 1.0 CD A:GLU45 4.2 21.6 1.0 OE1 A:GLU45 4.2 23.3 1.0 CD A:ARG17 4.3 26.0 1.0 NH1 A:ARG17 4.3 26.0 1.0 SG A:CYS43 4.7 18.9 1.0 SG A:CYS10 4.8 19.8 1.0 CB A:SER101 4.8 17.9 1.0 CA A:ARG17 5.0 19.4 1.0 CG A:GLU45 5.0 19.1 1.0 SG A:CYS104 5.0 17.9 1.0

Iron binding site 2 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:16.6 occ:0.90 FE2 A:SF4301 0.0 16.6 0.9 SG A:CYS10 2.3 19.8 1.0 S3 A:SF4301 2.3 18.3 0.9 S1 A:SF4301 2.3 17.1 0.9 S4 A:SF4301 2.3 18.0 0.9 FE4 A:SF4301 2.7 16.5 0.9 FE1 A:SF4301 2.8 18.9 0.9 FE3 A:SF4301 2.8 16.4 0.9 CB A:CYS10 3.2 18.6 1.0 S2 A:SF4301 4.0 17.4 0.9 N A:CYS10 4.0 18.1 1.0 CD A:ARG17 4.1 26.0 1.0 CB A:SER8 4.2 18.6 1.0 CA A:CYS10 4.2 18.8 1.0 CB A:LYS98 4.4 18.6 1.0 O2 A:EDO302 4.4 24.7 1.0 OG A:SER8 4.5 20.3 1.0 NH1 A:ARG17 4.7 26.0 1.0 SG A:CYS104 4.7 17.9 1.0 CG A:LYS98 4.8 19.8 1.0 CG2 A:VAL16 4.8 21.8 1.0 CG A:ARG17 4.8 24.2 1.0 N A:ALA9 4.9 16.8 1.0 SG A:CYS43 4.9 18.9 1.0 C A:SER8 4.9 17.3 1.0 CA A:SER8 5.0 16.9 1.0

Iron binding site 3 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:16.4 occ:0.90 FE3 A:SF4301 0.0 16.4 0.9 SG A:CYS43 2.3 18.9 1.0 S1 A:SF4301 2.3 17.1 0.9 S4 A:SF4301 2.3 18.0 0.9 S2 A:SF4301 2.3 17.4 0.9 FE1 A:SF4301 2.7 18.9 0.9 FE4 A:SF4301 2.8 16.5 0.9 FE2 A:SF4301 2.8 16.6 0.9 CB A:CYS43 3.3 16.6 1.0 CA A:CYS43 3.7 16.9 1.0 S3 A:SF4301 3.9 18.3 0.9 CD A:PRO44 4.1 16.2 1.0 C A:CYS43 4.2 17.1 1.0 NH2 A:ARG54 4.3 19.3 1.0 CG2 A:VAL16 4.3 21.8 1.0 N A:PRO44 4.3 16.6 1.0 O2 A:EDO302 4.5 24.7 1.0 N A:GLU45 4.6 17.2 1.0 O A:VAL16 4.7 20.0 1.0 SG A:CYS104 4.9 17.9 1.0 CB A:GLU45 4.9 17.9 1.0 SG A:CYS10 4.9 19.8 1.0 O1 A:EDO302 4.9 24.3 1.0 CB A:VAL16 5.0 21.6 1.0

Iron binding site 4 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:16.5 occ:0.90 FE4 A:SF4301 0.0 16.5 0.9 S3 A:SF4301 2.3 18.3 0.9 S2 A:SF4301 2.3 17.4 0.9 S1 A:SF4301 2.3 17.1 0.9 SG A:CYS104 2.3 17.9 1.0 FE2 A:SF4301 2.7 16.6 0.9 FE1 A:SF4301 2.8 18.9 0.9 FE3 A:SF4301 2.8 16.4 0.9 CB A:CYS104 3.4 15.5 1.0 S4 A:SF4301 3.9 18.0 0.9 OG A:SER8 3.9 20.3 1.0 CD A:PRO44 3.9 16.2 1.0 OG A:SER101 4.0 19.9 1.0 O1 A:EDO302 4.1 24.3 1.0 CB A:SER8 4.4 18.6 1.0 CB A:SER103 4.5 16.8 1.0 N A:CYS104 4.5 15.2 1.0 CA A:CYS104 4.6 15.7 1.0 CG A:PRO44 4.7 18.1 1.0 SG A:CYS10 4.7 19.8 1.0 CB A:SER101 4.7 17.9 1.0 CB A:LYS98 4.8 18.6 1.0 SG A:CYS43 4.8 18.9 1.0 N A:PRO44 5.0 16.6 1.0

Iron binding site 5 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:21.7 occ:0.90 FE1 B:SF4301 0.0 21.7 0.9 S3 B:SF4301 2.3 19.9 0.9 S4 B:SF4301 2.3 20.6 0.9 S2 B:SF4301 2.3 19.6 0.9 O2 B:EDO302 2.4 26.7 1.0 O1 B:EDO302 2.4 27.2 1.0 FE3 B:SF4301 2.7 17.2 0.9 FE2 B:SF4301 2.8 18.0 0.9 FE4 B:SF4301 2.8 17.8 0.9 C1 B:EDO302 3.2 28.3 1.0 C2 B:EDO302 3.3 27.9 1.0 S1 B:SF4301 3.9 17.1 0.9 NH2 B:ARG54 4.0 23.1 1.0 OG B:SER101 4.1 21.7 1.0 OE2 B:GLU45 4.1 22.6 1.0 CD B:GLU45 4.2 22.3 1.0 OE1 B:GLU45 4.2 22.7 1.0 CD B:ARG17 4.3 35.9 1.0 NH2 B:ARG17 4.5 41.4 1.0 CB B:SER101 4.7 20.3 1.0 SG B:CYS43 4.7 18.7 1.0 SG B:CYS10 4.8 20.4 1.0 CG B:GLU45 4.9 18.5 1.0 SG B:CYS104 5.0 19.4 1.0

Iron binding site 6 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:18.0 occ:0.90 FE2 B:SF4301 0.0 18.0 0.9 SG B:CYS10 2.3 20.4 1.0 S4 B:SF4301 2.3 20.6 0.9 S3 B:SF4301 2.3 19.9 0.9 S1 B:SF4301 2.3 17.1 0.9 FE4 B:SF4301 2.7 17.8 0.9 FE1 B:SF4301 2.8 21.7 0.9 FE3 B:SF4301 2.8 17.2 0.9 CB B:CYS10 3.2 20.0 1.0 S2 B:SF4301 3.9 19.6 0.9 N B:CYS10 4.0 19.5 1.0 CD B:ARG17 4.1 35.9 1.0 CB B:SER8 4.2 17.4 1.0 CA B:CYS10 4.2 20.4 1.0 CB B:LYS98 4.4 20.8 1.0 O1 B:EDO302 4.6 27.2 1.0 OG B:SER8 4.6 18.3 1.0 NH2 B:ARG17 4.6 41.4 1.0 SG B:CYS104 4.7 19.4 1.0 CG B:LYS98 4.8 22.6 1.0 CG2 B:VAL16 4.8 24.6 1.0 CG B:ARG17 4.9 33.3 1.0 SG B:CYS43 4.9 18.7 1.0 O2 B:EDO302 4.9 26.7 1.0 N B:ALA9 5.0 17.7 1.0

Iron binding site 7 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:17.2 occ:0.90 FE3 B:SF4301 0.0 17.2 0.9 SG B:CYS43 2.3 18.7 1.0 S1 B:SF4301 2.3 17.1 0.9 S2 B:SF4301 2.3 19.6 0.9 S4 B:SF4301 2.3 20.6 0.9 FE1 B:SF4301 2.7 21.7 0.9 FE4 B:SF4301 2.8 17.8 0.9 FE2 B:SF4301 2.8 18.0 0.9 CB B:CYS43 3.3 17.4 1.0 CA B:CYS43 3.7 15.9 1.0 S3 B:SF4301 3.9 19.9 0.9 CD B:PRO44 4.2 15.9 1.0 NH2 B:ARG54 4.2 23.1 1.0 C B:CYS43 4.2 15.2 1.0 CG2 B:VAL16 4.3 24.6 1.0 N B:PRO44 4.4 16.1 1.0 N B:GLU45 4.6 16.1 1.0 O1 B:EDO302 4.6 27.2 1.0 O B:VAL16 4.7 24.2 1.0 CB B:GLU45 4.8 18.1 1.0 SG B:CYS104 4.9 19.4 1.0 O2 B:EDO302 4.9 26.7 1.0 SG B:CYS10 4.9 20.4 1.0 CB B:VAL16 4.9 24.2 1.0

Iron binding site 8 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:17.8 occ:0.90 FE4 B:SF4301 0.0 17.8 0.9 S3 B:SF4301 2.3 19.9 0.9 SG B:CYS104 2.3 19.4 1.0 S1 B:SF4301 2.3 17.1 0.9 S2 B:SF4301 2.3 19.6 0.9 FE2 B:SF4301 2.7 18.0 0.9 FE3 B:SF4301 2.8 17.2 0.9 FE1 B:SF4301 2.8 21.7 0.9 CB B:CYS104 3.5 18.3 1.0 OG B:SER8 3.9 18.3 1.0 CD B:PRO44 3.9 15.9 1.0 S4 B:SF4301 3.9 20.6 0.9 OG B:SER101 4.0 21.7 1.0 O2 B:EDO302 4.2 26.7 1.0 CB B:SER8 4.4 17.4 1.0 CB B:SER103 4.4 15.8 0.5 OG B:SER103 4.4 23.7 0.5 N B:CYS104 4.5 18.1 1.0 CA B:CYS104 4.6 18.1 1.0 CB B:SER103 4.7 20.8 0.5 CG B:PRO44 4.7 17.4 1.0 SG B:CYS10 4.7 20.4 1.0 CB B:SER101 4.7 20.3 1.0 CB B:LYS98 4.8 20.8 1.0 SG B:CYS43 4.8 18.7 1.0 N B:PRO44 4.9 16.1 1.0

J.Zhou, L.Pecqueur, A.Aucynaite, J.Fuchs, R.Rutkiene, J.Vaitekunas, R.Meskys, M.Boll, M.Fontecave, J.Urbonavicius, B.Golinelli-Pimpaneau. Structural Evidence For A [4FE-5S] Intermediate in the Non-Redox Desulfuration of Thiouracil. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 32929873
DOI: 10.1002/ANIE.202011211