Iron in PDB 6z94: [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)(S-Sad Data)

The structure of [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)(S-Sad Data), PDB code: 6z94 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)	72.17 / 1.76
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.759, 85.797, 39.444, 90.00, 93.88, 90.00
R / Rfree (%)	18.3 / 20.7

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

Chlorine

(Cl)

3 atoms

The binding sites of Iron atom in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)(S-Sad Data) (pdb code 6z94). 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)(S-Sad Data), PDB code: 6z94:
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)(S-Sad Data)


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)(S-Sad Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:26.0 occ:0.85 FE1 A:SF4301 0.0 26.0 0.8 O2 A:EDO302 2.1 25.4 0.8 S2 A:SF4301 2.3 24.8 0.8 S3 A:SF4301 2.3 24.8 0.8 S4 A:SF4301 2.3 25.3 0.8 O1 A:EDO302 2.7 26.2 0.8 FE3 A:SF4301 2.8 23.9 0.8 FE4 A:SF4301 2.8 23.6 0.8 FE2 A:SF4301 2.8 24.1 0.8 C2 A:EDO302 3.1 26.7 0.8 C1 A:EDO302 3.2 27.2 0.8 NH2 A:ARG54 3.9 26.4 1.0 S1 A:SF4301 3.9 24.2 0.8 OG A:SER101 4.1 25.4 1.0 OE1 A:GLU45 4.1 29.6 1.0 OE2 A:GLU45 4.1 28.9 1.0 CD A:GLU45 4.2 28.7 1.0 CD A:ARG17 4.3 34.1 1.0 NH1 A:ARG17 4.4 36.7 1.0 SG A:CYS43 4.7 26.1 1.0 SG A:CYS10 4.8 29.2 1.0 CB A:SER101 4.8 25.7 1.0 CA A:ARG17 4.9 27.3 1.0 SG A:CYS104 5.0 25.3 1.0

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


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)(S-Sad Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:24.1 occ:0.85 FE2 A:SF4301 0.0 24.1 0.8 SG A:CYS10 2.3 29.2 1.0 S4 A:SF4301 2.3 25.3 0.8 S3 A:SF4301 2.3 24.8 0.8 S1 A:SF4301 2.3 24.2 0.8 FE4 A:SF4301 2.8 23.6 0.8 FE1 A:SF4301 2.8 26.0 0.8 FE3 A:SF4301 2.8 23.9 0.8 CB A:CYS10 3.2 27.0 1.0 S2 A:SF4301 4.0 24.8 0.8 N A:CYS10 4.0 26.6 1.0 CD A:ARG17 4.1 34.1 1.0 CB A:SER8 4.1 26.9 1.0 O2 A:EDO302 4.2 25.4 0.8 CA A:CYS10 4.2 27.3 1.0 CB A:LYS98 4.3 24.9 1.0 OG A:SER8 4.5 28.3 1.0 NH1 A:ARG17 4.7 36.7 1.0 CG A:LYS98 4.7 24.6 1.0 SG A:CYS104 4.7 25.3 1.0 CG A:ARG17 4.8 32.4 1.0 SG A:CYS43 4.9 26.1 1.0 N A:ALA9 4.9 26.5 1.0 C A:SER8 4.9 26.8 1.0 CA A:SER8 5.0 26.5 1.0 CG2 A:VAL16 5.0 28.0 1.0

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


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)(S-Sad Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:23.9 occ:0.85 FE3 A:SF4301 0.0 23.9 0.8 SG A:CYS43 2.3 26.1 1.0 S4 A:SF4301 2.3 25.3 0.8 S1 A:SF4301 2.3 24.2 0.8 S2 A:SF4301 2.3 24.8 0.8 FE1 A:SF4301 2.8 26.0 0.8 FE2 A:SF4301 2.8 24.1 0.8 FE4 A:SF4301 2.8 23.6 0.8 CB A:CYS43 3.2 24.7 1.0 CA A:CYS43 3.6 25.0 1.0 S3 A:SF4301 4.0 24.8 0.8 CD A:PRO44 4.0 25.2 1.0 NH2 A:ARG54 4.2 26.4 1.0 C A:CYS43 4.2 25.2 1.0 N A:PRO44 4.3 25.4 1.0 O2 A:EDO302 4.4 25.4 0.8 CG2 A:VAL16 4.4 28.0 1.0 N A:GLU45 4.6 24.4 1.0 O A:VAL16 4.7 27.1 1.0 SG A:CYS104 4.8 25.3 1.0 CB A:GLU45 4.9 25.5 1.0 SG A:CYS10 4.9 29.2 1.0 N A:CYS43 5.0 25.3 1.0

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


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)(S-Sad Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:23.6 occ:0.85 FE4 A:SF4301 0.0 23.6 0.8 S3 A:SF4301 2.3 24.8 0.8 SG A:CYS104 2.3 25.3 1.0 S1 A:SF4301 2.3 24.2 0.8 S2 A:SF4301 2.3 24.8 0.8 FE2 A:SF4301 2.8 24.1 0.8 FE1 A:SF4301 2.8 26.0 0.8 FE3 A:SF4301 2.8 23.9 0.8 CB A:CYS104 3.4 23.1 1.0 CD A:PRO44 3.8 25.2 1.0 OG A:SER8 3.9 28.3 1.0 S4 A:SF4301 3.9 25.3 0.8 OG A:SER101 4.0 25.4 1.0 O1 A:EDO302 4.3 26.2 0.8 CB A:SER8 4.4 26.9 1.0 CB A:SER103 4.4 22.6 1.0 N A:CYS104 4.4 23.0 1.0 CG A:PRO44 4.6 27.5 1.0 CA A:CYS104 4.6 23.4 1.0 CB A:SER101 4.7 25.7 1.0 SG A:CYS10 4.7 29.2 1.0 CB A:LYS98 4.7 24.9 1.0 SG A:CYS43 4.9 26.1 1.0 O2 A:EDO302 4.9 25.4 0.8 N A:PRO44 4.9 25.4 1.0

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


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)(S-Sad Data) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:26.2 occ:0.80 FE1 B:SF4301 0.0 26.2 0.8 S3 B:SF4301 2.3 25.5 0.8 S2 B:SF4301 2.3 24.7 0.8 S4 B:SF4301 2.3 25.2 0.8 O1 B:EDO302 2.4 26.2 0.8 O2 B:EDO302 2.6 27.1 0.8 FE3 B:SF4301 2.8 23.0 0.8 FE2 B:SF4301 2.8 24.7 0.8 FE4 B:SF4301 2.8 23.9 0.8 C1 B:EDO302 3.1 27.6 0.8 C2 B:EDO302 3.3 27.6 0.8 NH2 B:ARG54 3.9 30.3 1.0 S1 B:SF4301 4.0 23.8 0.8 OG B:SER101 4.1 26.5 1.0 OE2 B:GLU45 4.1 26.2 1.0 OE1 B:GLU45 4.1 26.0 1.0 CD B:GLU45 4.2 25.4 1.0 CD B:ARG17 4.3 46.1 1.0 NH1 B:ARG17 4.5 51.0 1.0 SG B:CYS43 4.7 25.7 1.0 CB B:SER101 4.8 25.8 1.0 SG B:CYS10 4.8 28.6 1.0 SG B:CYS104 5.0 26.9 1.0 CG B:GLU45 5.0 23.4 1.0

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


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)(S-Sad Data) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:24.7 occ:0.80 FE2 B:SF4301 0.0 24.7 0.8 S4 B:SF4301 2.3 25.2 0.8 S1 B:SF4301 2.3 23.8 0.8 S3 B:SF4301 2.3 25.5 0.8 SG B:CYS10 2.3 28.6 1.0 FE4 B:SF4301 2.7 23.9 0.8 FE1 B:SF4301 2.8 26.2 0.8 FE3 B:SF4301 2.8 23.0 0.8 CB B:CYS10 3.2 27.8 1.0 S2 B:SF4301 3.9 24.7 0.8 N B:CYS10 4.0 27.7 1.0 CD B:ARG17 4.1 46.1 1.0 CB B:SER8 4.2 24.6 1.0 CA B:CYS10 4.2 28.3 1.0 CB B:LYS98 4.3 27.5 1.0 OG B:SER8 4.5 25.2 1.0 CG2 B:VAL16 4.6 34.9 1.0 O1 B:EDO302 4.6 26.2 0.8 CG B:LYS98 4.7 28.5 1.0 NH1 B:ARG17 4.7 51.0 1.0 SG B:CYS104 4.7 26.9 1.0 CG B:ARG17 4.8 43.8 1.0 SG B:CYS43 4.9 25.7 1.0 N B:ALA9 5.0 26.2 1.0 C B:SER8 5.0 25.7 1.0 CA B:SER8 5.0 24.8 1.0

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


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)(S-Sad Data) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:23.0 occ:0.80 FE3 B:SF4301 0.0 23.0 0.8 SG B:CYS43 2.3 25.7 1.0 S2 B:SF4301 2.3 24.7 0.8 S4 B:SF4301 2.3 25.2 0.8 S1 B:SF4301 2.3 23.8 0.8 FE1 B:SF4301 2.8 26.2 0.8 FE2 B:SF4301 2.8 24.7 0.8 FE4 B:SF4301 2.8 23.9 0.8 CB B:CYS43 3.3 24.1 1.0 CA B:CYS43 3.7 23.7 1.0 S3 B:SF4301 4.0 25.5 0.8 CD B:PRO44 4.0 23.4 1.0 CG2 B:VAL16 4.0 34.9 1.0 NH2 B:ARG54 4.1 30.3 1.0 C B:CYS43 4.2 23.6 1.0 N B:PRO44 4.3 24.4 1.0 O1 B:EDO302 4.5 26.2 0.8 N B:GLU45 4.6 24.5 1.0 CB B:VAL16 4.7 35.3 1.0 O B:VAL16 4.7 35.2 1.0 CB B:GLU45 4.8 25.0 1.0 SG B:CYS104 4.9 26.9 1.0 SG B:CYS10 4.9 28.6 1.0 N B:CYS43 5.0 23.5 1.0

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


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)(S-Sad Data) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:23.9 occ:0.80 FE4 B:SF4301 0.0 23.9 0.8 SG B:CYS104 2.3 26.9 1.0 S3 B:SF4301 2.3 25.5 0.8 S1 B:SF4301 2.3 23.8 0.8 S2 B:SF4301 2.4 24.7 0.8 FE2 B:SF4301 2.7 24.7 0.8 FE1 B:SF4301 2.8 26.2 0.8 FE3 B:SF4301 2.8 23.0 0.8 CB B:CYS104 3.4 25.0 1.0 CD B:PRO44 3.8 23.4 1.0 OG B:SER8 3.9 25.2 1.0 S4 B:SF4301 4.0 25.2 0.8 OG B:SER101 4.0 26.5 1.0 O2 B:EDO302 4.3 27.1 0.8 OG B:SER103 4.3 28.4 0.5 CB B:SER8 4.4 24.6 1.0 CB B:SER103 4.4 22.7 0.5 N B:CYS104 4.4 24.1 1.0 CG B:PRO44 4.5 24.8 1.0 CA B:CYS104 4.6 24.9 1.0 CB B:SER103 4.6 25.7 0.5 CB B:SER101 4.7 25.8 1.0 CB B:LYS98 4.7 27.5 1.0 SG B:CYS10 4.8 28.6 1.0 SG B:CYS43 4.9 25.7 1.0 N B:PRO44 4.9 24.4 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