Iron in PDB 6z92: [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Solved By Fe-Sad Phasing

The structure of [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Solved By Fe-Sad Phasing, PDB code: 6z92 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)	66.51 / 2.07
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.280, 85.911, 39.565, 90.00, 93.64, 90.00
R / Rfree (%)	19.5 / 22

The binding sites of Iron atom in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Solved By Fe-Sad Phasing (pdb code 6z92). 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) Solved By Fe-Sad Phasing, PDB code: 6z92:
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) Solved By Fe-Sad Phasing


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) Solved By Fe-Sad Phasing within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:26.4 occ:0.90 FE1 A:SF4301 0.0 26.4 0.9 O2 A:EDO302 2.2 19.3 0.9 S2 A:SF4301 2.3 26.9 0.9 S3 A:SF4301 2.3 27.0 0.9 S4 A:SF4301 2.3 26.9 0.9 FE3 A:SF4301 2.7 27.4 0.9 FE4 A:SF4301 2.8 26.8 0.9 O1 A:EDO302 2.8 21.6 0.9 FE2 A:SF4301 2.8 27.6 0.9 C2 A:EDO302 3.1 20.1 0.9 C1 A:EDO302 3.2 21.2 0.9 NH2 A:ARG54 3.9 27.7 1.0 S1 A:SF4301 3.9 26.9 0.9 OE2 A:GLU45 4.0 33.4 1.0 OG A:SER101 4.2 30.4 1.0 CD A:GLU45 4.2 33.9 1.0 OE1 A:GLU45 4.3 35.6 1.0 CD A:ARG17 4.5 43.4 1.0 NH1 A:ARG17 4.5 46.6 1.0 SG A:CYS43 4.6 32.5 1.0 SG A:CYS10 4.8 33.6 1.0 CB A:SER101 4.9 28.4 1.0

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


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) Solved By Fe-Sad Phasing within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:27.6 occ:0.90 FE2 A:SF4301 0.0 27.6 0.9 SG A:CYS10 2.2 33.6 1.0 S1 A:SF4301 2.3 26.9 0.9 S4 A:SF4301 2.3 26.9 0.9 S3 A:SF4301 2.3 27.0 0.9 FE4 A:SF4301 2.8 26.8 0.9 FE3 A:SF4301 2.8 27.4 0.9 FE1 A:SF4301 2.8 26.4 0.9 CB A:CYS10 3.2 32.1 1.0 S2 A:SF4301 3.9 26.9 0.9 N A:CYS10 4.0 32.3 1.0 CD A:ARG17 4.1 43.4 1.0 O2 A:EDO302 4.2 19.3 0.9 CB A:SER8 4.2 27.4 1.0 CA A:CYS10 4.2 32.2 1.0 CB A:LYS98 4.3 29.0 1.0 OG A:SER8 4.4 27.6 1.0 NH1 A:ARG17 4.6 46.6 1.0 SG A:CYS104 4.7 32.3 1.0 CG A:LYS98 4.7 32.7 1.0 SG A:CYS43 4.9 32.5 1.0 N A:ALA9 4.9 32.3 1.0 CG2 A:VAL16 4.9 29.3 1.0 C A:SER8 4.9 31.6 1.0 CA A:SER8 5.0 29.3 1.0 CG A:ARG17 5.0 40.8 1.0

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


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) Solved By Fe-Sad Phasing within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:27.4 occ:0.90 FE3 A:SF4301 0.0 27.4 0.9 S4 A:SF4301 2.3 26.9 0.9 SG A:CYS43 2.3 32.5 1.0 S1 A:SF4301 2.3 26.9 0.9 S2 A:SF4301 2.3 26.9 0.9 FE1 A:SF4301 2.7 26.4 0.9 FE2 A:SF4301 2.8 27.6 0.9 FE4 A:SF4301 2.8 26.8 0.9 CB A:CYS43 3.3 29.7 1.0 CA A:CYS43 3.7 29.4 1.0 S3 A:SF4301 3.9 27.0 0.9 CD A:PRO44 4.1 26.6 1.0 NH2 A:ARG54 4.3 27.7 1.0 C A:CYS43 4.3 28.2 1.0 CG2 A:VAL16 4.3 29.3 1.0 N A:PRO44 4.4 27.1 1.0 O2 A:EDO302 4.4 19.3 0.9 O A:VAL16 4.6 32.8 1.0 N A:GLU45 4.7 27.1 1.0 SG A:CYS10 4.8 33.6 1.0 SG A:CYS104 4.9 32.3 1.0 CB A:GLU45 4.9 29.0 1.0 O A:PHE42 5.0 31.9 1.0 N A:CYS43 5.0 30.2 1.0

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


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) Solved By Fe-Sad Phasing within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:26.8 occ:0.90 FE4 A:SF4301 0.0 26.8 0.9 S3 A:SF4301 2.3 27.0 0.9 S2 A:SF4301 2.3 26.9 0.9 S1 A:SF4301 2.3 26.9 0.9 SG A:CYS104 2.4 32.3 1.0 FE2 A:SF4301 2.8 27.6 0.9 FE1 A:SF4301 2.8 26.4 0.9 FE3 A:SF4301 2.8 27.4 0.9 CB A:CYS104 3.5 30.4 1.0 OG A:SER8 3.9 27.6 1.0 OG A:SER101 3.9 30.4 1.0 CD A:PRO44 3.9 26.6 1.0 S4 A:SF4301 3.9 26.9 0.9 CB A:SER103 4.3 28.7 1.0 O1 A:EDO302 4.4 21.6 0.9 N A:CYS104 4.4 29.1 1.0 CB A:SER8 4.5 27.4 1.0 CA A:CYS104 4.6 29.8 1.0 CG A:PRO44 4.7 28.1 1.0 CB A:SER101 4.7 28.4 1.0 SG A:CYS10 4.7 33.6 1.0 CB A:LYS98 4.7 29.0 1.0 SG A:CYS43 4.8 32.5 1.0 O2 A:EDO302 4.9 19.3 0.9 OE2 A:GLU45 4.9 33.4 1.0 N A:PRO44 5.0 27.1 1.0

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


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) Solved By Fe-Sad Phasing within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:29.9 occ:0.90 FE1 B:SF4301 0.0 29.9 0.9 S4 B:SF4301 2.3 29.0 0.9 S3 B:SF4301 2.3 29.6 0.9 S2 B:SF4301 2.3 29.0 0.9 O2 B:EDO302 2.4 42.7 0.9 O1 B:EDO302 2.5 41.5 0.9 FE2 B:SF4301 2.7 28.9 0.9 FE3 B:SF4301 2.8 29.0 0.9 FE4 B:SF4301 2.8 27.8 0.9 C1 B:EDO302 3.0 41.9 0.9 C2 B:EDO302 3.2 42.4 0.9 NH2 B:ARG54 3.9 40.0 1.0 S1 B:SF4301 3.9 28.0 0.9 OE2 B:GLU45 4.0 31.1 1.0 OG B:SER101 4.2 31.7 1.0 CD B:GLU45 4.2 32.1 1.0 OE1 B:GLU45 4.3 31.8 1.0 CD B:ARG17 4.4 60.5 1.0 NH1 B:ARG17 4.4 65.0 1.0 SG B:CYS43 4.7 31.8 1.0 SG B:CYS10 4.7 36.8 1.0 CB B:SER101 4.9 30.3 1.0 SG B:CYS104 4.9 29.3 1.0

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


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) Solved By Fe-Sad Phasing within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:28.9 occ:0.90 FE2 B:SF4301 0.0 28.9 0.9 SG B:CYS10 2.3 36.8 1.0 S3 B:SF4301 2.3 29.6 0.9 S1 B:SF4301 2.3 28.0 0.9 S4 B:SF4301 2.3 29.0 0.9 FE4 B:SF4301 2.7 27.8 0.9 FE1 B:SF4301 2.7 29.9 0.9 FE3 B:SF4301 2.8 29.0 0.9 CB B:CYS10 3.2 33.5 1.0 S2 B:SF4301 3.9 29.0 0.9 N B:CYS10 4.0 33.1 1.0 CD B:ARG17 4.1 60.5 1.0 CB B:SER8 4.2 29.5 1.0 CA B:CYS10 4.2 33.1 1.0 CB B:LYS98 4.3 30.4 1.0 OG B:SER8 4.5 30.6 1.0 NH1 B:ARG17 4.5 65.0 1.0 SG B:CYS104 4.7 29.3 1.0 CG B:LYS98 4.7 33.4 1.0 O1 B:EDO302 4.8 41.5 0.9 O2 B:EDO302 4.9 42.7 0.9 SG B:CYS43 4.9 31.8 1.0 CG2 B:VAL16 4.9 46.7 1.0 N B:ALA9 5.0 31.0 1.0 C B:SER8 5.0 30.2 1.0 CG B:ARG17 5.0 57.7 1.0

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


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) Solved By Fe-Sad Phasing within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:29.0 occ:0.90 FE3 B:SF4301 0.0 29.0 0.9 SG B:CYS43 2.3 31.8 1.0 S4 B:SF4301 2.3 29.0 0.9 S2 B:SF4301 2.3 29.0 0.9 S1 B:SF4301 2.3 28.0 0.9 FE1 B:SF4301 2.8 29.9 0.9 FE2 B:SF4301 2.8 28.9 0.9 FE4 B:SF4301 2.8 27.8 0.9 CB B:CYS43 3.3 29.1 1.0 CA B:CYS43 3.7 29.0 1.0 S3 B:SF4301 3.9 29.6 0.9 CD B:PRO44 4.0 25.3 1.0 NH2 B:ARG54 4.1 40.0 1.0 C B:CYS43 4.3 27.7 1.0 N B:PRO44 4.3 26.5 1.0 CG2 B:VAL16 4.3 46.7 1.0 O B:VAL16 4.6 47.9 1.0 N B:GLU45 4.7 25.3 1.0 O1 B:EDO302 4.7 41.5 0.9 SG B:CYS104 4.8 29.3 1.0 SG B:CYS10 4.8 36.8 1.0 CB B:GLU45 4.9 27.6 1.0 O2 B:EDO302 4.9 42.7 0.9 CB B:VAL16 5.0 46.4 1.0

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


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) Solved By Fe-Sad Phasing within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:27.8 occ:0.90 FE4 B:SF4301 0.0 27.8 0.9 SG B:CYS104 2.3 29.3 1.0 S3 B:SF4301 2.3 29.6 0.9 S1 B:SF4301 2.3 28.0 0.9 S2 B:SF4301 2.3 29.0 0.9 FE2 B:SF4301 2.7 28.9 0.9 FE3 B:SF4301 2.8 29.0 0.9 FE1 B:SF4301 2.8 29.9 0.9 CB B:CYS104 3.5 28.8 1.0 CD B:PRO44 3.8 25.3 1.0 OG B:SER8 3.9 30.6 1.0 S4 B:SF4301 3.9 29.0 0.9 OG B:SER101 3.9 31.7 1.0 O2 B:EDO302 4.0 42.7 0.9 CB B:SER8 4.4 29.5 1.0 CB B:SER103 4.5 31.1 1.0 N B:CYS104 4.6 29.0 1.0 CA B:CYS104 4.7 29.1 1.0 CG B:PRO44 4.7 27.0 1.0 CB B:SER101 4.7 30.3 1.0 SG B:CYS10 4.7 36.8 1.0 CB B:LYS98 4.8 30.4 1.0 SG B:CYS43 4.8 31.8 1.0 OE2 B:GLU45 4.9 31.1 1.0 N B:PRO44 4.9 26.5 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