Iron in PDB 6zw9: [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (S-Sad Data)

The structure of [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (S-Sad Data), PDB code: 6zw9 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)	24.12 / 1.76
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.165, 85.519, 39.576, 90.00, 94.01, 90.00
R / Rfree (%)	16.8 / 18.9

The binding sites of Iron atom in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (S-Sad Data) (pdb code 6zw9). 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) Soaked with 4-Thiouracil (S-Sad Data), PDB code: 6zw9:
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) Soaked with 4-Thiouracil (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) Soaked with 4-Thiouracil (S-Sad Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:6.9 occ:0.80 FE1 A:SF4301 0.0 6.9 0.8 S3 A:SF4301 2.3 7.2 0.8 S A:H2S303 2.3 10.7 0.8 S4 A:SF4301 2.3 7.1 0.8 S2 A:SF4301 2.3 6.5 0.8 FE3 A:SF4301 2.8 5.7 0.8 FE2 A:SF4301 2.8 5.5 0.8 FE4 A:SF4301 2.8 6.4 0.8 O A:HOH423 3.0 19.5 1.0 NH2 A:ARG54 3.9 10.1 1.0 S1 A:SF4301 3.9 6.5 0.8 OG A:SER101 4.2 11.9 1.0 CD A:ARG17 4.2 15.4 1.0 OE1 A:GLU45 4.2 11.0 1.0 OE2 A:GLU45 4.3 9.5 1.0 NH1 A:ARG17 4.3 15.8 1.0 CD A:GLU45 4.3 10.1 1.0 SG A:CYS43 4.7 9.6 1.0 SG A:CYS10 4.8 9.7 1.0 CB A:SER101 4.8 11.0 1.0 CA A:ARG17 4.9 8.8 1.0 SG A:CYS104 5.0 9.2 1.0

Iron binding site 2 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (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) Soaked with 4-Thiouracil (S-Sad Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:5.5 occ:0.80 FE2 A:SF4301 0.0 5.5 0.8 SG A:CYS10 2.3 9.7 1.0 S4 A:SF4301 2.3 7.1 0.8 S1 A:SF4301 2.3 6.5 0.8 S3 A:SF4301 2.3 7.2 0.8 FE4 A:SF4301 2.8 6.4 0.8 FE1 A:SF4301 2.8 6.9 0.8 FE3 A:SF4301 2.8 5.7 0.8 CB A:CYS10 3.2 9.1 1.0 S2 A:SF4301 3.9 6.5 0.8 N A:CYS10 4.0 7.3 1.0 CD A:ARG17 4.0 15.4 1.0 CB A:SER8 4.2 8.5 1.0 CA A:CYS10 4.2 8.4 1.0 CB A:LYS98 4.4 9.2 1.0 OG A:SER8 4.5 9.6 1.0 S A:H2S303 4.6 10.7 0.8 SG A:CYS104 4.7 9.2 1.0 CG A:ARG17 4.7 12.7 1.0 NH1 A:ARG17 4.8 15.8 1.0 CG A:LYS98 4.8 9.8 1.0 CG2 A:VAL16 4.8 10.0 1.0 N A:ALA9 4.9 7.4 1.0 SG A:CYS43 4.9 9.6 1.0 C A:SER8 4.9 7.9 1.0 CA A:SER8 5.0 7.7 1.0

Iron binding site 3 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (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) Soaked with 4-Thiouracil (S-Sad Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:5.7 occ:0.80 FE3 A:SF4301 0.0 5.7 0.8 S1 A:SF4301 2.3 6.5 0.8 SG A:CYS43 2.3 9.6 1.0 S4 A:SF4301 2.3 7.1 0.8 S2 A:SF4301 2.3 6.5 0.8 FE1 A:SF4301 2.8 6.9 0.8 FE4 A:SF4301 2.8 6.4 0.8 FE2 A:SF4301 2.8 5.5 0.8 CB A:CYS43 3.2 8.3 1.0 CA A:CYS43 3.7 8.1 1.0 S3 A:SF4301 3.9 7.2 0.8 CD A:PRO44 4.1 8.3 1.0 NH2 A:ARG54 4.1 10.1 1.0 C A:CYS43 4.2 8.0 1.0 CG2 A:VAL16 4.3 10.0 1.0 N A:PRO44 4.3 8.0 1.0 N A:GLU45 4.6 7.0 1.0 O A:VAL16 4.6 8.2 1.0 S A:H2S303 4.7 10.7 0.8 SG A:CYS104 4.9 9.2 1.0 CB A:GLU45 4.9 6.0 1.0 SG A:CYS10 4.9 9.7 1.0 CB A:VAL16 5.0 10.2 1.0

Iron binding site 4 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (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) Soaked with 4-Thiouracil (S-Sad Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:6.4 occ:0.80 FE4 A:SF4301 0.0 6.4 0.8 S2 A:SF4301 2.3 6.5 0.8 S3 A:SF4301 2.3 7.2 0.8 SG A:CYS104 2.3 9.2 1.0 S1 A:SF4301 2.3 6.5 0.8 FE2 A:SF4301 2.8 5.5 0.8 FE3 A:SF4301 2.8 5.7 0.8 FE1 A:SF4301 2.8 6.9 0.8 CB A:CYS104 3.4 7.6 1.0 CD A:PRO44 3.9 8.3 1.0 S4 A:SF4301 3.9 7.1 0.8 OG A:SER8 3.9 9.6 1.0 OG A:SER101 4.0 11.9 1.0 CB A:SER8 4.4 8.5 1.0 CB A:SER103 4.5 8.2 1.0 O A:HOH423 4.5 19.5 1.0 N A:CYS104 4.5 6.3 1.0 CA A:CYS104 4.6 7.1 1.0 CG A:PRO44 4.7 10.1 1.0 SG A:CYS10 4.7 9.7 1.0 CB A:SER101 4.7 11.0 1.0 SG A:CYS43 4.8 9.6 1.0 CB A:LYS98 4.8 9.2 1.0 N A:PRO44 4.9 8.0 1.0

Iron binding site 5 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (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) Soaked with 4-Thiouracil (S-Sad Data) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:9.9 occ:0.80 FE1 B:SF4301 0.0 9.9 0.8 S3 B:SF4301 2.3 8.7 0.8 S4 B:SF4301 2.3 8.4 0.8 S2 B:SF4301 2.3 7.9 0.8 S B:H2S302 2.4 16.0 0.7 S B:H2S302 2.7 7.4 0.3 FE2 B:SF4301 2.8 6.0 0.8 FE3 B:SF4301 2.8 5.3 0.8 FE4 B:SF4301 2.8 7.2 0.8 OG B:SER101 3.9 11.1 1.0 S1 B:SF4301 3.9 6.2 0.8 NH2 B:ARG54 4.1 12.4 1.0 NH1 B:ARG17 4.2 16.9 0.5 OE2 B:GLU45 4.2 10.4 1.0 OE1 B:GLU45 4.3 11.5 1.0 CD B:GLU45 4.3 11.3 1.0 CD B:ARG17 4.4 17.1 0.5 CB B:SER101 4.5 9.9 1.0 SG B:CYS43 4.8 8.6 1.0 SG B:CYS10 4.8 10.0 1.0 SG B:CYS104 4.9 10.3 1.0

Iron binding site 6 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (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) Soaked with 4-Thiouracil (S-Sad Data) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:6.0 occ:0.80 FE2 B:SF4301 0.0 6.0 0.8 S4 B:SF4301 2.3 8.4 0.8 S3 B:SF4301 2.3 8.7 0.8 SG B:CYS10 2.3 10.0 1.0 S1 B:SF4301 2.3 6.2 0.8 FE1 B:SF4301 2.8 9.9 0.8 FE4 B:SF4301 2.8 7.2 0.8 FE3 B:SF4301 2.8 5.3 0.8 CB B:CYS10 3.2 8.9 1.0 S2 B:SF4301 3.9 7.9 0.8 N B:CYS10 4.1 8.5 1.0 CD B:ARG17 4.1 17.1 0.5 CB B:SER8 4.2 6.9 1.0 CA B:CYS10 4.3 9.5 1.0 CB B:LYS98 4.4 8.4 1.0 CG2 B:VAL16 4.6 13.7 1.0 OG B:SER8 4.6 8.7 1.0 NH1 B:ARG17 4.6 16.9 0.5 S B:H2S302 4.7 7.4 0.3 SG B:CYS104 4.7 10.3 1.0 CG B:LYS98 4.8 9.6 1.0 CG B:ARG17 4.9 15.8 0.5 SG B:CYS43 4.9 8.6 1.0 S B:H2S302 4.9 16.0 0.7

Iron binding site 7 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (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) Soaked with 4-Thiouracil (S-Sad Data) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:5.3 occ:0.80 FE3 B:SF4301 0.0 5.3 0.8 SG B:CYS43 2.3 8.6 1.0 S1 B:SF4301 2.3 6.2 0.8 S2 B:SF4301 2.3 7.9 0.8 S4 B:SF4301 2.3 8.4 0.8 FE1 B:SF4301 2.8 9.9 0.8 FE2 B:SF4301 2.8 6.0 0.8 FE4 B:SF4301 2.8 7.2 0.8 CB B:CYS43 3.2 7.7 1.0 CA B:CYS43 3.7 7.2 1.0 S3 B:SF4301 3.9 8.7 0.8 NH2 B:ARG54 4.1 12.4 1.0 CD B:PRO44 4.1 7.7 1.0 CG2 B:VAL16 4.2 13.7 1.0 C B:CYS43 4.3 7.4 1.0 N B:PRO44 4.4 7.6 1.0 N B:GLU45 4.6 7.0 1.0 O B:VAL16 4.7 11.7 1.0 CB B:VAL16 4.7 13.5 1.0 CB B:GLU45 4.8 8.2 1.0 S B:H2S302 4.9 7.4 0.3 SG B:CYS104 4.9 10.3 1.0 SG B:CYS10 4.9 10.0 1.0

Iron binding site 8 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (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) Soaked with 4-Thiouracil (S-Sad Data) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:7.2 occ:0.80 FE4 B:SF4301 0.0 7.2 0.8 SG B:CYS104 2.3 10.3 1.0 S2 B:SF4301 2.3 7.9 0.8 S3 B:SF4301 2.3 8.7 0.8 S1 B:SF4301 2.3 6.2 0.8 FE2 B:SF4301 2.8 6.0 0.8 FE1 B:SF4301 2.8 9.9 0.8 FE3 B:SF4301 2.8 5.3 0.8 CB B:CYS104 3.4 7.7 1.0 CD B:PRO44 3.8 7.7 1.0 OG B:SER8 3.9 8.7 1.0 S4 B:SF4301 3.9 8.4 0.8 OG B:SER103 4.0 9.5 0.2 OG B:SER101 4.0 11.1 1.0 CB B:SER8 4.3 6.9 1.0 CB B:SER103 4.4 7.0 0.8 N B:CYS104 4.5 6.2 1.0 S B:H2S302 4.5 16.0 0.7 CA B:CYS104 4.6 7.0 1.0 CG B:PRO44 4.6 9.3 1.0 CB B:SER101 4.7 9.9 1.0 SG B:CYS10 4.7 10.0 1.0 CB B:SER103 4.7 8.2 0.2 CB B:LYS98 4.8 8.4 1.0 SG B:CYS43 4.8 8.6 1.0 N B:PRO44 4.9 7.6 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