Iron in PDB 6z96: [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (S-Sad) Data)

The structure of [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (S-Sad) Data), PDB code: 6z96 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)	39.69 / 1.33
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.666, 85.776, 39.515, 90.00, 94.10, 90.00
R / Rfree (%)	16.5 / 18.4

The binding sites of Iron atom in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (S-Sad) Data) (pdb code 6z96). 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 (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (S-Sad) Data), PDB code: 6z96:
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 (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (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 (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (S-Sad) Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:16.8 occ:0.80 FE1 A:SF4301 0.0 16.8 0.8 S3 A:SF4301 2.3 15.9 0.9 S4 A:SF4301 2.3 15.3 0.9 S A:H2S302 2.4 20.2 0.8 S2 A:SF4301 2.4 15.6 0.9 FE2 A:SF4301 2.7 14.5 0.9 O A:HOH406 2.7 29.2 1.0 FE3 A:SF4301 2.8 14.2 0.9 FE4 A:SF4301 2.8 14.8 0.9 S1 A:SF4301 3.9 14.4 0.9 NH2 A:ARG54 4.0 14.8 1.0 OG A:SER101 4.1 16.3 1.0 OE2 A:GLU45 4.2 17.3 1.0 CD A:ARG17 4.2 21.5 1.0 NH1 A:ARG17 4.2 24.6 1.0 OE1 A:GLU45 4.3 18.9 1.0 CD A:GLU45 4.3 17.6 1.0 SG A:CYS43 4.7 16.3 1.0 SG A:CYS10 4.7 17.2 1.0 CB A:SER101 4.8 16.2 1.0 SG A:CYS104 5.0 16.0 1.0 CA A:ARG17 5.0 16.0 1.0

Iron binding site 2 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (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 (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (S-Sad) Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:14.5 occ:0.90 FE2 A:SF4301 0.0 14.5 0.9 S4 A:SF4301 2.3 15.3 0.9 S3 A:SF4301 2.3 15.9 0.9 SG A:CYS10 2.3 17.2 1.0 S1 A:SF4301 2.3 14.4 0.9 FE1 A:SF4301 2.7 16.8 0.8 FE4 A:SF4301 2.7 14.8 0.9 FE3 A:SF4301 2.8 14.2 0.9 CB A:CYS10 3.3 16.4 1.0 S2 A:SF4301 3.9 15.6 0.9 N A:CYS10 4.0 15.3 1.0 CD A:ARG17 4.1 21.5 1.0 CB A:SER8 4.2 15.3 1.0 CA A:CYS10 4.3 15.4 1.0 CB A:LYS98 4.4 16.6 1.0 OG A:SER8 4.6 16.4 1.0 S A:H2S302 4.6 20.2 0.8 NH1 A:ARG17 4.7 24.6 1.0 SG A:CYS104 4.7 16.0 1.0 CG A:ARG17 4.8 20.4 1.0 CG A:LYS98 4.8 18.3 1.0 CG2 A:VAL16 4.9 19.9 1.0 N A:ALA9 4.9 14.9 1.0 SG A:CYS43 4.9 16.3 1.0

Iron binding site 3 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (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 (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (S-Sad) Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:14.2 occ:0.90 FE3 A:SF4301 0.0 14.2 0.9 S1 A:SF4301 2.3 14.4 0.9 S4 A:SF4301 2.3 15.3 0.9 S2 A:SF4301 2.3 15.6 0.9 SG A:CYS43 2.3 16.3 1.0 FE4 A:SF4301 2.7 14.8 0.9 FE1 A:SF4301 2.8 16.8 0.8 FE2 A:SF4301 2.8 14.5 0.9 CB A:CYS43 3.3 16.0 1.0 CA A:CYS43 3.7 15.1 1.0 S3 A:SF4301 3.9 15.9 0.9 CD A:PRO44 4.1 15.7 1.0 NH2 A:ARG54 4.2 14.8 1.0 C A:CYS43 4.2 15.4 1.0 N A:PRO44 4.3 14.6 1.0 CG2 A:VAL16 4.4 19.9 1.0 N A:GLU45 4.6 14.6 1.0 S A:H2S302 4.7 20.2 0.8 O A:VAL16 4.7 16.2 1.0 SG A:CYS104 4.9 16.0 1.0 SG A:CYS10 4.9 17.2 1.0 CB A:GLU45 4.9 15.1 1.0

Iron binding site 4 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (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 (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (S-Sad) Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:14.8 occ:0.90 FE4 A:SF4301 0.0 14.8 0.9 S2 A:SF4301 2.3 15.6 0.9 S3 A:SF4301 2.3 15.9 0.9 S1 A:SF4301 2.3 14.4 0.9 SG A:CYS104 2.3 16.0 1.0 FE2 A:SF4301 2.7 14.5 0.9 FE3 A:SF4301 2.7 14.2 0.9 FE1 A:SF4301 2.8 16.8 0.8 CB A:CYS104 3.5 15.6 1.0 S4 A:SF4301 3.9 15.3 0.9 CD A:PRO44 3.9 15.7 1.0 OG A:SER8 4.0 16.4 1.0 OG A:SER101 4.1 16.3 1.0 O A:HOH406 4.4 29.2 1.0 CB A:SER103 4.4 15.2 1.0 CB A:SER8 4.4 15.3 1.0 N A:CYS104 4.5 14.7 1.0 CA A:CYS104 4.6 14.5 1.0 CG A:PRO44 4.6 17.0 1.0 SG A:CYS10 4.7 17.2 1.0 CB A:SER101 4.8 16.2 1.0 SG A:CYS43 4.8 16.3 1.0 CB A:LYS98 4.9 16.6 1.0 N A:PRO44 4.9 14.6 1.0

Iron binding site 5 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (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 (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (S-Sad) Data) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:18.4 occ:0.75 FE1 B:SF4301 0.0 18.4 0.8 S3 B:SF4301 2.3 17.5 0.9 S B:H2S302 2.3 28.8 0.8 S4 B:SF4301 2.3 17.1 0.9 S2 B:SF4301 2.3 16.2 0.9 FE2 B:SF4301 2.7 15.1 0.9 FE3 B:SF4301 2.7 14.4 0.9 O B:HOH536 2.7 26.2 1.0 FE4 B:SF4301 2.8 15.2 0.9 S1 B:SF4301 3.9 14.0 0.9 OG B:SER101 3.9 17.2 1.0 OE2 B:GLU45 4.1 17.7 1.0 NH2 B:ARG54 4.1 18.7 1.0 NH2 B:ARG17 4.2 32.6 0.7 CD B:GLU45 4.2 18.4 1.0 OE1 B:GLU45 4.3 18.8 1.0 CD B:ARG17 4.5 28.0 0.7 CB B:SER101 4.5 16.9 1.0 SG B:CYS43 4.8 15.2 1.0 SG B:CYS10 4.8 17.1 1.0 SG B:CYS104 4.9 17.0 1.0

Iron binding site 6 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (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 (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (S-Sad) Data) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:15.1 occ:0.90 FE2 B:SF4301 0.0 15.1 0.9 S4 B:SF4301 2.3 17.1 0.9 S3 B:SF4301 2.3 17.5 0.9 SG B:CYS10 2.3 17.1 1.0 S1 B:SF4301 2.3 14.0 0.9 FE1 B:SF4301 2.7 18.4 0.8 FE4 B:SF4301 2.7 15.2 0.9 FE3 B:SF4301 2.7 14.4 0.9 CB B:CYS10 3.2 16.6 1.0 S2 B:SF4301 3.9 16.2 0.9 N B:CYS10 4.1 15.6 1.0 CD B:ARG17 4.1 28.0 0.7 CB B:SER8 4.3 13.6 1.0 CA B:CYS10 4.3 16.4 1.0 CB B:LYS98 4.4 16.0 1.0 CG2 B:VAL16 4.5 19.6 1.0 NH2 B:ARG17 4.6 32.6 0.7 OG B:SER8 4.7 15.2 1.0 O B:HOH536 4.7 26.2 1.0 SG B:CYS104 4.7 17.0 1.0 CG B:LYS98 4.8 19.0 1.0 S B:H2S302 4.8 28.8 0.8 SG B:CYS43 4.9 15.2 1.0 CG B:ARG17 4.9 24.5 0.7 N B:ALA9 5.0 15.0 1.0

Iron binding site 7 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (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 (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (S-Sad) Data) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:14.4 occ:0.90 FE3 B:SF4301 0.0 14.4 0.9 S1 B:SF4301 2.3 14.0 0.9 S2 B:SF4301 2.3 16.2 0.9 S4 B:SF4301 2.3 17.1 0.9 SG B:CYS43 2.3 15.2 1.0 FE1 B:SF4301 2.7 18.4 0.8 FE2 B:SF4301 2.7 15.1 0.9 FE4 B:SF4301 2.8 15.2 0.9 CB B:CYS43 3.3 15.3 1.0 CA B:CYS43 3.7 13.8 1.0 S3 B:SF4301 3.9 17.5 0.9 CG2 B:VAL16 4.1 19.6 1.0 NH2 B:ARG54 4.1 18.7 1.0 CD B:PRO44 4.2 13.8 1.0 C B:CYS43 4.3 14.4 1.0 N B:PRO44 4.4 14.2 1.0 N B:GLU45 4.6 14.0 1.0 O B:VAL16 4.7 18.9 1.0 CB B:VAL16 4.7 19.5 1.0 O B:HOH536 4.8 26.2 1.0 CB B:GLU45 4.8 15.2 1.0 S B:H2S302 4.9 28.8 0.8 SG B:CYS104 4.9 17.0 1.0 SG B:CYS10 4.9 17.1 1.0

Iron binding site 8 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) Soaked with 4-Thiouracil (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (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 (12.65 Kev, 7.125 Kev (Fe-Sad) and 6.5 Kev (S-Sad) Data) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:15.2 occ:0.90 FE4 B:SF4301 0.0 15.2 0.9 S2 B:SF4301 2.3 16.2 0.9 S3 B:SF4301 2.3 17.5 0.9 SG B:CYS104 2.3 17.0 1.0 S1 B:SF4301 2.3 14.0 0.9 FE2 B:SF4301 2.7 15.1 0.9 FE1 B:SF4301 2.8 18.4 0.8 FE3 B:SF4301 2.8 14.4 0.9 CB B:CYS104 3.4 16.1 1.0 CD B:PRO44 3.9 13.8 1.0 S4 B:SF4301 3.9 17.1 0.9 OG B:SER8 4.0 15.2 1.0 OG B:SER101 4.1 17.2 1.0 CB B:SER8 4.4 13.6 1.0 S B:H2S302 4.4 28.8 0.8 OG B:SER103 4.4 22.4 0.5 CB B:SER103 4.4 12.4 0.5 N B:CYS104 4.5 15.0 1.0 CB B:SER103 4.6 18.9 0.5 CA B:CYS104 4.6 15.4 1.0 CG B:PRO44 4.7 15.1 1.0 SG B:CYS10 4.7 17.1 1.0 CB B:SER101 4.7 16.9 1.0 SG B:CYS43 4.8 15.2 1.0 N B:PRO44 4.9 14.2 1.0 CB B:LYS98 4.9 16.0 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