Atomistry » Iron » PDB 6yj4-6zaf » 6z96
Atomistry »
  Iron »
    PDB 6yj4-6zaf »
      6z96 »

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)

Protein crystallography 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

Iron Binding Sites:

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 6z96

Go back to Iron Binding Sites List in 6z96
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 6z96

Go back to Iron Binding Sites List in 6z96
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 6z96

Go back to Iron Binding Sites List in 6z96
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 6z96

Go back to Iron Binding Sites List in 6z96
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 6z96

Go back to Iron Binding Sites List in 6z96
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 6z96

Go back to Iron Binding Sites List in 6z96
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 6z96

Go back to Iron Binding Sites List in 6z96
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 6z96

Go back to Iron Binding Sites List in 6z96
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

Reference:

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
Page generated: Wed Aug 7 17:24:35 2024

Last articles

Cl in 5L47
Cl in 5L3H
Cl in 5L3I
Cl in 5L2O
Cl in 5L3X
Cl in 5L39
Cl in 5L38
Cl in 5L35
Cl in 5L2U
Cl in 5L2N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy