Atomistry » Iron » PDB 6yj4-6zaf » 6z93
Atomistry »
  Iron »
    PDB 6yj4-6zaf »
      6z93 »

Iron in PDB 6z93: [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)

Protein crystallography data

The structure of [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ), PDB code: 6z93 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) 29.03 / 1.51
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.381, 85.812, 39.512, 90.00, 93.92, 90.00
R / Rfree (%) 16.8 / 19.4

Other elements in 6z93:

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

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ) (pdb code 6z93). 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), PDB code: 6z93:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6z93

Go back to Iron Binding Sites List in 6z93
Iron binding site 1 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:18.9
occ:0.90
FE1 A:SF4301 0.0 18.9 0.9
O2 A:EDO302 2.3 24.7 1.0
S3 A:SF4301 2.3 18.3 0.9
S2 A:SF4301 2.3 17.4 0.9
S4 A:SF4301 2.3 18.0 0.9
O1 A:EDO302 2.5 24.3 1.0
FE3 A:SF4301 2.7 16.4 0.9
FE4 A:SF4301 2.8 16.5 0.9
FE2 A:SF4301 2.8 16.6 0.9
C1 A:EDO302 3.2 25.4 1.0
C2 A:EDO302 3.2 25.9 1.0
S1 A:SF4301 3.9 17.1 0.9
NH2 A:ARG54 3.9 19.3 1.0
OG A:SER101 4.1 19.9 1.0
OE2 A:GLU45 4.1 18.9 1.0
CD A:GLU45 4.2 21.6 1.0
OE1 A:GLU45 4.2 23.3 1.0
CD A:ARG17 4.3 26.0 1.0
NH1 A:ARG17 4.3 26.0 1.0
SG A:CYS43 4.7 18.9 1.0
SG A:CYS10 4.8 19.8 1.0
CB A:SER101 4.8 17.9 1.0
CA A:ARG17 5.0 19.4 1.0
CG A:GLU45 5.0 19.1 1.0
SG A:CYS104 5.0 17.9 1.0

Iron binding site 2 out of 8 in 6z93

Go back to Iron Binding Sites List in 6z93
Iron binding site 2 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:16.6
occ:0.90
FE2 A:SF4301 0.0 16.6 0.9
SG A:CYS10 2.3 19.8 1.0
S3 A:SF4301 2.3 18.3 0.9
S1 A:SF4301 2.3 17.1 0.9
S4 A:SF4301 2.3 18.0 0.9
FE4 A:SF4301 2.7 16.5 0.9
FE1 A:SF4301 2.8 18.9 0.9
FE3 A:SF4301 2.8 16.4 0.9
CB A:CYS10 3.2 18.6 1.0
S2 A:SF4301 4.0 17.4 0.9
N A:CYS10 4.0 18.1 1.0
CD A:ARG17 4.1 26.0 1.0
CB A:SER8 4.2 18.6 1.0
CA A:CYS10 4.2 18.8 1.0
CB A:LYS98 4.4 18.6 1.0
O2 A:EDO302 4.4 24.7 1.0
OG A:SER8 4.5 20.3 1.0
NH1 A:ARG17 4.7 26.0 1.0
SG A:CYS104 4.7 17.9 1.0
CG A:LYS98 4.8 19.8 1.0
CG2 A:VAL16 4.8 21.8 1.0
CG A:ARG17 4.8 24.2 1.0
N A:ALA9 4.9 16.8 1.0
SG A:CYS43 4.9 18.9 1.0
C A:SER8 4.9 17.3 1.0
CA A:SER8 5.0 16.9 1.0

Iron binding site 3 out of 8 in 6z93

Go back to Iron Binding Sites List in 6z93
Iron binding site 3 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:16.4
occ:0.90
FE3 A:SF4301 0.0 16.4 0.9
SG A:CYS43 2.3 18.9 1.0
S1 A:SF4301 2.3 17.1 0.9
S4 A:SF4301 2.3 18.0 0.9
S2 A:SF4301 2.3 17.4 0.9
FE1 A:SF4301 2.7 18.9 0.9
FE4 A:SF4301 2.8 16.5 0.9
FE2 A:SF4301 2.8 16.6 0.9
CB A:CYS43 3.3 16.6 1.0
CA A:CYS43 3.7 16.9 1.0
S3 A:SF4301 3.9 18.3 0.9
CD A:PRO44 4.1 16.2 1.0
C A:CYS43 4.2 17.1 1.0
NH2 A:ARG54 4.3 19.3 1.0
CG2 A:VAL16 4.3 21.8 1.0
N A:PRO44 4.3 16.6 1.0
O2 A:EDO302 4.5 24.7 1.0
N A:GLU45 4.6 17.2 1.0
O A:VAL16 4.7 20.0 1.0
SG A:CYS104 4.9 17.9 1.0
CB A:GLU45 4.9 17.9 1.0
SG A:CYS10 4.9 19.8 1.0
O1 A:EDO302 4.9 24.3 1.0
CB A:VAL16 5.0 21.6 1.0

Iron binding site 4 out of 8 in 6z93

Go back to Iron Binding Sites List in 6z93
Iron binding site 4 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:16.5
occ:0.90
FE4 A:SF4301 0.0 16.5 0.9
S3 A:SF4301 2.3 18.3 0.9
S2 A:SF4301 2.3 17.4 0.9
S1 A:SF4301 2.3 17.1 0.9
SG A:CYS104 2.3 17.9 1.0
FE2 A:SF4301 2.7 16.6 0.9
FE1 A:SF4301 2.8 18.9 0.9
FE3 A:SF4301 2.8 16.4 0.9
CB A:CYS104 3.4 15.5 1.0
S4 A:SF4301 3.9 18.0 0.9
OG A:SER8 3.9 20.3 1.0
CD A:PRO44 3.9 16.2 1.0
OG A:SER101 4.0 19.9 1.0
O1 A:EDO302 4.1 24.3 1.0
CB A:SER8 4.4 18.6 1.0
CB A:SER103 4.5 16.8 1.0
N A:CYS104 4.5 15.2 1.0
CA A:CYS104 4.6 15.7 1.0
CG A:PRO44 4.7 18.1 1.0
SG A:CYS10 4.7 19.8 1.0
CB A:SER101 4.7 17.9 1.0
CB A:LYS98 4.8 18.6 1.0
SG A:CYS43 4.8 18.9 1.0
N A:PRO44 5.0 16.6 1.0

Iron binding site 5 out of 8 in 6z93

Go back to Iron Binding Sites List in 6z93
Iron binding site 5 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:21.7
occ:0.90
FE1 B:SF4301 0.0 21.7 0.9
S3 B:SF4301 2.3 19.9 0.9
S4 B:SF4301 2.3 20.6 0.9
S2 B:SF4301 2.3 19.6 0.9
O2 B:EDO302 2.4 26.7 1.0
O1 B:EDO302 2.4 27.2 1.0
FE3 B:SF4301 2.7 17.2 0.9
FE2 B:SF4301 2.8 18.0 0.9
FE4 B:SF4301 2.8 17.8 0.9
C1 B:EDO302 3.2 28.3 1.0
C2 B:EDO302 3.3 27.9 1.0
S1 B:SF4301 3.9 17.1 0.9
NH2 B:ARG54 4.0 23.1 1.0
OG B:SER101 4.1 21.7 1.0
OE2 B:GLU45 4.1 22.6 1.0
CD B:GLU45 4.2 22.3 1.0
OE1 B:GLU45 4.2 22.7 1.0
CD B:ARG17 4.3 35.9 1.0
NH2 B:ARG17 4.5 41.4 1.0
CB B:SER101 4.7 20.3 1.0
SG B:CYS43 4.7 18.7 1.0
SG B:CYS10 4.8 20.4 1.0
CG B:GLU45 4.9 18.5 1.0
SG B:CYS104 5.0 19.4 1.0

Iron binding site 6 out of 8 in 6z93

Go back to Iron Binding Sites List in 6z93
Iron binding site 6 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:18.0
occ:0.90
FE2 B:SF4301 0.0 18.0 0.9
SG B:CYS10 2.3 20.4 1.0
S4 B:SF4301 2.3 20.6 0.9
S3 B:SF4301 2.3 19.9 0.9
S1 B:SF4301 2.3 17.1 0.9
FE4 B:SF4301 2.7 17.8 0.9
FE1 B:SF4301 2.8 21.7 0.9
FE3 B:SF4301 2.8 17.2 0.9
CB B:CYS10 3.2 20.0 1.0
S2 B:SF4301 3.9 19.6 0.9
N B:CYS10 4.0 19.5 1.0
CD B:ARG17 4.1 35.9 1.0
CB B:SER8 4.2 17.4 1.0
CA B:CYS10 4.2 20.4 1.0
CB B:LYS98 4.4 20.8 1.0
O1 B:EDO302 4.6 27.2 1.0
OG B:SER8 4.6 18.3 1.0
NH2 B:ARG17 4.6 41.4 1.0
SG B:CYS104 4.7 19.4 1.0
CG B:LYS98 4.8 22.6 1.0
CG2 B:VAL16 4.8 24.6 1.0
CG B:ARG17 4.9 33.3 1.0
SG B:CYS43 4.9 18.7 1.0
O2 B:EDO302 4.9 26.7 1.0
N B:ALA9 5.0 17.7 1.0

Iron binding site 7 out of 8 in 6z93

Go back to Iron Binding Sites List in 6z93
Iron binding site 7 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:17.2
occ:0.90
FE3 B:SF4301 0.0 17.2 0.9
SG B:CYS43 2.3 18.7 1.0
S1 B:SF4301 2.3 17.1 0.9
S2 B:SF4301 2.3 19.6 0.9
S4 B:SF4301 2.3 20.6 0.9
FE1 B:SF4301 2.7 21.7 0.9
FE4 B:SF4301 2.8 17.8 0.9
FE2 B:SF4301 2.8 18.0 0.9
CB B:CYS43 3.3 17.4 1.0
CA B:CYS43 3.7 15.9 1.0
S3 B:SF4301 3.9 19.9 0.9
CD B:PRO44 4.2 15.9 1.0
NH2 B:ARG54 4.2 23.1 1.0
C B:CYS43 4.2 15.2 1.0
CG2 B:VAL16 4.3 24.6 1.0
N B:PRO44 4.4 16.1 1.0
N B:GLU45 4.6 16.1 1.0
O1 B:EDO302 4.6 27.2 1.0
O B:VAL16 4.7 24.2 1.0
CB B:GLU45 4.8 18.1 1.0
SG B:CYS104 4.9 19.4 1.0
O2 B:EDO302 4.9 26.7 1.0
SG B:CYS10 4.9 20.4 1.0
CB B:VAL16 4.9 24.2 1.0

Iron binding site 8 out of 8 in 6z93

Go back to Iron Binding Sites List in 6z93
Iron binding site 8 out of 8 in the [4FE-4S]-Dependent Thiouracil Desulfidase Tuds (DUF523VCZ)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:17.8
occ:0.90
FE4 B:SF4301 0.0 17.8 0.9
S3 B:SF4301 2.3 19.9 0.9
SG B:CYS104 2.3 19.4 1.0
S1 B:SF4301 2.3 17.1 0.9
S2 B:SF4301 2.3 19.6 0.9
FE2 B:SF4301 2.7 18.0 0.9
FE3 B:SF4301 2.8 17.2 0.9
FE1 B:SF4301 2.8 21.7 0.9
CB B:CYS104 3.5 18.3 1.0
OG B:SER8 3.9 18.3 1.0
CD B:PRO44 3.9 15.9 1.0
S4 B:SF4301 3.9 20.6 0.9
OG B:SER101 4.0 21.7 1.0
O2 B:EDO302 4.2 26.7 1.0
CB B:SER8 4.4 17.4 1.0
CB B:SER103 4.4 15.8 0.5
OG B:SER103 4.4 23.7 0.5
N B:CYS104 4.5 18.1 1.0
CA B:CYS104 4.6 18.1 1.0
CB B:SER103 4.7 20.8 0.5
CG B:PRO44 4.7 17.4 1.0
SG B:CYS10 4.7 20.4 1.0
CB B:SER101 4.7 20.3 1.0
CB B:LYS98 4.8 20.8 1.0
SG B:CYS43 4.8 18.7 1.0
N B:PRO44 4.9 16.1 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 17:17:19 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy