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: Sun Dec 13 17:49:04 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy