Iron in PDB 5mkq: Ttua Enzyme Containing A [4FE-4S]

Protein crystallography data

The structure of Ttua Enzyme Containing A [4FE-4S], PDB code: 5mkq was solved by S.Arragain, O.Bimai, P.Legrand, B.Golinelli-Pimpaneau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.88 / 2.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.450, 72.190, 127.950, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.4

Other elements in 5mkq:

The structure of Ttua Enzyme Containing A [4FE-4S] also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Ttua Enzyme Containing A [4FE-4S] (pdb code 5mkq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Ttua Enzyme Containing A [4FE-4S], PDB code: 5mkq:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5mkq

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Iron binding site 1 out of 8 in the Ttua Enzyme Containing A [4FE-4S]


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ttua Enzyme Containing A [4FE-4S] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:0.1
occ:0.95
 FE1 A:SF4403 0.0 0.1 1.0
S3 A:SF4403 2.3 0.9 0.7
S2 A:SF4403 2.3 0.6 0.7
S4 A:SF4403 2.3 0.8 1.0
CB A:CYS220 2.5 0.5 1.0
SG A:CYS220 2.5 0.3 1.0
FE2 A:SF4403 2.7 0.8 1.0
FE3 A:SF4403 2.7 0.7 1.0
FE4 A:SF4403 2.8 0.7 0.7
S1 A:SF4403 3.9 0.7 0.7
CA A:CYS220 4.0 1.0 1.0
SG A:CYS128 4.5 0.3 1.0
C A:CYS220 4.6 0.9 1.0
N A:CYS220 4.6 0.1 1.0
SG A:CYS131 4.7 0.0 1.0
O A:CYS220 4.9 0.2 1.0

Iron binding site 2 out of 8 in 5mkq

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Iron binding site 2 out of 8 in the Ttua Enzyme Containing A [4FE-4S]


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ttua Enzyme Containing A [4FE-4S] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:0.8
occ:0.95
 FE2 A:SF4403 0.0 0.8 1.0
SG A:CYS131 2.1 0.0 1.0
S4 A:SF4403 2.3 0.8 1.0
S3 A:SF4403 2.3 0.9 0.7
S1 A:SF4403 2.3 0.7 0.7
FE1 A:SF4403 2.7 0.1 1.0
FE3 A:SF4403 2.7 0.7 1.0
FE4 A:SF4403 2.8 0.7 0.7
CB A:CYS131 3.1 0.6 1.0
S2 A:SF4403 3.9 0.6 0.7
CE A:LYS135 4.2 0.3 1.0
CA A:CYS131 4.4 0.5 1.0
CD1 A:LEU81 4.5 82.2 1.0
NZ A:LYS135 4.6 0.7 1.0
C A:CYS131 4.6 99.3 1.0
SG A:CYS220 4.7 0.3 1.0
N A:GLY132 4.8 92.2 1.0
CA A:CYS128 4.9 1.0 1.0

Iron binding site 3 out of 8 in 5mkq

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Iron binding site 3 out of 8 in the Ttua Enzyme Containing A [4FE-4S]


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ttua Enzyme Containing A [4FE-4S] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:0.7
occ:0.95
 FE3 A:SF4403 0.0 0.7 1.0
S2 A:SF4403 2.3 0.6 0.7
S1 A:SF4403 2.3 0.7 0.7
S4 A:SF4403 2.3 0.8 1.0
SG A:CYS128 2.5 0.3 1.0
FE1 A:SF4403 2.7 0.1 1.0
FE2 A:SF4403 2.7 0.8 1.0
FE4 A:SF4403 2.8 0.7 0.7
CA A:CYS128 3.4 1.0 1.0
CB A:CYS128 3.4 0.1 1.0
S3 A:SF4403 3.9 0.9 0.7
O A:CYS128 4.2 0.3 1.0
N A:CYS128 4.3 0.1 1.0
C A:CYS128 4.3 0.8 1.0
SG A:CYS131 4.6 0.0 1.0
CB A:CYS131 4.6 0.6 1.0
SG A:CYS220 4.8 0.3 1.0
CB A:CYS220 5.0 0.5 1.0
C A:TYR222 5.0 0.7 1.0

Iron binding site 4 out of 8 in 5mkq

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Iron binding site 4 out of 8 in the Ttua Enzyme Containing A [4FE-4S]


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ttua Enzyme Containing A [4FE-4S] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:0.7
occ:0.70
 FE4 A:SF4403 0.0 0.7 0.7
S1 A:SF4403 2.3 0.7 0.7
S2 A:SF4403 2.3 0.6 0.7
S3 A:SF4403 2.3 0.9 0.7
FE2 A:SF4403 2.8 0.8 1.0
FE1 A:SF4403 2.8 0.1 1.0
FE3 A:SF4403 2.8 0.7 1.0
S4 A:SF4403 3.9 0.8 1.0
NZ A:LYS135 4.2 0.7 1.0
SG A:CYS131 4.6 0.0 1.0
CE A:LYS135 4.6 0.3 1.0
CB A:CYS220 4.6 0.5 1.0

Iron binding site 5 out of 8 in 5mkq

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Iron binding site 5 out of 8 in the Ttua Enzyme Containing A [4FE-4S]


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ttua Enzyme Containing A [4FE-4S] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:0.6
occ:0.95
 FE1 B:SF4403 0.0 0.6 1.0
S4 B:SF4403 2.3 0.0 0.7
S3 B:SF4403 2.3 0.1 1.0
S2 B:SF4403 2.3 0.7 0.7
SG B:CYS128 2.5 1.0 1.0
FE2 B:SF4403 2.7 0.8 1.0
FE4 B:SF4403 2.7 0.8 1.0
FE3 B:SF4403 2.7 0.9 0.7
CA B:CYS128 3.4 0.4 1.0
CB B:CYS128 3.4 0.7 1.0
S1 B:SF4403 3.9 0.0 0.7
O B:CYS128 4.1 0.8 1.0
C B:CYS128 4.3 0.2 1.0
N B:CYS128 4.3 0.2 1.0
SG B:CYS131 4.6 93.4 1.0
CB B:CYS131 4.7 90.1 1.0
SG B:CYS220 4.9 0.5 1.0
C B:TYR222 5.0 0.8 1.0

Iron binding site 6 out of 8 in 5mkq

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Iron binding site 6 out of 8 in the Ttua Enzyme Containing A [4FE-4S]


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Ttua Enzyme Containing A [4FE-4S] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:0.8
occ:0.95
 FE2 B:SF4403 0.0 0.8 1.0
SG B:CYS131 2.1 93.4 1.0
S3 B:SF4403 2.3 0.1 1.0
S4 B:SF4403 2.3 0.0 0.7
S1 B:SF4403 2.3 0.0 0.7
FE4 B:SF4403 2.7 0.8 1.0
FE1 B:SF4403 2.7 0.6 1.0
FE3 B:SF4403 2.7 0.9 0.7
CB B:CYS131 3.0 90.1 1.0
S2 B:SF4403 3.9 0.7 0.7
CE B:LYS135 4.2 0.4 1.0
CA B:CYS131 4.3 90.3 1.0
C B:CYS131 4.5 91.1 1.0
NZ B:LYS135 4.6 0.3 1.0
N B:GLY132 4.6 86.0 1.0
CD1 B:LEU81 4.7 75.6 1.0
CA B:CYS128 4.7 0.4 1.0
SG B:CYS220 4.8 0.5 1.0
O B:CYS128 4.9 0.8 1.0
O B:PRO127 4.9 0.0 1.0

Iron binding site 7 out of 8 in 5mkq

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Iron binding site 7 out of 8 in the Ttua Enzyme Containing A [4FE-4S]


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Ttua Enzyme Containing A [4FE-4S] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:0.9
occ:0.70
 FE3 B:SF4403 0.0 0.9 0.7
S2 B:SF4403 2.3 0.7 0.7
S1 B:SF4403 2.3 0.0 0.7
S4 B:SF4403 2.3 0.0 0.7
FE2 B:SF4403 2.7 0.8 1.0
FE1 B:SF4403 2.7 0.6 1.0
FE4 B:SF4403 2.7 0.8 1.0
S3 B:SF4403 3.9 0.1 1.0
NZ B:LYS135 4.2 0.3 1.0
CE B:LYS135 4.6 0.4 1.0
SG B:CYS131 4.6 93.4 1.0
CB B:CYS220 4.9 0.7 1.0

Iron binding site 8 out of 8 in 5mkq

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Iron binding site 8 out of 8 in the Ttua Enzyme Containing A [4FE-4S]


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Ttua Enzyme Containing A [4FE-4S] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:0.8
occ:0.95
 FE4 B:SF4403 0.0 0.8 1.0
S3 B:SF4403 2.3 0.1 1.0
S1 B:SF4403 2.3 0.0 0.7
S2 B:SF4403 2.3 0.7 0.7
CB B:CYS220 2.6 0.7 1.0
SG B:CYS220 2.7 0.5 1.0
FE2 B:SF4403 2.7 0.8 1.0
FE1 B:SF4403 2.7 0.6 1.0
FE3 B:SF4403 2.7 0.9 0.7
S4 B:SF4403 3.9 0.0 0.7
CA B:CYS220 4.1 0.9 1.0
SG B:CYS128 4.5 1.0 1.0
SG B:CYS131 4.6 93.4 1.0
N B:CYS220 4.7 0.5 1.0
C B:CYS220 4.8 0.3 1.0
O B:CYS220 5.0 0.9 1.0

Reference:

S.Arragain, O.Bimai, P.Legrand, S.Caillat, J.L.Ravanat, N.Touati, L.Binet, M.Atta, M.Fontecave, B.Golinelli-Pimpaneau. Nonredox Thiolation in Trna Occurring Via Sulfur Activation By A [4FE-4S] Cluster. Proc. Natl. Acad. Sci. V. 114 7355 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28655838
DOI: 10.1073/PNAS.1700902114
Page generated: Tue Aug 6 06:01:40 2024

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