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Iron in PDB 7mjz: The Structure of Miab with Pentasulfide Bridge

Enzymatic activity of The Structure of Miab with Pentasulfide Bridge

All present enzymatic activity of The Structure of Miab with Pentasulfide Bridge:
2.8.4.3;

Protein crystallography data

The structure of The Structure of Miab with Pentasulfide Bridge, PDB code: 7mjz was solved by O.A.Esakova, T.L.Grove, N.H.Yennawar, A.J.Arcinas, B.Wang, C.Krebs, S.C.Almo, S.J.Booker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.68 / 2.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.215, 81.125, 118.326, 90, 90, 90
R / Rfree (%) 18.2 / 22.1

Other elements in 7mjz:

The structure of The Structure of Miab with Pentasulfide Bridge also contains other interesting chemical elements:

Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the The Structure of Miab with Pentasulfide Bridge (pdb code 7mjz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the The Structure of Miab with Pentasulfide Bridge, PDB code: 7mjz:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 7mjz

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Iron binding site 1 out of 8 in the The Structure of Miab with Pentasulfide Bridge


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Structure of Miab with Pentasulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:27.4
occ:1.00
 FE1 A:SF4501 0.0 27.4 1.0
SG A:CYS97 2.2 32.3 1.0
S4 A:SF4501 2.3 30.3 1.0
S3 A:SF4501 2.3 28.1 1.0
S2 A:SF4501 2.3 29.3 1.0
FE2 A:SF4501 2.7 27.2 1.0
FE4 A:SF4501 2.7 27.7 1.0
FE3 A:SF4501 2.7 31.4 1.0
CB A:CYS97 3.3 32.0 1.0
S1 A:SF4501 3.9 28.7 1.0
NH1 A:ARG184 4.3 31.0 1.0
CD A:ARG184 4.5 27.1 1.0
CA A:CYS97 4.6 30.0 1.0
SG A:CYS63 4.7 31.4 1.0
N A:SER64 4.7 38.4 1.0
CA A:CYS63 4.7 29.1 1.0
SG A:CYS27 4.8 28.7 1.0
OG A:SER64 4.9 52.9 1.0
CG2 A:VAL180 5.0 25.7 1.0
CB A:CYS63 5.0 33.7 1.0

Iron binding site 2 out of 8 in 7mjz

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Iron binding site 2 out of 8 in the The Structure of Miab with Pentasulfide Bridge


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Structure of Miab with Pentasulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:27.2
occ:1.00
 FE2 A:SF4501 0.0 27.2 1.0
SG A:CYS27 2.2 28.7 1.0
S3 A:SF4501 2.3 28.1 1.0
S4 A:SF4501 2.3 30.3 1.0
S1 A:SF4501 2.3 28.7 1.0
FE4 A:SF4501 2.7 27.7 1.0
FE1 A:SF4501 2.7 27.4 1.0
FE3 A:SF4501 2.7 31.4 1.0
CB A:CYS27 3.3 27.3 1.0
N A:CYS27 3.6 28.5 1.0
S2 A:SF4501 3.9 29.3 1.0
CA A:CYS27 4.1 28.7 1.0
CB A:ASN30 4.5 27.5 1.0
C A:GLY26 4.6 31.7 1.0
CA A:GLY26 4.7 30.2 1.0
SG A:CYS97 4.7 32.3 1.0
SG A:CYS63 4.8 31.4 1.0
C A:CYS27 4.9 27.9 1.0
N A:ASN30 5.0 23.6 1.0

Iron binding site 3 out of 8 in 7mjz

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Iron binding site 3 out of 8 in the The Structure of Miab with Pentasulfide Bridge


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Structure of Miab with Pentasulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:31.4
occ:1.00
 FE3 A:SF4501 0.0 31.4 1.0
S1 A:SF4501 2.3 28.7 1.0
S2 A:SF4501 2.3 29.3 1.0
S4 A:SF4501 2.3 30.3 1.0
S5 A:PS5503 2.6 54.6 1.0
FE4 A:SF4501 2.7 27.7 1.0
FE2 A:SF4501 2.7 27.2 1.0
FE1 A:SF4501 2.7 27.4 1.0
S4 A:PS5503 3.5 93.3 1.0
S3 A:SF4501 3.9 28.1 1.0
CG2 A:VAL180 3.9 25.7 1.0
S3 A:PS5503 4.4 99.0 1.0
SG A:CYS27 4.6 28.7 1.0
SG A:CYS97 4.7 32.3 1.0
CB A:ILE65 4.7 45.5 1.0
SG A:CYS63 4.8 31.4 1.0
CD1 A:ILE179 4.8 32.9 1.0
CG1 A:ILE65 4.8 54.5 1.0

Iron binding site 4 out of 8 in 7mjz

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Iron binding site 4 out of 8 in the The Structure of Miab with Pentasulfide Bridge


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Structure of Miab with Pentasulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:27.7
occ:1.00
 FE4 A:SF4501 0.0 27.7 1.0
SG A:CYS63 2.2 31.4 1.0
S1 A:SF4501 2.3 28.7 1.0
S3 A:SF4501 2.3 28.1 1.0
S2 A:SF4501 2.3 29.3 1.0
FE3 A:SF4501 2.7 31.4 1.0
FE2 A:SF4501 2.7 27.2 1.0
FE1 A:SF4501 2.7 27.4 1.0
CB A:CYS63 3.2 33.7 1.0
CA A:CYS63 3.8 29.1 1.0
S4 A:SF4501 3.9 30.3 1.0
N A:SER64 4.0 38.4 1.0
CA A:GLY26 4.1 30.2 1.0
CB A:ILE65 4.1 45.5 1.0
N A:ILE65 4.2 53.3 1.0
C A:CYS63 4.3 47.3 1.0
N A:CYS27 4.4 28.5 1.0
CA A:ILE65 4.7 53.4 1.0
SG A:CYS97 4.7 32.3 1.0
CG2 A:ILE65 4.8 52.0 1.0
SG A:CYS27 4.8 28.7 1.0
C A:GLY26 4.8 31.7 1.0
CG1 A:ILE65 5.0 54.5 1.0

Iron binding site 5 out of 8 in 7mjz

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Iron binding site 5 out of 8 in the The Structure of Miab with Pentasulfide Bridge


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Structure of Miab with Pentasulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:31.5
occ:1.00
 FE1 A:SF4502 0.0 31.5 1.0
S4 A:SF4502 2.3 33.8 1.0
S3 A:SF4502 2.3 32.6 1.0
S2 A:SF4502 2.3 30.1 1.0
SG A:CYS175 2.3 29.5 1.0
FE3 A:SF4502 2.7 28.5 1.0
FE4 A:SF4502 2.7 25.8 1.0
FE2 A:SF4502 2.7 35.4 1.0
CB A:CYS175 3.3 26.2 1.0
S1 A:SF4502 3.9 32.8 1.0
NH1 A:ARG293 3.9 22.6 1.0
N A:CYS175 4.0 31.4 1.0
CB A:ASN173 4.2 33.7 1.0
CA A:CYS175 4.3 31.9 1.0
CB A:CYS178 4.5 31.0 1.0
O A:HOH804 4.6 27.7 1.0
SG A:CYS178 4.7 33.8 1.0
OH A:TYR177 4.7 23.5 1.0
SG A:CYS171 4.7 28.8 1.0
ND2 A:ASN173 4.7 26.6 1.0
N A:PHE174 5.0 34.8 1.0
S1 A:PS5503 5.0 41.7 1.0

Iron binding site 6 out of 8 in 7mjz

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Iron binding site 6 out of 8 in the The Structure of Miab with Pentasulfide Bridge


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Structure of Miab with Pentasulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:35.4
occ:1.00
 FE2 A:SF4502 0.0 35.4 1.0
S4 A:SF4502 2.3 33.8 1.0
S1 A:SF4502 2.3 32.8 1.0
S3 A:SF4502 2.3 32.6 1.0
S1 A:PS5503 2.4 41.7 1.0
FE3 A:SF4502 2.7 28.5 1.0
FE4 A:SF4502 2.7 25.8 1.0
FE1 A:SF4502 2.7 31.5 1.0
S2 A:PS5503 3.5 100.6 1.0
S2 A:SF4502 3.9 30.1 1.0
O A:HOH723 4.1 30.5 1.0
S3 A:PS5503 4.4 99.0 1.0
O A:HOH817 4.4 27.3 1.0
O A:HOH884 4.6 36.4 1.0
NH1 A:ARG293 4.6 22.6 1.0
SG A:CYS178 4.7 33.8 1.0
SG A:CYS171 4.7 28.8 1.0
O A:GLN215 4.7 23.8 1.0
NE2 A:GLN215 4.8 30.7 1.0
SG A:CYS175 4.8 29.5 1.0
CB A:GLN215 4.9 27.9 1.0

Iron binding site 7 out of 8 in 7mjz

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Iron binding site 7 out of 8 in the The Structure of Miab with Pentasulfide Bridge


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Structure of Miab with Pentasulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:28.5
occ:1.00
 FE3 A:SF4502 0.0 28.5 1.0
SG A:CYS178 2.2 33.8 1.0
S4 A:SF4502 2.3 33.8 1.0
S2 A:SF4502 2.3 30.1 1.0
S1 A:SF4502 2.3 32.8 1.0
FE2 A:SF4502 2.7 35.4 1.0
FE1 A:SF4502 2.7 31.5 1.0
FE4 A:SF4502 2.7 25.8 1.0
CB A:CYS178 3.0 31.0 1.0
S3 A:SF4502 3.9 32.6 1.0
CB A:VAL180 4.1 29.9 1.0
CD A:PRO181 4.3 38.7 1.0
CG2 A:VAL180 4.3 25.7 1.0
CA A:CYS178 4.5 32.2 1.0
SG A:CYS175 4.6 29.5 1.0
N A:VAL180 4.8 38.2 1.0
CB A:CYS175 4.8 26.2 1.0
S1 A:PS5503 4.8 41.7 1.0
SG A:CYS171 4.9 28.8 1.0
CG1 A:VAL180 4.9 27.2 1.0
S2 A:PS5503 5.0 100.6 1.0

Iron binding site 8 out of 8 in 7mjz

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Iron binding site 8 out of 8 in the The Structure of Miab with Pentasulfide Bridge


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Structure of Miab with Pentasulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:25.8
occ:1.00
 FE4 A:SF4502 0.0 25.8 1.0
S1 A:SF4502 2.3 32.8 1.0
S2 A:SF4502 2.3 30.1 1.0
SG A:CYS171 2.3 28.8 1.0
S3 A:SF4502 2.3 32.6 1.0
FE1 A:SF4502 2.7 31.5 1.0
FE2 A:SF4502 2.7 35.4 1.0
FE3 A:SF4502 2.7 28.5 1.0
CB A:CYS171 3.3 28.4 1.0
S4 A:SF4502 3.9 33.8 1.0
ND2 A:ASN173 4.0 26.6 1.0
CB A:ASN173 4.0 33.7 1.0
CG A:ASN173 4.5 31.0 1.0
CB A:GLN215 4.5 27.9 1.0
N A:ASN173 4.7 28.3 1.0
CA A:CYS171 4.7 29.6 1.0
SG A:CYS178 4.8 33.8 1.0
SG A:CYS175 4.8 29.5 1.0
CD A:PRO181 4.9 38.7 1.0
CG A:PRO181 4.9 37.5 1.0
S1 A:PS5503 4.9 41.7 1.0
CA A:ASN173 4.9 37.2 1.0
N A:PHE174 5.0 34.8 1.0

Reference:

O.A.Esakova, T.L.Grove, N.H.Yennawar, A.J.Arcinas, B.Wang, C.Krebs, S.C.Almo, S.J.Booker. Structural Basis For Trna Methylthiolation By the Radical Sam Enzyme Miab Nature 2021.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-021-03904-6
Page generated: Thu Aug 8 09:18:07 2024

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