Iron in PDB 7mjv: Miab in the Complex with S-Adenosylmethionine and Rna

Enzymatic activity of Miab in the Complex with S-Adenosylmethionine and Rna

All present enzymatic activity of Miab in the Complex with S-Adenosylmethionine and Rna:
2.8.4.3;

Protein crystallography data

The structure of Miab in the Complex with S-Adenosylmethionine and Rna, PDB code: 7mjv 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) 45.51 / 2.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.155, 81.442, 109.751, 90, 90, 90
R / Rfree (%) 24.3 / 27.3

Other elements in 7mjv:

The structure of Miab in the Complex with S-Adenosylmethionine and Rna also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Miab in the Complex with S-Adenosylmethionine and Rna (pdb code 7mjv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Miab in the Complex with S-Adenosylmethionine and Rna, PDB code: 7mjv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 7mjv

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Iron binding site 1 out of 7 in the Miab in the Complex with S-Adenosylmethionine and Rna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Miab in the Complex with S-Adenosylmethionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:42.6
occ:1.00
FE1 A:F3S501 0.0 42.6 1.0
SG A:CYS97 2.2 48.8 1.0
S3 A:F3S501 2.2 44.2 1.0
S1 A:F3S501 2.3 44.0 1.0
S2 A:F3S501 2.3 48.5 1.0
FE4 A:F3S501 2.5 43.4 1.0
FE3 A:F3S501 2.7 40.1 1.0
CB A:CYS97 3.2 55.2 1.0
S4 A:F3S501 3.6 41.1 1.0
CA A:CYS63 4.4 55.9 1.0
SG A:CYS63 4.5 49.5 1.0
O A:THR62 4.5 63.3 1.0
N A:SER64 4.6 56.6 1.0
CA A:CYS97 4.6 57.1 1.0
OG1 A:THR183 4.6 47.8 1.0
CB A:CYS63 4.8 55.4 1.0
SG A:CYS27 4.8 47.4 1.0
OD1 A:ASN30 4.9 54.2 1.0
N A:CYS97 4.9 53.2 1.0

Iron binding site 2 out of 7 in 7mjv

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Iron binding site 2 out of 7 in the Miab in the Complex with S-Adenosylmethionine and Rna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Miab in the Complex with S-Adenosylmethionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:40.1
occ:1.00
FE3 A:F3S501 0.0 40.1 1.0
S3 A:F3S501 2.1 44.2 1.0
SG A:CYS27 2.2 47.4 1.0
S4 A:F3S501 2.2 41.1 1.0
S1 A:F3S501 2.2 44.0 1.0
FE1 A:F3S501 2.7 42.6 1.0
FE4 A:F3S501 2.8 43.4 1.0
CB A:CYS27 3.4 42.4 1.0
N A:CYS27 3.9 44.6 1.0
S2 A:F3S501 4.0 48.5 1.0
CA A:CYS27 4.3 45.0 1.0
SG A:CYS63 4.6 49.5 1.0
SG A:CYS97 4.6 48.8 1.0
NE2 A:GLN215 4.7 52.5 1.0
OD1 A:ASN30 4.8 54.2 1.0
CB A:MET29 4.9 50.7 1.0

Iron binding site 3 out of 7 in 7mjv

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Iron binding site 3 out of 7 in the Miab in the Complex with S-Adenosylmethionine and Rna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Miab in the Complex with S-Adenosylmethionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:43.4
occ:1.00
FE4 A:F3S501 0.0 43.4 1.0
S4 A:F3S501 2.1 41.1 1.0
S2 A:F3S501 2.1 48.5 1.0
SG A:CYS63 2.2 49.5 1.0
S3 A:F3S501 2.4 44.2 1.0
FE1 A:F3S501 2.5 42.6 1.0
FE3 A:F3S501 2.8 40.1 1.0
CB A:CYS63 3.2 55.4 1.0
CA A:CYS63 3.5 55.9 1.0
N A:SER64 3.7 56.6 1.0
S1 A:F3S501 3.8 44.0 1.0
N A:ILE65 4.0 45.5 1.0
CB A:ILE65 4.0 41.1 1.0
C A:CYS63 4.1 57.0 1.0
SG A:CYS97 4.4 48.8 1.0
CG2 A:ILE65 4.4 46.0 1.0
CA A:ILE65 4.5 46.3 1.0
CB A:CYS97 4.7 55.2 1.0
SG A:CYS27 4.8 47.4 1.0
C A:SER64 4.8 48.4 1.0
N A:CYS63 4.8 61.1 1.0
CA A:SER64 4.8 55.6 1.0
N A:CYS27 4.9 44.6 1.0
O A:THR62 5.0 63.3 1.0

Iron binding site 4 out of 7 in 7mjv

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Iron binding site 4 out of 7 in the Miab in the Complex with S-Adenosylmethionine and Rna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Miab in the Complex with S-Adenosylmethionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:35.1
occ:1.00
FE1 A:SF4502 0.0 35.1 1.0
S2 A:SF4502 2.3 37.0 1.0
S4 A:SF4502 2.3 36.9 1.0
S3 A:SF4502 2.3 34.3 1.0
SG A:CYS175 2.4 35.5 1.0
FE3 A:SF4502 2.7 38.0 1.0
FE4 A:SF4502 2.7 35.8 1.0
FE2 A:SF4502 2.7 40.2 1.0
CB A:CYS175 3.3 36.7 1.0
NH1 A:ARG293 3.7 39.3 1.0
S1 A:SF4502 3.9 35.9 1.0
OXT A:SAM503 3.9 44.9 1.0
N A:CYS175 4.1 43.7 1.0
CB A:ASN173 4.3 44.0 1.0
CA A:CYS175 4.3 37.9 1.0
O A:HOH632 4.4 41.9 1.0
OH A:TYR177 4.5 34.5 1.0
SG A:CYS171 4.7 36.8 1.0
CB A:CYS178 4.7 38.4 1.0
ND2 A:ASN173 4.7 46.0 1.0
SG A:CYS178 4.8 42.0 1.0
N A:PHE174 5.0 39.2 1.0
CZ A:ARG293 5.0 35.8 1.0
CZ A:TYR177 5.0 35.5 1.0

Iron binding site 5 out of 7 in 7mjv

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Iron binding site 5 out of 7 in the Miab in the Complex with S-Adenosylmethionine and Rna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Miab in the Complex with S-Adenosylmethionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:40.2
occ:1.00
FE2 A:SF4502 0.0 40.2 1.0
S1 A:SF4502 2.3 35.9 1.0
S4 A:SF4502 2.3 36.9 1.0
S3 A:SF4502 2.3 34.3 1.0
OXT A:SAM503 2.5 44.9 1.0
FE4 A:SF4502 2.7 35.8 1.0
FE3 A:SF4502 2.7 38.0 1.0
FE1 A:SF4502 2.7 35.1 1.0
N A:SAM503 3.1 45.9 1.0
CB A:SAM503 3.1 48.3 1.0
C A:SAM503 3.2 47.4 1.0
CA A:SAM503 3.2 46.1 1.0
CG A:SAM503 3.6 53.0 1.0
S2 A:SF4502 3.9 37.0 1.0
O A:HOH619 4.0 32.4 1.0
O A:SAM503 4.4 47.9 1.0
OE1 A:GLN215 4.4 57.8 1.0
NH1 A:ARG293 4.5 39.3 1.0
O A:GLN215 4.6 32.9 1.0
SG A:CYS171 4.7 36.8 1.0
SG A:CYS178 4.8 42.0 1.0
SD A:SAM503 4.9 44.1 1.0
SG A:CYS175 5.0 35.5 1.0

Iron binding site 6 out of 7 in 7mjv

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Iron binding site 6 out of 7 in the Miab in the Complex with S-Adenosylmethionine and Rna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Miab in the Complex with S-Adenosylmethionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:38.0
occ:1.00
FE3 A:SF4502 0.0 38.0 1.0
S1 A:SF4502 2.3 35.9 1.0
S2 A:SF4502 2.3 37.0 1.0
S4 A:SF4502 2.3 36.9 1.0
SG A:CYS178 2.3 42.0 1.0
FE1 A:SF4502 2.7 35.1 1.0
FE2 A:SF4502 2.7 40.2 1.0
FE4 A:SF4502 2.7 35.8 1.0
CB A:CYS178 3.1 38.4 1.0
S3 A:SF4502 3.9 34.3 1.0
CB A:VAL180 4.2 40.8 1.0
CG2 A:VAL180 4.4 40.5 1.0
CD A:PRO181 4.4 42.1 1.0
CA A:CYS178 4.6 39.8 1.0
CB A:CYS175 4.6 36.7 1.0
SG A:CYS175 4.7 35.5 1.0
CB A:SAM503 4.7 48.3 1.0
CG A:SAM503 4.7 53.0 1.0
CE1 A:TYR177 4.8 36.2 1.0
SG A:CYS171 4.8 36.8 1.0
OXT A:SAM503 4.9 44.9 1.0
CG A:PRO181 4.9 43.6 1.0
CG1 A:VAL180 5.0 40.0 1.0

Iron binding site 7 out of 7 in 7mjv

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Iron binding site 7 out of 7 in the Miab in the Complex with S-Adenosylmethionine and Rna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Miab in the Complex with S-Adenosylmethionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:35.8
occ:1.00
FE4 A:SF4502 0.0 35.8 1.0
SG A:CYS171 2.2 36.8 1.0
S3 A:SF4502 2.3 34.3 1.0
S1 A:SF4502 2.3 35.9 1.0
S2 A:SF4502 2.3 37.0 1.0
FE1 A:SF4502 2.7 35.1 1.0
FE2 A:SF4502 2.7 40.2 1.0
FE3 A:SF4502 2.7 38.0 1.0
CB A:CYS171 3.4 38.0 1.0
S4 A:SF4502 3.9 36.9 1.0
ND2 A:ASN173 4.1 46.0 1.0
CB A:ASN173 4.3 44.0 1.0
CG A:PRO181 4.7 43.6 1.0
CG A:ASN173 4.7 53.3 1.0
CA A:CYS171 4.8 40.3 1.0
CB A:GLN215 4.8 36.7 1.0
N A:ASN173 4.8 38.6 1.0
CD A:PRO181 4.8 42.1 1.0
SG A:CYS178 4.9 42.0 1.0
OXT A:SAM503 4.9 44.9 1.0
SG A:CYS175 4.9 35.5 1.0
N A:PHE174 5.0 39.2 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: Fri Sep 24 14:09:57 2021

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