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Iron in PDB 7mjx: Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna

Enzymatic activity of Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna

All present enzymatic activity of Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna:
2.8.4.3;

Protein crystallography data

The structure of Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna, PDB code: 7mjx 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) 41.02 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.69, 97.12, 80.606, 90, 108.1, 90
R / Rfree (%) 14.9 / 17

Other elements in 7mjx:

The structure of Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iron atom in the Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna (pdb code 7mjx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 14 binding sites of Iron where determined in the Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna, PDB code: 7mjx:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 14 in 7mjx

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Iron binding site 1 out of 14 in the Miab in the Complex with 5'-Deoxyadenosine, Methionine 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 5'-Deoxyadenosine, Methionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:8.0
occ:1.00
 FE1 A:F3S501 0.0 8.0 1.0
S1 A:F3S501 2.2 12.9 1.0
S2 A:F3S501 2.3 9.1 1.0
S3 A:F3S501 2.3 8.2 1.0
SG A:CYS97 2.4 9.3 1.0
FE3 A:F3S501 2.7 8.7 1.0
FE4 A:F3S501 2.7 7.9 1.0
CB A:CYS97 3.3 9.2 1.0
S4 A:F3S501 3.7 15.5 1.0
NE A:ARG184 4.1 13.3 1.0
NH2 A:ARG184 4.2 15.4 1.0
O A:HOH701 4.4 11.1 1.0
OG1 A:THR183 4.4 9.1 1.0
CZ A:ARG184 4.6 8.8 1.0
CA A:CYS97 4.6 9.1 1.0
CG A:ARG184 4.7 15.3 1.0
CA A:CYS63 4.7 6.9 1.0
N A:SER64 4.7 9.6 1.0
SG A:CYS63 4.8 8.1 1.0
O A:THR62 4.8 9.8 1.0
SG A:CYS27 4.8 9.2 1.0
CG2 A:VAL180 4.9 7.8 1.0
N A:CYS97 5.0 8.2 1.0

Iron binding site 2 out of 14 in 7mjx

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Iron binding site 2 out of 14 in the Miab in the Complex with 5'-Deoxyadenosine, Methionine 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 5'-Deoxyadenosine, Methionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:8.7
occ:1.00
 FE3 A:F3S501 0.0 8.7 1.0
S4 A:F3S501 2.2 15.5 1.0
S1 A:F3S501 2.3 12.9 1.0
S3 A:F3S501 2.3 8.2 1.0
SG A:CYS27 2.3 9.2 1.0
FE1 A:F3S501 2.7 8.0 1.0
FE4 A:F3S501 2.7 7.9 1.0
CB A:CYS27 3.3 9.7 1.0
NH2 A:ARG184 3.9 15.4 1.0
N A:CYS27 3.9 9.6 1.0
S2 A:F3S501 4.0 9.1 1.0
CA A:CYS27 4.3 6.9 1.0
C15 M:ZJS37 4.7 12.8 1.0
NE A:ARG184 4.7 13.3 1.0
NE2 A:GLN215 4.8 11.4 1.0
SG A:CYS63 4.8 8.1 1.0
CZ A:ARG184 4.8 8.8 1.0
SG A:CYS97 4.8 9.3 1.0
OD1 A:ASN30 4.8 10.8 1.0
CG A:ASN30 4.9 9.9 1.0

Iron binding site 3 out of 14 in 7mjx

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Iron binding site 3 out of 14 in the Miab in the Complex with 5'-Deoxyadenosine, Methionine 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 5'-Deoxyadenosine, Methionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:7.9
occ:1.00
 FE4 A:F3S501 0.0 7.9 1.0
S4 A:F3S501 2.2 15.5 1.0
S3 A:F3S501 2.3 8.2 1.0
S2 A:F3S501 2.3 9.1 1.0
SG A:CYS63 2.3 8.1 1.0
FE1 A:F3S501 2.7 8.0 1.0
FE3 A:F3S501 2.7 8.7 1.0
CB A:CYS63 3.3 6.7 1.0
CA A:CYS63 3.6 6.9 1.0
N A:SER64 3.9 9.6 1.0
S1 A:F3S501 4.0 12.9 1.0
CB A:ILE65 4.1 9.0 1.0
N A:ILE65 4.2 9.1 1.0
C A:CYS63 4.2 9.0 1.0
CA A:GLY26 4.6 7.4 1.0
N A:CYS27 4.6 9.6 1.0
CG2 A:ILE65 4.6 9.0 1.0
CA A:ILE65 4.7 10.5 1.0
SG A:CYS27 4.7 9.2 1.0
SG A:CYS97 4.8 9.3 1.0
CB A:CYS97 4.9 9.2 1.0
N A:CYS63 4.9 8.3 1.0
CD1 A:ILE65 5.0 14.5 1.0

Iron binding site 4 out of 14 in 7mjx

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Iron binding site 4 out of 14 in the Miab in the Complex with 5'-Deoxyadenosine, Methionine 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 5'-Deoxyadenosine, Methionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:7.8
occ:1.00
 FE1 A:SF4502 0.0 7.8 1.0
S2 A:SF4502 2.2 7.5 1.0
S4 A:SF4502 2.3 7.3 1.0
SG A:CYS178 2.3 7.7 1.0
S3 A:SF4502 2.3 7.6 1.0
FE2 A:SF4502 2.7 6.9 1.0
FE4 A:SF4502 2.7 7.8 1.0
FE3 A:SF4502 2.9 8.1 1.0
CB A:CYS178 3.1 8.2 1.0
S1 A:SF4502 3.9 8.4 1.0
CB A:VAL180 4.1 6.9 1.0
SD A:MET504 4.2 7.6 1.0
CG2 A:VAL180 4.4 7.8 1.0
CD A:PRO181 4.5 8.2 1.0
CA A:CYS178 4.6 7.8 1.0
SG A:CYS175 4.7 8.8 1.0
CE1 A:TYR177 4.8 6.8 1.0
OXT A:MET504 4.8 7.6 1.0
SG A:CYS171 4.8 8.3 1.0
CE A:MET504 4.9 7.9 1.0
CB A:CYS175 4.9 8.1 1.0
N A:VAL180 4.9 7.6 1.0
N A:MET504 4.9 8.3 1.0
CG1 A:VAL180 5.0 8.3 1.0

Iron binding site 5 out of 14 in 7mjx

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Iron binding site 5 out of 14 in the Miab in the Complex with 5'-Deoxyadenosine, Methionine 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 5'-Deoxyadenosine, Methionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:6.9
occ:1.00
 FE2 A:SF4502 0.0 6.9 1.0
S1 A:SF4502 2.2 8.4 1.0
S3 A:SF4502 2.3 7.6 1.0
S4 A:SF4502 2.3 7.3 1.0
SG A:CYS175 2.3 8.8 1.0
FE1 A:SF4502 2.7 7.8 1.0
FE4 A:SF4502 2.7 7.8 1.0
FE3 A:SF4502 2.9 8.1 1.0
CB A:CYS175 3.2 8.1 1.0
NH1 A:ARG293 3.6 7.3 1.0
S2 A:SF4502 3.8 7.5 1.0
OXT A:MET504 3.8 7.6 1.0
N A:CYS175 4.0 7.6 1.0
OH A:TYR177 4.1 10.1 1.0
CA A:CYS175 4.2 7.6 1.0
CB A:CYS178 4.4 8.2 1.0
O A:HOH920 4.6 10.1 1.0
SG A:CYS178 4.6 7.7 1.0
SG A:CYS171 4.6 8.3 1.0
CZ A:TYR177 4.6 6.9 1.0
N A:MET504 4.7 8.3 1.0
CB A:ASN173 4.7 7.7 1.0
CE1 A:TYR177 4.8 6.8 1.0
C A:MET504 4.9 7.7 1.0
CZ A:ARG293 4.9 7.1 1.0

Iron binding site 6 out of 14 in 7mjx

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Iron binding site 6 out of 14 in the Miab in the Complex with 5'-Deoxyadenosine, Methionine 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 5'-Deoxyadenosine, Methionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:8.1
occ:1.00
 FE3 A:SF4502 0.0 8.1 1.0
N A:MET504 2.2 8.3 1.0
OXT A:MET504 2.2 7.6 1.0
S4 A:SF4502 2.4 7.3 1.0
S2 A:SF4502 2.4 7.5 1.0
S1 A:SF4502 2.4 8.4 1.0
SD A:MET504 2.6 7.6 1.0
FE2 A:SF4502 2.9 6.9 1.0
FE1 A:SF4502 2.9 7.8 1.0
FE4 A:SF4502 3.0 7.8 1.0
C A:MET504 3.0 7.7 1.0
CA A:MET504 3.0 7.7 1.0
CG A:MET504 3.5 10.0 1.0
CE A:MET504 3.6 7.9 1.0
CB A:MET504 3.7 6.7 1.0
NH1 A:ARG293 4.2 7.3 1.0
S3 A:SF4502 4.2 7.6 1.0
O A:MET504 4.2 8.5 1.0
OD1 A:ASN216 4.6 8.3 1.0
O A:GLN215 4.8 6.7 1.0
SG A:CYS171 4.9 8.3 1.0
SG A:CYS175 4.9 8.8 1.0

Iron binding site 7 out of 14 in 7mjx

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Iron binding site 7 out of 14 in the Miab in the Complex with 5'-Deoxyadenosine, Methionine 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 5'-Deoxyadenosine, Methionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:7.8
occ:1.00
 FE4 A:SF4502 0.0 7.8 1.0
S3 A:SF4502 2.2 7.6 1.0
SG A:CYS171 2.2 8.3 1.0
S2 A:SF4502 2.3 7.5 1.0
S1 A:SF4502 2.3 8.4 1.0
FE2 A:SF4502 2.7 6.9 1.0
FE1 A:SF4502 2.7 7.8 1.0
FE3 A:SF4502 3.0 8.1 1.0
CB A:CYS171 3.4 7.2 1.0
S4 A:SF4502 3.9 7.3 1.0
N A:MET504 4.0 8.3 1.0
ND2 A:ASN216 4.2 8.0 1.0
ND2 A:ASN173 4.3 10.0 1.0
CB A:ASN173 4.3 7.7 1.0
CG A:PRO181 4.4 7.4 1.0
CD A:PRO181 4.6 8.2 1.0
OD1 A:ASN216 4.6 8.3 1.0
SG A:CYS175 4.7 8.8 1.0
CA A:CYS171 4.7 9.0 1.0
N A:PHE174 4.7 7.7 1.0
SG A:CYS178 4.8 7.7 1.0
OXT A:MET504 4.8 7.6 1.0
N A:ASN173 4.9 8.2 1.0
CG A:ASN173 4.9 8.6 1.0
CG A:ASN216 4.9 6.8 1.0
CB A:VAL180 5.0 6.9 1.0

Iron binding site 8 out of 14 in 7mjx

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Iron binding site 8 out of 14 in the Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:10.1
occ:1.00
 FE1 B:F3S602 0.0 10.1 1.0
S2 B:F3S602 2.2 9.9 1.0
S1 B:F3S602 2.3 16.4 1.0
S3 B:F3S602 2.4 8.7 1.0
SG B:CYS97 2.4 10.2 1.0
FE4 B:F3S602 2.7 10.5 1.0
FE3 B:F3S602 2.7 10.2 1.0
CB B:CYS97 3.2 8.6 1.0
S4 B:F3S602 3.7 18.8 1.0
NE B:ARG184 4.1 12.3 1.0
NH2 B:ARG184 4.3 15.7 1.0
OG1 B:THR183 4.4 12.4 1.0
O B:HOH744 4.4 14.1 1.0
CA B:CYS63 4.6 7.6 1.0
CZ B:ARG184 4.7 10.6 1.0
CA B:CYS97 4.7 8.7 1.0
CG B:ARG184 4.7 11.1 1.0
SG B:CYS63 4.8 9.7 1.0
CG2 B:VAL180 4.8 8.6 1.0
O B:THR62 4.8 10.1 1.0
N B:SER64 4.8 8.5 1.0
SG B:CYS27 4.9 10.0 1.0
CD B:ARG184 5.0 9.9 1.0

Iron binding site 9 out of 14 in 7mjx

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Iron binding site 9 out of 14 in the Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:10.2
occ:1.00
 FE3 B:F3S602 0.0 10.2 1.0
S4 B:F3S602 2.2 18.8 1.0
S1 B:F3S602 2.3 16.4 1.0
S3 B:F3S602 2.3 8.7 1.0
SG B:CYS27 2.4 10.0 1.0
FE1 B:F3S602 2.7 10.1 1.0
FE4 B:F3S602 2.7 10.5 1.0
CB B:CYS27 3.3 9.3 1.0
N B:CYS27 3.9 10.3 1.0
S2 B:F3S602 3.9 9.9 1.0
NH2 B:ARG184 4.0 15.7 1.0
CA B:CYS27 4.3 7.7 1.0
C15 D:ZJS37 4.7 11.5 1.0
SG B:CYS63 4.7 9.7 1.0
OD1 B:ASN30 4.8 11.9 1.0
NE B:ARG184 4.8 12.3 1.0
SG B:CYS97 4.8 10.2 1.0
NE2 B:GLN215 4.8 11.8 1.0
CZ B:ARG184 4.9 10.6 1.0
CG B:ASN30 5.0 10.2 1.0
C2 D:ZJS37 5.0 13.0 1.0

Iron binding site 10 out of 14 in 7mjx

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Iron binding site 10 out of 14 in the Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:10.5
occ:1.00
 FE4 B:F3S602 0.0 10.5 1.0
S4 B:F3S602 2.2 18.8 1.0
S2 B:F3S602 2.3 9.9 1.0
S3 B:F3S602 2.3 8.7 1.0
SG B:CYS63 2.3 9.7 1.0
FE1 B:F3S602 2.7 10.1 1.0
FE3 B:F3S602 2.7 10.2 1.0
CB B:CYS63 3.2 8.5 1.0
CA B:CYS63 3.6 7.6 1.0
S1 B:F3S602 4.0 16.4 1.0
N B:SER64 4.0 8.5 1.0
CB B:ILE65 4.0 9.1 1.0
N B:ILE65 4.2 9.6 1.0
C B:CYS63 4.2 8.7 1.0
CG2 B:ILE65 4.4 13.8 1.0
CA B:GLY26 4.6 9.2 1.0
N B:CYS27 4.6 10.3 1.0
CA B:ILE65 4.7 8.2 1.0
SG B:CYS27 4.8 10.0 1.0
SG B:CYS97 4.8 10.2 1.0
N B:CYS63 4.8 8.7 1.0
CB B:CYS97 4.8 8.6 1.0
O4' D:ZJS37 4.9 12.4 1.0
N3 D:ZJS37 5.0 13.7 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 09:17:55 2024

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