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:
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
Go back to
Iron Binding Sites List in 7mjz
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
Go back to
Iron Binding Sites List in 7mjz
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
Go back to
Iron Binding Sites List in 7mjz
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
Go back to
Iron Binding Sites List in 7mjz
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
Go back to
Iron Binding Sites List in 7mjz
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
Go back to
Iron Binding Sites List in 7mjz
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
Go back to
Iron Binding Sites List in 7mjz
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
Go back to
Iron Binding Sites List in 7mjz
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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