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:
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
Go back to
Iron Binding Sites List in 7mjv
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
Go back to
Iron Binding Sites List in 7mjv
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
Go back to
Iron Binding Sites List in 7mjv
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
Go back to
Iron Binding Sites List in 7mjv
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
Go back to
Iron Binding Sites List in 7mjv
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
Go back to
Iron Binding Sites List in 7mjv
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
Go back to
Iron Binding Sites List in 7mjv
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: Thu Aug 8 09:16:25 2024
|