Iron in PDB 6fz6: Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus
Enzymatic activity of Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus
All present enzymatic activity of Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus:
2.1.1.192;
Protein crystallography data
The structure of Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus, PDB code: 6fz6
was solved by
P.Hinchliffe,
J.M.Shaw,
J.Spencer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.29 /
1.42
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.840,
53.140,
113.570,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.6 /
18.7
|
Other elements in 6fz6:
The structure of Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus
(pdb code 6fz6). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus, PDB code: 6fz6:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 6fz6
Go back to
Iron Binding Sites List in 6fz6
Iron binding site 1 out
of 8 in the Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:18.9
occ:1.00
|
FE1
|
A:SF4401
|
0.0
|
18.9
|
1.0
|
S2
|
A:SF4401
|
2.2
|
18.9
|
1.0
|
S3
|
A:SF4401
|
2.3
|
17.9
|
1.0
|
SG
|
A:CYS110
|
2.3
|
17.3
|
1.0
|
S4
|
A:SF4401
|
2.3
|
19.5
|
1.0
|
FE3
|
A:SF4401
|
2.7
|
19.4
|
1.0
|
FE2
|
A:SF4401
|
2.7
|
18.7
|
1.0
|
FE4
|
A:SF4401
|
2.9
|
19.2
|
1.0
|
CB
|
A:CYS110
|
3.2
|
16.5
|
1.0
|
S1
|
A:SF4401
|
3.9
|
18.8
|
1.0
|
N
|
A:SAH402
|
4.0
|
18.6
|
1.0
|
CB
|
A:VAL112
|
4.0
|
17.1
|
1.0
|
CG2
|
A:VAL112
|
4.4
|
20.2
|
1.0
|
C
|
A:GLY160
|
4.6
|
16.1
|
1.0
|
N
|
A:VAL112
|
4.6
|
17.2
|
1.0
|
CA
|
A:CYS110
|
4.6
|
15.8
|
1.0
|
O
|
A:GLY160
|
4.7
|
16.9
|
1.0
|
N
|
A:GLU161
|
4.7
|
15.3
|
1.0
|
N
|
A:GLY113
|
4.8
|
18.6
|
1.0
|
SG
|
A:CYS117
|
4.8
|
20.3
|
1.0
|
CA
|
A:VAL112
|
4.9
|
17.7
|
1.0
|
CB
|
A:GLU161
|
4.9
|
17.7
|
1.0
|
SG
|
A:CYS114
|
4.9
|
19.2
|
1.0
|
CA
|
A:GLY160
|
4.9
|
18.1
|
1.0
|
CG1
|
A:VAL112
|
4.9
|
20.5
|
1.0
|
O
|
A:SAH402
|
5.0
|
20.0
|
1.0
|
|
Iron binding site 2 out
of 8 in 6fz6
Go back to
Iron Binding Sites List in 6fz6
Iron binding site 2 out
of 8 in the Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:18.7
occ:1.00
|
FE2
|
A:SF4401
|
0.0
|
18.7
|
1.0
|
S1
|
A:SF4401
|
2.2
|
18.8
|
1.0
|
S3
|
A:SF4401
|
2.3
|
17.9
|
1.0
|
S4
|
A:SF4401
|
2.3
|
19.5
|
1.0
|
SG
|
A:CYS114
|
2.3
|
19.2
|
1.0
|
FE3
|
A:SF4401
|
2.7
|
19.4
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
18.9
|
1.0
|
FE4
|
A:SF4401
|
2.8
|
19.2
|
1.0
|
CB
|
A:CYS114
|
3.2
|
20.8
|
1.0
|
S2
|
A:SF4401
|
3.8
|
18.9
|
1.0
|
O
|
A:HOH688
|
3.8
|
20.1
|
1.0
|
N
|
A:CYS114
|
3.9
|
18.7
|
1.0
|
O
|
A:SAH402
|
4.1
|
20.0
|
1.0
|
CG1
|
A:VAL112
|
4.2
|
20.5
|
1.0
|
CA
|
A:CYS114
|
4.2
|
17.0
|
1.0
|
CB
|
A:VAL112
|
4.2
|
17.1
|
1.0
|
CB
|
A:CYS117
|
4.5
|
21.6
|
1.0
|
SG
|
A:CYS117
|
4.6
|
20.3
|
1.0
|
N
|
A:SAH402
|
4.8
|
18.6
|
1.0
|
SG
|
A:CYS110
|
4.8
|
17.3
|
1.0
|
CB
|
A:SER194
|
4.8
|
19.2
|
1.0
|
N
|
A:GLY113
|
4.8
|
18.6
|
1.0
|
|
Iron binding site 3 out
of 8 in 6fz6
Go back to
Iron Binding Sites List in 6fz6
Iron binding site 3 out
of 8 in the Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:19.4
occ:1.00
|
FE3
|
A:SF4401
|
0.0
|
19.4
|
1.0
|
S1
|
A:SF4401
|
2.3
|
18.8
|
1.0
|
S2
|
A:SF4401
|
2.3
|
18.9
|
1.0
|
S4
|
A:SF4401
|
2.3
|
19.5
|
1.0
|
SG
|
A:CYS117
|
2.3
|
20.3
|
1.0
|
FE2
|
A:SF4401
|
2.7
|
18.7
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
18.9
|
1.0
|
FE4
|
A:SF4401
|
2.9
|
19.2
|
1.0
|
CB
|
A:CYS117
|
3.1
|
21.6
|
1.0
|
S3
|
A:SF4401
|
3.9
|
17.9
|
1.0
|
N
|
A:GLY120
|
4.3
|
21.9
|
1.0
|
SD
|
A:SAH402
|
4.4
|
20.1
|
1.0
|
CB
|
A:THR119
|
4.4
|
21.6
|
1.0
|
CA
|
A:CYS117
|
4.6
|
20.5
|
1.0
|
C8
|
A:SAH402
|
4.6
|
19.7
|
1.0
|
SG
|
A:CYS114
|
4.7
|
19.2
|
1.0
|
CB
|
A:CYS114
|
4.8
|
20.8
|
1.0
|
SG
|
A:CYS110
|
4.8
|
17.3
|
1.0
|
CA
|
A:GLY120
|
4.8
|
23.4
|
1.0
|
O
|
A:SAH402
|
4.9
|
20.0
|
1.0
|
CB
|
A:CYS110
|
4.9
|
16.5
|
1.0
|
N
|
A:SAH402
|
4.9
|
18.6
|
1.0
|
|
Iron binding site 4 out
of 8 in 6fz6
Go back to
Iron Binding Sites List in 6fz6
Iron binding site 4 out
of 8 in the Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:19.2
occ:1.00
|
FE4
|
A:SF4401
|
0.0
|
19.2
|
1.0
|
O
|
A:SAH402
|
2.3
|
20.0
|
1.0
|
N
|
A:SAH402
|
2.3
|
18.6
|
1.0
|
S1
|
A:SF4401
|
2.3
|
18.8
|
1.0
|
S3
|
A:SF4401
|
2.3
|
17.9
|
1.0
|
S2
|
A:SF4401
|
2.4
|
18.9
|
1.0
|
FE2
|
A:SF4401
|
2.8
|
18.7
|
1.0
|
FE1
|
A:SF4401
|
2.9
|
18.9
|
1.0
|
FE3
|
A:SF4401
|
2.9
|
19.4
|
1.0
|
C
|
A:SAH402
|
3.0
|
18.6
|
1.0
|
CA
|
A:SAH402
|
3.1
|
17.1
|
1.0
|
SD
|
A:SAH402
|
3.2
|
20.1
|
1.0
|
CG
|
A:SAH402
|
3.6
|
17.6
|
1.0
|
CB
|
A:SAH402
|
3.9
|
17.6
|
1.0
|
O
|
A:HOH688
|
4.0
|
20.1
|
1.0
|
S4
|
A:SF4401
|
4.0
|
19.5
|
1.0
|
OXT
|
A:SAH402
|
4.2
|
19.5
|
1.0
|
O
|
A:GLY160
|
4.4
|
16.9
|
1.0
|
C2'
|
A:SAH402
|
4.6
|
22.3
|
1.0
|
OE1
|
A:GLU161
|
4.7
|
18.6
|
1.0
|
C5'
|
A:SAH402
|
4.8
|
20.3
|
1.0
|
C3'
|
A:SAH402
|
4.8
|
20.8
|
1.0
|
SG
|
A:CYS114
|
4.8
|
19.2
|
1.0
|
CB
|
A:SER194
|
4.8
|
19.2
|
1.0
|
SG
|
A:CYS110
|
4.8
|
17.3
|
1.0
|
|
Iron binding site 5 out
of 8 in 6fz6
Go back to
Iron Binding Sites List in 6fz6
Iron binding site 5 out
of 8 in the Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:16.4
occ:1.00
|
FE1
|
B:SF4401
|
0.0
|
16.4
|
1.0
|
S4
|
B:SF4401
|
2.3
|
15.3
|
1.0
|
S3
|
B:SF4401
|
2.3
|
16.9
|
1.0
|
S2
|
B:SF4401
|
2.3
|
17.0
|
1.0
|
SG
|
B:CYS110
|
2.3
|
15.3
|
1.0
|
FE4
|
B:SF4401
|
2.7
|
17.2
|
1.0
|
FE3
|
B:SF4401
|
2.7
|
16.3
|
1.0
|
FE2
|
B:SF4401
|
2.8
|
17.2
|
1.0
|
CB
|
B:CYS110
|
3.2
|
15.5
|
1.0
|
S1
|
B:SF4401
|
3.9
|
16.5
|
1.0
|
N
|
B:SAH402
|
3.9
|
16.4
|
1.0
|
CB
|
B:VAL112
|
4.0
|
15.2
|
1.0
|
CG2
|
B:VAL112
|
4.4
|
18.1
|
1.0
|
C
|
B:GLY160
|
4.6
|
15.7
|
1.0
|
N
|
B:VAL112
|
4.6
|
15.2
|
1.0
|
CA
|
B:CYS110
|
4.6
|
14.6
|
1.0
|
N
|
B:GLU161
|
4.7
|
15.1
|
1.0
|
O
|
B:GLY160
|
4.8
|
16.3
|
1.0
|
CB
|
B:GLU161
|
4.8
|
16.2
|
1.0
|
SG
|
B:CYS114
|
4.8
|
16.8
|
1.0
|
CA
|
B:GLY160
|
4.8
|
14.6
|
1.0
|
CA
|
B:VAL112
|
4.8
|
14.2
|
1.0
|
SG
|
B:CYS117
|
4.9
|
17.6
|
1.0
|
N
|
B:GLY113
|
4.9
|
16.4
|
1.0
|
CG1
|
B:VAL112
|
4.9
|
17.7
|
1.0
|
O
|
B:SAH402
|
4.9
|
18.0
|
1.0
|
|
Iron binding site 6 out
of 8 in 6fz6
Go back to
Iron Binding Sites List in 6fz6
Iron binding site 6 out
of 8 in the Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:17.2
occ:1.00
|
FE2
|
B:SF4401
|
0.0
|
17.2
|
1.0
|
N
|
B:SAH402
|
2.3
|
16.4
|
1.0
|
O
|
B:SAH402
|
2.3
|
18.0
|
1.0
|
S4
|
B:SF4401
|
2.3
|
15.3
|
1.0
|
S1
|
B:SF4401
|
2.3
|
16.5
|
1.0
|
S3
|
B:SF4401
|
2.4
|
16.9
|
1.0
|
FE3
|
B:SF4401
|
2.8
|
16.3
|
1.0
|
FE1
|
B:SF4401
|
2.8
|
16.4
|
1.0
|
FE4
|
B:SF4401
|
2.9
|
17.2
|
1.0
|
C
|
B:SAH402
|
3.0
|
17.8
|
1.0
|
CA
|
B:SAH402
|
3.1
|
17.4
|
1.0
|
SD
|
B:SAH402
|
3.1
|
19.2
|
1.0
|
CG
|
B:SAH402
|
3.6
|
18.2
|
1.0
|
CB
|
B:SAH402
|
3.8
|
18.6
|
1.0
|
S2
|
B:SF4401
|
4.0
|
17.0
|
1.0
|
O
|
B:HOH677
|
4.1
|
19.4
|
1.0
|
OXT
|
B:SAH402
|
4.2
|
18.8
|
1.0
|
O
|
B:GLY160
|
4.4
|
16.3
|
1.0
|
C2'
|
B:SAH402
|
4.7
|
24.0
|
1.0
|
OE1
|
B:GLU161
|
4.7
|
17.5
|
1.0
|
C5'
|
B:SAH402
|
4.7
|
20.1
|
1.0
|
C3'
|
B:SAH402
|
4.8
|
22.9
|
1.0
|
SG
|
B:CYS114
|
4.8
|
16.8
|
1.0
|
SG
|
B:CYS110
|
4.8
|
15.3
|
1.0
|
CB
|
B:SER194
|
4.9
|
15.4
|
1.0
|
C
|
B:GLY160
|
5.0
|
15.7
|
1.0
|
|
Iron binding site 7 out
of 8 in 6fz6
Go back to
Iron Binding Sites List in 6fz6
Iron binding site 7 out
of 8 in the Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:16.3
occ:1.00
|
FE3
|
B:SF4401
|
0.0
|
16.3
|
1.0
|
S4
|
B:SF4401
|
2.3
|
15.3
|
1.0
|
S1
|
B:SF4401
|
2.3
|
16.5
|
1.0
|
SG
|
B:CYS114
|
2.3
|
16.8
|
1.0
|
S2
|
B:SF4401
|
2.3
|
17.0
|
1.0
|
FE4
|
B:SF4401
|
2.7
|
17.2
|
1.0
|
FE1
|
B:SF4401
|
2.7
|
16.4
|
1.0
|
FE2
|
B:SF4401
|
2.8
|
17.2
|
1.0
|
CB
|
B:CYS114
|
3.2
|
17.5
|
1.0
|
O
|
B:HOH677
|
3.8
|
19.4
|
1.0
|
S3
|
B:SF4401
|
3.9
|
16.9
|
1.0
|
N
|
B:CYS114
|
3.9
|
15.0
|
1.0
|
O
|
B:SAH402
|
4.1
|
18.0
|
1.0
|
CA
|
B:CYS114
|
4.2
|
15.1
|
1.0
|
CG1
|
B:VAL112
|
4.2
|
17.7
|
1.0
|
CB
|
B:VAL112
|
4.2
|
15.2
|
1.0
|
CB
|
B:CYS117
|
4.5
|
18.8
|
1.0
|
SG
|
B:CYS117
|
4.7
|
17.6
|
1.0
|
N
|
B:SAH402
|
4.7
|
16.4
|
1.0
|
CB
|
B:SER194
|
4.8
|
15.4
|
1.0
|
SG
|
B:CYS110
|
4.8
|
15.3
|
1.0
|
N
|
B:GLY113
|
4.9
|
16.4
|
1.0
|
|
Iron binding site 8 out
of 8 in 6fz6
Go back to
Iron Binding Sites List in 6fz6
Iron binding site 8 out
of 8 in the Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:17.2
occ:1.00
|
FE4
|
B:SF4401
|
0.0
|
17.2
|
1.0
|
S3
|
B:SF4401
|
2.2
|
16.9
|
1.0
|
S1
|
B:SF4401
|
2.3
|
16.5
|
1.0
|
S2
|
B:SF4401
|
2.3
|
17.0
|
1.0
|
SG
|
B:CYS117
|
2.3
|
17.6
|
1.0
|
FE1
|
B:SF4401
|
2.7
|
16.4
|
1.0
|
FE3
|
B:SF4401
|
2.7
|
16.3
|
1.0
|
FE2
|
B:SF4401
|
2.9
|
17.2
|
1.0
|
CB
|
B:CYS117
|
3.2
|
18.8
|
1.0
|
S4
|
B:SF4401
|
3.9
|
15.3
|
1.0
|
N
|
B:GLY120
|
4.2
|
16.9
|
1.0
|
SD
|
B:SAH402
|
4.3
|
19.2
|
1.0
|
CB
|
B:THR119
|
4.4
|
17.9
|
1.0
|
CA
|
B:CYS117
|
4.6
|
18.2
|
1.0
|
C8
|
B:SAH402
|
4.7
|
21.1
|
1.0
|
CB
|
B:CYS114
|
4.7
|
17.5
|
1.0
|
SG
|
B:CYS114
|
4.7
|
16.8
|
1.0
|
SG
|
B:CYS110
|
4.8
|
15.3
|
1.0
|
CA
|
B:GLY120
|
4.8
|
18.9
|
1.0
|
CB
|
B:CYS110
|
4.9
|
15.5
|
1.0
|
N
|
B:SAH402
|
4.9
|
16.4
|
1.0
|
O
|
B:SAH402
|
4.9
|
18.0
|
1.0
|
|
Reference:
J.M.Shaw,
P.Hinchliffe,
J.Spencer.
Crystal Structure of A Radical Sam Methyltransferase From Sphaerobacter Thermophilus To Be Published.
Page generated: Tue Aug 6 18:49:28 2024
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