Iron in PDB 4u0p: The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine
Enzymatic activity of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine
All present enzymatic activity of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine:
2.8.1.8;
Protein crystallography data
The structure of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine, PDB code: 4u0p
was solved by
J.E.Harmer,
M.J.Hiscox,
J.Sandy,
P.C.Dinis,
P.L.Roach,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
43.89 /
1.62
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
71.090,
161.130,
59.470,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
17.8 /
20.7
|
Other elements in 4u0p:
The structure of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine
(pdb code 4u0p). 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 Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine, PDB code: 4u0p:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 4u0p
Go back to
Iron Binding Sites List in 4u0p
Iron binding site 1 out
of 8 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe301
b:36.8
occ:1.00
|
FE1
|
B:SF4301
|
0.0
|
36.8
|
1.0
|
|
N
|
B:SAH303
|
1.3
|
28.7
|
1.0
|
|
S2
|
B:SF4301
|
2.1
|
35.6
|
1.0
|
|
S4
|
B:SF4301
|
2.2
|
34.1
|
1.0
|
|
S3
|
B:SF4301
|
2.2
|
32.7
|
1.0
|
|
OXT
|
B:SAH303
|
2.3
|
39.4
|
1.0
|
|
CA
|
B:SAH303
|
2.4
|
50.2
|
1.0
|
|
C
|
B:SAH303
|
2.6
|
41.5
|
1.0
|
|
FE3
|
B:SF4301
|
2.7
|
32.2
|
1.0
|
|
FE2
|
B:SF4301
|
2.7
|
30.0
|
1.0
|
|
FE4
|
B:SF4301
|
2.7
|
31.5
|
1.0
|
|
HA
|
B:SAH303
|
2.8
|
60.2
|
1.0
|
|
O
|
B:SAH303
|
3.6
|
52.6
|
1.0
|
|
HB1
|
B:SAH303
|
3.6
|
63.5
|
1.0
|
|
CB
|
B:SAH303
|
3.7
|
52.9
|
1.0
|
|
S1
|
B:SF4301
|
3.7
|
31.9
|
1.0
|
|
H
|
B:ALA107
|
3.8
|
39.3
|
1.0
|
|
HA
|
B:VAL106
|
4.1
|
34.4
|
1.0
|
|
HB2
|
B:ALA107
|
4.1
|
41.8
|
1.0
|
|
HB2
|
B:SAH303
|
4.2
|
63.5
|
1.0
|
|
N
|
B:ALA107
|
4.4
|
32.8
|
1.0
|
|
CG
|
B:SAH303
|
4.7
|
50.4
|
1.0
|
|
HG2
|
B:SAH303
|
4.7
|
60.4
|
1.0
|
|
SG
|
B:CYS63
|
4.7
|
31.3
|
1.0
|
|
SG
|
B:CYS67
|
4.8
|
35.2
|
1.0
|
|
SD
|
B:SAH303
|
4.8
|
56.3
|
1.0
|
|
CB
|
B:ALA107
|
4.8
|
34.9
|
1.0
|
|
HB3
|
B:ALA107
|
4.8
|
41.8
|
1.0
|
|
C5'
|
B:SAH303
|
4.9
|
44.9
|
1.0
|
|
SG
|
B:CYS70
|
4.9
|
32.0
|
1.0
|
|
CA
|
B:VAL106
|
4.9
|
28.7
|
1.0
|
|
O
|
B:HOH479
|
4.9
|
35.8
|
1.0
|
|
O
|
B:SER105
|
4.9
|
31.0
|
1.0
|
|
HB2
|
B:ARG65
|
5.0
|
45.5
|
1.0
|
|
Iron binding site 2 out
of 8 in 4u0p
Go back to
Iron Binding Sites List in 4u0p
Iron binding site 2 out
of 8 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe301
b:30.0
occ:1.00
|
FE2
|
B:SF4301
|
0.0
|
30.0
|
1.0
|
|
S1
|
B:SF4301
|
2.1
|
31.9
|
1.0
|
|
S3
|
B:SF4301
|
2.1
|
32.7
|
1.0
|
|
S4
|
B:SF4301
|
2.2
|
34.1
|
1.0
|
|
SG
|
B:CYS70
|
2.3
|
32.0
|
1.0
|
|
FE3
|
B:SF4301
|
2.7
|
32.2
|
1.0
|
|
FE4
|
B:SF4301
|
2.7
|
31.5
|
1.0
|
|
FE1
|
B:SF4301
|
2.7
|
36.8
|
1.0
|
|
N
|
B:SAH303
|
2.9
|
28.7
|
1.0
|
|
HB2
|
B:CYS70
|
3.2
|
37.2
|
1.0
|
|
CB
|
B:CYS70
|
3.2
|
31.0
|
1.0
|
|
HB3
|
B:CYS70
|
3.4
|
37.2
|
1.0
|
|
HB
|
B:VAL72
|
3.6
|
39.0
|
1.0
|
|
S2
|
B:SF4301
|
3.7
|
35.6
|
1.0
|
|
HG21
|
B:VAL72
|
4.0
|
42.0
|
1.0
|
|
HB2
|
B:CYS67
|
4.0
|
36.0
|
1.0
|
|
HG23
|
B:VAL72
|
4.2
|
42.0
|
1.0
|
|
O
|
B:HOH474
|
4.4
|
38.0
|
1.0
|
|
CG2
|
B:VAL72
|
4.4
|
35.0
|
1.0
|
|
CA
|
B:SAH303
|
4.4
|
50.2
|
1.0
|
|
CB
|
B:VAL72
|
4.4
|
32.5
|
1.0
|
|
HB3
|
B:CYS63
|
4.5
|
39.2
|
1.0
|
|
H
|
B:VAL72
|
4.5
|
39.0
|
1.0
|
|
H
|
B:CYS67
|
4.6
|
46.2
|
1.0
|
|
SG
|
B:CYS67
|
4.7
|
35.2
|
1.0
|
|
CA
|
B:CYS70
|
4.7
|
30.9
|
1.0
|
|
H5'1
|
B:SAH303
|
4.7
|
53.9
|
1.0
|
|
HA
|
B:SAH303
|
4.7
|
60.2
|
1.0
|
|
HB2
|
B:CYS63
|
4.7
|
39.2
|
1.0
|
|
CB
|
B:CYS67
|
4.8
|
30.0
|
1.0
|
|
HB1
|
B:SAH303
|
4.8
|
63.5
|
1.0
|
|
C5'
|
B:SAH303
|
4.8
|
44.9
|
1.0
|
|
SG
|
B:CYS63
|
4.8
|
31.3
|
1.0
|
|
HG11
|
B:VAL72
|
4.9
|
40.4
|
1.0
|
|
HA
|
B:CYS70
|
4.9
|
37.1
|
1.0
|
|
CB
|
B:CYS63
|
4.9
|
32.6
|
1.0
|
|
SD
|
B:SAH303
|
5.0
|
56.3
|
1.0
|
|
Iron binding site 3 out
of 8 in 4u0p
Go back to
Iron Binding Sites List in 4u0p
Iron binding site 3 out
of 8 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe301
b:32.2
occ:1.00
|
FE3
|
B:SF4301
|
0.0
|
32.2
|
1.0
|
|
S4
|
B:SF4301
|
2.1
|
34.1
|
1.0
|
|
S2
|
B:SF4301
|
2.2
|
35.6
|
1.0
|
|
S1
|
B:SF4301
|
2.2
|
31.9
|
1.0
|
|
SG
|
B:CYS67
|
2.3
|
35.2
|
1.0
|
|
FE4
|
B:SF4301
|
2.7
|
31.5
|
1.0
|
|
FE2
|
B:SF4301
|
2.7
|
30.0
|
1.0
|
|
FE1
|
B:SF4301
|
2.7
|
36.8
|
1.0
|
|
HB2
|
B:CYS67
|
3.0
|
36.0
|
1.0
|
|
CB
|
B:CYS67
|
3.3
|
30.0
|
1.0
|
|
H
|
B:CYS67
|
3.3
|
46.2
|
1.0
|
|
HB2
|
B:ARG65
|
3.4
|
45.5
|
1.0
|
|
N
|
B:SAH303
|
3.6
|
28.7
|
1.0
|
|
S3
|
B:SF4301
|
3.7
|
32.7
|
1.0
|
|
HB3
|
B:CYS67
|
4.0
|
36.0
|
1.0
|
|
HB3
|
B:ARG65
|
4.0
|
45.5
|
1.0
|
|
HB2
|
B:CYS70
|
4.1
|
37.2
|
1.0
|
|
N
|
B:CYS67
|
4.1
|
38.5
|
1.0
|
|
CB
|
B:ARG65
|
4.1
|
37.9
|
1.0
|
|
CA
|
B:CYS67
|
4.3
|
33.7
|
1.0
|
|
HB3
|
B:CYS70
|
4.4
|
37.2
|
1.0
|
|
HG3
|
B:ARG65
|
4.4
|
53.4
|
1.0
|
|
OXT
|
B:SAH303
|
4.5
|
39.4
|
1.0
|
|
CB
|
B:CYS70
|
4.5
|
31.0
|
1.0
|
|
SG
|
B:CYS70
|
4.6
|
32.0
|
1.0
|
|
O
|
B:HOH479
|
4.7
|
35.8
|
1.0
|
|
SG
|
B:CYS63
|
4.7
|
31.3
|
1.0
|
|
HA
|
B:CYS67
|
4.8
|
40.5
|
1.0
|
|
H
|
B:ARG182
|
4.8
|
49.1
|
1.0
|
|
CG
|
B:ARG65
|
4.8
|
44.5
|
1.0
|
|
HD2
|
B:ARG65
|
4.8
|
52.9
|
1.0
|
|
HZ
|
B:PHE69
|
4.9
|
40.1
|
1.0
|
|
HH11
|
B:ARG65
|
4.9
|
52.9
|
1.0
|
|
C
|
B:SAH303
|
4.9
|
41.5
|
1.0
|
|
H
|
B:ALA66
|
4.9
|
41.5
|
1.0
|
|
CA
|
B:SAH303
|
4.9
|
50.2
|
1.0
|
|
HE1
|
B:PHE69
|
5.0
|
44.1
|
1.0
|
|
Iron binding site 4 out
of 8 in 4u0p
Go back to
Iron Binding Sites List in 4u0p
Iron binding site 4 out
of 8 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe301
b:31.5
occ:1.00
|
FE4
|
B:SF4301
|
0.0
|
31.5
|
1.0
|
|
S1
|
B:SF4301
|
2.2
|
31.9
|
1.0
|
|
S3
|
B:SF4301
|
2.2
|
32.7
|
1.0
|
|
S2
|
B:SF4301
|
2.2
|
35.6
|
1.0
|
|
SG
|
B:CYS63
|
2.3
|
31.3
|
1.0
|
|
FE3
|
B:SF4301
|
2.7
|
32.2
|
1.0
|
|
FE2
|
B:SF4301
|
2.7
|
30.0
|
1.0
|
|
FE1
|
B:SF4301
|
2.7
|
36.8
|
1.0
|
|
HB2
|
B:ARG65
|
3.0
|
45.5
|
1.0
|
|
HB3
|
B:CYS63
|
3.0
|
39.2
|
1.0
|
|
CB
|
B:CYS63
|
3.1
|
32.6
|
1.0
|
|
HB2
|
B:CYS63
|
3.2
|
39.2
|
1.0
|
|
H
|
B:ALA107
|
3.3
|
39.3
|
1.0
|
|
S4
|
B:SF4301
|
3.7
|
34.1
|
1.0
|
|
HG3
|
B:ARG65
|
3.8
|
53.4
|
1.0
|
|
N
|
B:SAH303
|
3.8
|
28.7
|
1.0
|
|
HB
|
B:VAL106
|
3.9
|
36.5
|
1.0
|
|
H
|
B:ARG65
|
4.0
|
44.4
|
1.0
|
|
CB
|
B:ARG65
|
4.0
|
37.9
|
1.0
|
|
HA
|
B:VAL106
|
4.1
|
34.4
|
1.0
|
|
HB3
|
B:ALA107
|
4.1
|
41.8
|
1.0
|
|
N
|
B:ALA107
|
4.2
|
32.8
|
1.0
|
|
H
|
B:ALA66
|
4.3
|
41.5
|
1.0
|
|
CG
|
B:ARG65
|
4.4
|
44.5
|
1.0
|
|
HB2
|
B:ALA107
|
4.4
|
41.8
|
1.0
|
|
HB3
|
B:ARG65
|
4.4
|
45.5
|
1.0
|
|
OXT
|
B:SAH303
|
4.4
|
39.4
|
1.0
|
|
H
|
B:CYS67
|
4.5
|
46.2
|
1.0
|
|
CA
|
B:CYS63
|
4.6
|
34.1
|
1.0
|
|
HB
|
B:VAL72
|
4.6
|
39.0
|
1.0
|
|
CB
|
B:ALA107
|
4.7
|
34.9
|
1.0
|
|
N
|
B:ARG65
|
4.7
|
37.0
|
1.0
|
|
CB
|
B:VAL106
|
4.7
|
30.4
|
1.0
|
|
CA
|
B:VAL106
|
4.8
|
28.7
|
1.0
|
|
SG
|
B:CYS67
|
4.8
|
35.2
|
1.0
|
|
HG11
|
B:VAL72
|
4.8
|
40.4
|
1.0
|
|
HG12
|
B:VAL106
|
4.8
|
38.0
|
1.0
|
|
SG
|
B:CYS70
|
4.8
|
32.0
|
1.0
|
|
CA
|
B:ARG65
|
4.8
|
35.7
|
1.0
|
|
HG2
|
B:ARG65
|
4.9
|
53.4
|
1.0
|
|
O
|
B:HOH468
|
4.9
|
40.1
|
1.0
|
|
N
|
B:ALA66
|
4.9
|
34.6
|
1.0
|
|
HA
|
B:CYS63
|
4.9
|
40.9
|
1.0
|
|
O
|
B:HOH474
|
4.9
|
38.0
|
1.0
|
|
CA
|
B:SAH303
|
4.9
|
50.2
|
1.0
|
|
Iron binding site 5 out
of 8 in 4u0p
Go back to
Iron Binding Sites List in 4u0p
Iron binding site 5 out
of 8 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe302
b:28.1
occ:1.00
|
FE1
|
B:SF4302
|
0.0
|
28.1
|
1.0
|
|
S3
|
B:SF4302
|
2.2
|
30.4
|
1.0
|
|
S4
|
B:SF4302
|
2.2
|
27.0
|
1.0
|
|
S2
|
B:SF4302
|
2.3
|
29.1
|
1.0
|
|
SG
|
B:CYS48
|
2.3
|
31.1
|
1.0
|
|
FE4
|
B:SF4302
|
2.7
|
29.2
|
1.0
|
|
FE3
|
B:SF4302
|
2.7
|
27.2
|
1.0
|
|
FE2
|
B:SF4302
|
2.8
|
27.1
|
1.0
|
|
HB2
|
B:CYS48
|
3.0
|
36.5
|
1.0
|
|
CB
|
B:CYS48
|
3.1
|
30.4
|
1.0
|
|
HB3
|
B:CYS48
|
3.2
|
36.5
|
1.0
|
|
HB2
|
B:ASN44
|
3.4
|
35.8
|
1.0
|
|
S1
|
B:SF4302
|
3.8
|
29.6
|
1.0
|
|
HA
|
B:TYR284
|
3.9
|
36.9
|
1.0
|
|
HD1
|
B:TYR284
|
4.0
|
41.0
|
1.0
|
|
HB3
|
B:ASN44
|
4.0
|
35.8
|
1.0
|
|
CB
|
B:ASN44
|
4.1
|
29.8
|
1.0
|
|
OG
|
B:SER283
|
4.4
|
29.2
|
1.0
|
|
HD22
|
B:ASN44
|
4.4
|
33.7
|
1.0
|
|
HB2
|
B:SER283
|
4.4
|
36.0
|
1.0
|
|
O
|
B:ASN44
|
4.6
|
29.3
|
1.0
|
|
CA
|
B:CYS48
|
4.6
|
32.5
|
1.0
|
|
HA
|
B:ARG45
|
4.7
|
35.2
|
1.0
|
|
H
|
B:CYS48
|
4.7
|
41.1
|
1.0
|
|
O
|
B:SER283
|
4.7
|
30.4
|
1.0
|
|
SG
|
B:CYS42
|
4.7
|
29.7
|
1.0
|
|
O
|
B:HOH540
|
4.7
|
40.6
|
1.0
|
|
C
|
B:ASN44
|
4.7
|
29.2
|
1.0
|
|
CA
|
B:TYR284
|
4.8
|
30.7
|
1.0
|
|
SG
|
B:CYS37
|
4.8
|
27.8
|
1.0
|
|
HG1
|
B:THR55
|
4.9
|
31.8
|
1.0
|
|
HB2
|
B:TYR284
|
4.9
|
34.8
|
1.0
|
|
HA
|
B:CYS48
|
4.9
|
39.0
|
1.0
|
|
CD1
|
B:TYR284
|
4.9
|
34.2
|
1.0
|
|
C
|
B:SER283
|
4.9
|
28.2
|
1.0
|
|
CB
|
B:SER283
|
4.9
|
30.0
|
1.0
|
|
N
|
B:TYR284
|
5.0
|
27.9
|
1.0
|
|
Iron binding site 6 out
of 8 in 4u0p
Go back to
Iron Binding Sites List in 4u0p
Iron binding site 6 out
of 8 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe302
b:27.1
occ:1.00
|
FE2
|
B:SF4302
|
0.0
|
27.1
|
1.0
|
|
S4
|
B:SF4302
|
2.2
|
27.0
|
1.0
|
|
S3
|
B:SF4302
|
2.2
|
30.4
|
1.0
|
|
S1
|
B:SF4302
|
2.2
|
29.6
|
1.0
|
|
SG
|
B:CYS37
|
2.3
|
27.8
|
1.0
|
|
FE3
|
B:SF4302
|
2.7
|
27.2
|
1.0
|
|
FE1
|
B:SF4302
|
2.8
|
28.1
|
1.0
|
|
FE4
|
B:SF4302
|
2.8
|
29.2
|
1.0
|
|
HB3
|
B:CYS37
|
3.2
|
34.1
|
1.0
|
|
CB
|
B:CYS37
|
3.2
|
28.5
|
1.0
|
|
HA
|
B:CYS37
|
3.3
|
33.8
|
1.0
|
|
CA
|
B:CYS37
|
3.7
|
28.2
|
1.0
|
|
HG1
|
B:THR55
|
3.8
|
31.8
|
1.0
|
|
HB
|
B:THR55
|
3.8
|
32.6
|
1.0
|
|
S2
|
B:SF4302
|
3.8
|
29.1
|
1.0
|
|
H
|
B:THR55
|
3.9
|
30.1
|
1.0
|
|
H
|
B:CYS37
|
3.9
|
36.6
|
1.0
|
|
HA
|
B:ALA54
|
4.0
|
32.5
|
1.0
|
|
HB2
|
B:CYS37
|
4.1
|
34.1
|
1.0
|
|
N
|
B:CYS37
|
4.1
|
30.5
|
1.0
|
|
HB3
|
B:CYS42
|
4.2
|
37.5
|
1.0
|
|
OG1
|
B:THR55
|
4.3
|
26.5
|
1.0
|
|
HB2
|
B:CYS48
|
4.4
|
36.5
|
1.0
|
|
N
|
B:THR55
|
4.4
|
25.0
|
1.0
|
|
HE1
|
B:TYR49
|
4.4
|
36.3
|
1.0
|
|
OG
|
B:SER283
|
4.4
|
29.2
|
1.0
|
|
CB
|
B:THR55
|
4.5
|
27.2
|
1.0
|
|
HB2
|
B:CYS42
|
4.5
|
37.5
|
1.0
|
|
HG2
|
B:ARG45
|
4.6
|
33.5
|
1.0
|
|
HB3
|
B:CYS48
|
4.6
|
36.5
|
1.0
|
|
CB
|
B:CYS42
|
4.7
|
31.2
|
1.0
|
|
SG
|
B:CYS42
|
4.7
|
29.7
|
1.0
|
|
HB
|
B:ILE36
|
4.8
|
35.8
|
1.0
|
|
CB
|
B:CYS48
|
4.8
|
30.4
|
1.0
|
|
SG
|
B:CYS48
|
4.8
|
31.1
|
1.0
|
|
HG22
|
B:ILE36
|
4.9
|
42.6
|
1.0
|
|
CA
|
B:ALA54
|
4.9
|
27.1
|
1.0
|
|
HB2
|
B:SER283
|
4.9
|
36.0
|
1.0
|
|
HG3
|
B:ARG45
|
4.9
|
33.5
|
1.0
|
|
HA
|
B:ARG45
|
4.9
|
35.2
|
1.0
|
|
C
|
B:ALA54
|
5.0
|
28.3
|
1.0
|
|
Iron binding site 7 out
of 8 in 4u0p
Go back to
Iron Binding Sites List in 4u0p
Iron binding site 7 out
of 8 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe302
b:27.2
occ:1.00
|
FE3
|
B:SF4302
|
0.0
|
27.2
|
1.0
|
|
S1
|
B:SF4302
|
2.2
|
29.6
|
1.0
|
|
S2
|
B:SF4302
|
2.2
|
29.1
|
1.0
|
|
S4
|
B:SF4302
|
2.3
|
27.0
|
1.0
|
|
SG
|
B:CYS42
|
2.3
|
29.7
|
1.0
|
|
FE2
|
B:SF4302
|
2.7
|
27.1
|
1.0
|
|
FE1
|
B:SF4302
|
2.7
|
28.1
|
1.0
|
|
FE4
|
B:SF4302
|
2.7
|
29.2
|
1.0
|
|
HB3
|
B:CYS42
|
3.0
|
37.5
|
1.0
|
|
HB2
|
B:ASN44
|
3.1
|
35.8
|
1.0
|
|
CB
|
B:CYS42
|
3.1
|
31.2
|
1.0
|
|
HB2
|
B:CYS42
|
3.2
|
37.5
|
1.0
|
|
HD22
|
B:ASN44
|
3.6
|
33.7
|
1.0
|
|
S3
|
B:SF4302
|
3.8
|
30.4
|
1.0
|
|
HG3
|
B:ARG281
|
3.9
|
39.9
|
1.0
|
|
HA
|
B:CYS37
|
3.9
|
33.8
|
1.0
|
|
H
|
B:ASN44
|
4.0
|
35.5
|
1.0
|
|
O
|
B:HOH553
|
4.0
|
37.5
|
1.0
|
|
CB
|
B:ASN44
|
4.0
|
29.8
|
1.0
|
|
ND2
|
B:ASN44
|
4.3
|
28.1
|
1.0
|
|
HB2
|
B:ARG281
|
4.3
|
39.2
|
1.0
|
|
HB3
|
B:ASN44
|
4.5
|
35.8
|
1.0
|
|
HB3
|
B:CYS37
|
4.6
|
34.1
|
1.0
|
|
CA
|
B:CYS42
|
4.6
|
34.1
|
1.0
|
|
HG3
|
B:ARG45
|
4.6
|
33.5
|
1.0
|
|
OG
|
B:SER283
|
4.6
|
29.2
|
1.0
|
|
N
|
B:ASN44
|
4.7
|
29.6
|
1.0
|
|
SG
|
B:CYS48
|
4.7
|
31.1
|
1.0
|
|
CG
|
B:ASN44
|
4.7
|
28.2
|
1.0
|
|
CA
|
B:ASN44
|
4.8
|
28.6
|
1.0
|
|
CG
|
B:ARG281
|
4.8
|
33.2
|
1.0
|
|
SG
|
B:CYS37
|
4.8
|
27.8
|
1.0
|
|
HH21
|
B:ARG281
|
4.8
|
43.0
|
1.0
|
|
CA
|
B:CYS37
|
4.8
|
28.2
|
1.0
|
|
HA
|
B:CYS42
|
4.9
|
40.9
|
1.0
|
|
C
|
B:ASN44
|
4.9
|
29.2
|
1.0
|
|
CB
|
B:CYS37
|
4.9
|
28.5
|
1.0
|
|
CB
|
B:ARG281
|
5.0
|
32.7
|
1.0
|
|
N
|
B:ARG45
|
5.0
|
29.3
|
1.0
|
|
HD2
|
B:PRO43
|
5.0
|
40.0
|
1.0
|
|
C
|
B:CYS42
|
5.0
|
30.2
|
1.0
|
|
H
|
B:ARG45
|
5.0
|
35.1
|
1.0
|
|
Iron binding site 8 out
of 8 in 4u0p
Go back to
Iron Binding Sites List in 4u0p
Iron binding site 8 out
of 8 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe302
b:29.2
occ:1.00
|
FE4
|
B:SF4302
|
0.0
|
29.2
|
1.0
|
|
OG
|
B:SER283
|
2.0
|
29.2
|
1.0
|
|
S1
|
B:SF4302
|
2.2
|
29.6
|
1.0
|
|
S2
|
B:SF4302
|
2.2
|
29.1
|
1.0
|
|
S3
|
B:SF4302
|
2.3
|
30.4
|
1.0
|
|
FE1
|
B:SF4302
|
2.7
|
28.1
|
1.0
|
|
FE3
|
B:SF4302
|
2.7
|
27.2
|
1.0
|
|
FE2
|
B:SF4302
|
2.8
|
27.1
|
1.0
|
|
HB2
|
B:SER283
|
3.0
|
36.0
|
1.0
|
|
CB
|
B:SER283
|
3.1
|
30.0
|
1.0
|
|
NA
|
B:NA304
|
3.5
|
45.7
|
1.0
|
|
HG1
|
B:THR55
|
3.5
|
31.8
|
1.0
|
|
H
|
B:SER283
|
3.7
|
34.6
|
1.0
|
|
HB3
|
B:SER283
|
3.7
|
36.0
|
1.0
|
|
OG1
|
B:THR55
|
3.8
|
26.5
|
1.0
|
|
S4
|
B:SF4302
|
3.8
|
27.0
|
1.0
|
|
HB2
|
B:ARG281
|
3.8
|
39.2
|
1.0
|
|
CA
|
B:SER283
|
4.0
|
27.1
|
1.0
|
|
C
|
B:SER283
|
4.0
|
28.2
|
1.0
|
|
N
|
B:TYR284
|
4.2
|
27.9
|
1.0
|
|
N
|
B:SER283
|
4.3
|
28.9
|
1.0
|
|
HB
|
B:THR55
|
4.3
|
32.6
|
1.0
|
|
O
|
B:SER283
|
4.3
|
30.4
|
1.0
|
|
HA
|
B:TYR284
|
4.4
|
36.9
|
1.0
|
|
H
|
B:TYR284
|
4.4
|
33.5
|
1.0
|
|
HB3
|
B:ARG281
|
4.5
|
39.2
|
1.0
|
|
CB
|
B:ARG281
|
4.6
|
32.7
|
1.0
|
|
CB
|
B:THR55
|
4.6
|
27.2
|
1.0
|
|
HG3
|
B:ARG281
|
4.7
|
39.9
|
1.0
|
|
HB2
|
B:TYR284
|
4.7
|
34.8
|
1.0
|
|
SG
|
B:CYS48
|
4.7
|
31.1
|
1.0
|
|
SG
|
B:CYS37
|
4.8
|
27.8
|
1.0
|
|
CA
|
B:TYR284
|
4.8
|
30.7
|
1.0
|
|
SG
|
B:CYS42
|
4.8
|
29.7
|
1.0
|
|
HA
|
B:SER283
|
4.8
|
32.6
|
1.0
|
|
O
|
B:HOH570
|
4.9
|
42.3
|
1.0
|
|
HD22
|
B:ASN44
|
4.9
|
33.7
|
1.0
|
|
O
|
B:HOH553
|
4.9
|
37.5
|
1.0
|
|
HB2
|
B:ASN44
|
5.0
|
35.8
|
1.0
|
|
Reference:
J.E.Harmer,
M.J.Hiscox,
P.C.Dinis,
S.J.Fox,
A.Iliopoulos,
J.E.Hussey,
J.Sandy,
F.T.Van Beek,
J.W.Essex,
P.L.Roach.
Structures of Lipoyl Synthase Reveal A Compact Active Site For Controlling Sequential Sulfur Insertion Reactions. Biochem.J. V. 464 123 2014.
ISSN: ESSN 1470-8728
PubMed: 25100160
DOI: 10.1042/BJ20140895
Page generated: Mon Aug 5 11:51:56 2024
|
