Iron in PDB 1m54: Cystathionine-Beta Synthase: Reduced Vicinal Thiols
Enzymatic activity of Cystathionine-Beta Synthase: Reduced Vicinal Thiols
All present enzymatic activity of Cystathionine-Beta Synthase: Reduced Vicinal Thiols:
4.2.1.22;
Protein crystallography data
The structure of Cystathionine-Beta Synthase: Reduced Vicinal Thiols, PDB code: 1m54
was solved by
S.Taoka,
B.W.Lepore,
O.Kabil,
S.Ojha,
D.Ringe,
R.Banerjee,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
50.00 /
2.90
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.740,
85.626,
97.082,
102.01,
101.53,
112.60
|
|
R / Rfree (%)
|
27.1 /
36.5
|
Iron Binding Sites:
The binding sites of Iron atom in the Cystathionine-Beta Synthase: Reduced Vicinal Thiols
(pdb code 1m54). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Cystathionine-Beta Synthase: Reduced Vicinal Thiols, PDB code: 1m54:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 1m54
Go back to
Iron Binding Sites List in 1m54
Iron binding site 1 out
of 6 in the Cystathionine-Beta Synthase: Reduced Vicinal Thiols
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Cystathionine-Beta Synthase: Reduced Vicinal Thiols within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1120
b:40.4
occ:1.00
|
FE
|
A:HEM1120
|
0.0
|
40.4
|
1.0
|
|
ND
|
A:HEM1120
|
2.0
|
37.5
|
1.0
|
|
NE2
|
A:HIS65
|
2.0
|
18.0
|
1.0
|
|
NC
|
A:HEM1120
|
2.0
|
39.2
|
1.0
|
|
NB
|
A:HEM1120
|
2.0
|
39.8
|
1.0
|
|
NA
|
A:HEM1120
|
2.1
|
39.6
|
1.0
|
|
SG
|
A:CYS52
|
2.5
|
32.4
|
1.0
|
|
CD2
|
A:HIS65
|
3.0
|
20.8
|
1.0
|
|
CE1
|
A:HIS65
|
3.0
|
18.7
|
1.0
|
|
C4D
|
A:HEM1120
|
3.0
|
37.2
|
1.0
|
|
C1D
|
A:HEM1120
|
3.0
|
37.1
|
1.0
|
|
C1B
|
A:HEM1120
|
3.0
|
40.4
|
1.0
|
|
C1C
|
A:HEM1120
|
3.0
|
38.2
|
1.0
|
|
C4C
|
A:HEM1120
|
3.1
|
38.9
|
1.0
|
|
C4A
|
A:HEM1120
|
3.1
|
39.8
|
1.0
|
|
C1A
|
A:HEM1120
|
3.1
|
37.4
|
1.0
|
|
C4B
|
A:HEM1120
|
3.1
|
39.4
|
1.0
|
|
CHB
|
A:HEM1120
|
3.4
|
40.2
|
1.0
|
|
CHD
|
A:HEM1120
|
3.4
|
38.2
|
1.0
|
|
CHA
|
A:HEM1120
|
3.4
|
37.4
|
1.0
|
|
CHC
|
A:HEM1120
|
3.4
|
38.4
|
1.0
|
|
CB
|
A:CYS52
|
3.6
|
31.7
|
1.0
|
|
ND1
|
A:HIS65
|
4.1
|
21.6
|
1.0
|
|
CG
|
A:HIS65
|
4.1
|
22.4
|
1.0
|
|
CA
|
A:CYS52
|
4.2
|
29.2
|
1.0
|
|
C2D
|
A:HEM1120
|
4.3
|
36.4
|
1.0
|
|
C3D
|
A:HEM1120
|
4.3
|
35.0
|
1.0
|
|
C2B
|
A:HEM1120
|
4.3
|
40.4
|
1.0
|
|
C3C
|
A:HEM1120
|
4.3
|
39.1
|
1.0
|
|
C2C
|
A:HEM1120
|
4.3
|
39.2
|
1.0
|
|
C3A
|
A:HEM1120
|
4.3
|
39.4
|
1.0
|
|
C2A
|
A:HEM1120
|
4.3
|
38.0
|
1.0
|
|
C3B
|
A:HEM1120
|
4.3
|
40.4
|
1.0
|
|
NH1
|
A:ARG266
|
4.4
|
22.5
|
1.0
|
|
C
|
A:CYS52
|
4.8
|
27.6
|
1.0
|
|
N
|
A:THR53
|
4.8
|
28.1
|
1.0
|
|
CB
|
A:TRP54
|
4.9
|
29.1
|
1.0
|
|
Iron binding site 2 out
of 6 in 1m54
Go back to
Iron Binding Sites List in 1m54
Iron binding site 2 out
of 6 in the Cystathionine-Beta Synthase: Reduced Vicinal Thiols
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Cystathionine-Beta Synthase: Reduced Vicinal Thiols within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1220
b:36.5
occ:1.00
|
FE
|
B:HEM1220
|
0.0
|
36.5
|
1.0
|
|
ND
|
B:HEM1220
|
2.0
|
35.5
|
1.0
|
|
NC
|
B:HEM1220
|
2.0
|
37.1
|
1.0
|
|
NE2
|
B:HIS65
|
2.0
|
21.5
|
1.0
|
|
NB
|
B:HEM1220
|
2.0
|
36.2
|
1.0
|
|
NA
|
B:HEM1220
|
2.1
|
37.7
|
1.0
|
|
SG
|
B:CYS52
|
2.4
|
27.8
|
1.0
|
|
CD2
|
B:HIS65
|
3.0
|
23.5
|
1.0
|
|
CE1
|
B:HIS65
|
3.0
|
20.9
|
1.0
|
|
C1C
|
B:HEM1220
|
3.0
|
37.3
|
1.0
|
|
C1B
|
B:HEM1220
|
3.1
|
37.2
|
1.0
|
|
C4D
|
B:HEM1220
|
3.1
|
34.5
|
1.0
|
|
C4C
|
B:HEM1220
|
3.1
|
35.6
|
1.0
|
|
C1D
|
B:HEM1220
|
3.1
|
34.2
|
1.0
|
|
C4B
|
B:HEM1220
|
3.1
|
37.5
|
1.0
|
|
C4A
|
B:HEM1220
|
3.1
|
38.5
|
1.0
|
|
C1A
|
B:HEM1220
|
3.1
|
35.7
|
1.0
|
|
CHD
|
B:HEM1220
|
3.4
|
34.0
|
1.0
|
|
CHC
|
B:HEM1220
|
3.4
|
37.8
|
1.0
|
|
CHB
|
B:HEM1220
|
3.4
|
38.1
|
1.0
|
|
CHA
|
B:HEM1220
|
3.4
|
34.5
|
1.0
|
|
CB
|
B:CYS52
|
3.5
|
25.9
|
1.0
|
|
ND1
|
B:HIS65
|
4.1
|
23.8
|
1.0
|
|
CG
|
B:HIS65
|
4.1
|
25.1
|
1.0
|
|
C2C
|
B:HEM1220
|
4.3
|
37.0
|
1.0
|
|
C3C
|
B:HEM1220
|
4.3
|
35.8
|
1.0
|
|
C3D
|
B:HEM1220
|
4.3
|
32.9
|
1.0
|
|
C2D
|
B:HEM1220
|
4.3
|
33.3
|
1.0
|
|
C3B
|
B:HEM1220
|
4.3
|
37.1
|
1.0
|
|
C2B
|
B:HEM1220
|
4.3
|
36.9
|
1.0
|
|
C3A
|
B:HEM1220
|
4.3
|
37.5
|
1.0
|
|
C2A
|
B:HEM1220
|
4.3
|
35.7
|
1.0
|
|
N
|
B:THR53
|
4.4
|
27.8
|
1.0
|
|
CA
|
B:CYS52
|
4.5
|
26.7
|
1.0
|
|
C
|
B:CYS52
|
4.9
|
27.2
|
1.0
|
|
Iron binding site 3 out
of 6 in 1m54
Go back to
Iron Binding Sites List in 1m54
Iron binding site 3 out
of 6 in the Cystathionine-Beta Synthase: Reduced Vicinal Thiols
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Cystathionine-Beta Synthase: Reduced Vicinal Thiols within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe1320
b:37.4
occ:1.00
|
FE
|
C:HEM1320
|
0.0
|
37.4
|
1.0
|
|
ND
|
C:HEM1320
|
2.0
|
36.5
|
1.0
|
|
NE2
|
C:HIS65
|
2.0
|
26.8
|
1.0
|
|
NC
|
C:HEM1320
|
2.0
|
36.4
|
1.0
|
|
NB
|
C:HEM1320
|
2.0
|
38.1
|
1.0
|
|
NA
|
C:HEM1320
|
2.1
|
38.1
|
1.0
|
|
SG
|
C:CYS52
|
2.3
|
20.7
|
1.0
|
|
CD2
|
C:HIS65
|
2.9
|
29.1
|
1.0
|
|
CE1
|
C:HIS65
|
3.0
|
27.2
|
1.0
|
|
C4D
|
C:HEM1320
|
3.0
|
36.0
|
1.0
|
|
C1C
|
C:HEM1320
|
3.0
|
36.6
|
1.0
|
|
C1B
|
C:HEM1320
|
3.0
|
38.8
|
1.0
|
|
C1D
|
C:HEM1320
|
3.0
|
35.6
|
1.0
|
|
C4C
|
C:HEM1320
|
3.1
|
34.9
|
1.0
|
|
C1A
|
C:HEM1320
|
3.1
|
37.3
|
1.0
|
|
C4B
|
C:HEM1320
|
3.1
|
39.1
|
1.0
|
|
C4A
|
C:HEM1320
|
3.1
|
38.0
|
1.0
|
|
CHA
|
C:HEM1320
|
3.4
|
37.1
|
1.0
|
|
CHD
|
C:HEM1320
|
3.4
|
34.9
|
1.0
|
|
CHB
|
C:HEM1320
|
3.4
|
39.3
|
1.0
|
|
CHC
|
C:HEM1320
|
3.4
|
39.2
|
1.0
|
|
CB
|
C:CYS52
|
3.6
|
20.5
|
1.0
|
|
CG
|
C:HIS65
|
4.1
|
29.7
|
1.0
|
|
ND1
|
C:HIS65
|
4.1
|
28.8
|
1.0
|
|
C3D
|
C:HEM1320
|
4.3
|
35.2
|
1.0
|
|
C2D
|
C:HEM1320
|
4.3
|
35.3
|
1.0
|
|
C2B
|
C:HEM1320
|
4.3
|
39.4
|
1.0
|
|
C2C
|
C:HEM1320
|
4.3
|
35.1
|
1.0
|
|
C3C
|
C:HEM1320
|
4.3
|
34.5
|
1.0
|
|
C3B
|
C:HEM1320
|
4.3
|
39.7
|
1.0
|
|
C2A
|
C:HEM1320
|
4.3
|
36.5
|
1.0
|
|
C3A
|
C:HEM1320
|
4.3
|
36.2
|
1.0
|
|
CA
|
C:CYS52
|
4.4
|
20.5
|
1.0
|
|
NH1
|
C:ARG266
|
4.9
|
23.2
|
1.0
|
|
N
|
C:THR53
|
4.9
|
19.0
|
1.0
|
|
Iron binding site 4 out
of 6 in 1m54
Go back to
Iron Binding Sites List in 1m54
Iron binding site 4 out
of 6 in the Cystathionine-Beta Synthase: Reduced Vicinal Thiols
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Cystathionine-Beta Synthase: Reduced Vicinal Thiols within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1420
b:31.6
occ:1.00
|
FE
|
D:HEM1420
|
0.0
|
31.6
|
1.0
|
|
ND
|
D:HEM1420
|
2.0
|
32.3
|
1.0
|
|
NE2
|
D:HIS65
|
2.0
|
24.2
|
1.0
|
|
NC
|
D:HEM1420
|
2.0
|
32.1
|
1.0
|
|
NB
|
D:HEM1420
|
2.0
|
32.8
|
1.0
|
|
NA
|
D:HEM1420
|
2.1
|
33.6
|
1.0
|
|
SG
|
D:CYS52
|
2.3
|
33.5
|
1.0
|
|
CD2
|
D:HIS65
|
2.9
|
26.0
|
1.0
|
|
C1C
|
D:HEM1420
|
3.0
|
30.4
|
1.0
|
|
C1B
|
D:HEM1420
|
3.0
|
33.3
|
1.0
|
|
C4D
|
D:HEM1420
|
3.0
|
32.0
|
1.0
|
|
CE1
|
D:HIS65
|
3.0
|
26.0
|
1.0
|
|
C1D
|
D:HEM1420
|
3.0
|
31.8
|
1.0
|
|
C4C
|
D:HEM1420
|
3.0
|
31.2
|
1.0
|
|
C4A
|
D:HEM1420
|
3.1
|
34.2
|
1.0
|
|
C1A
|
D:HEM1420
|
3.1
|
31.7
|
1.0
|
|
C4B
|
D:HEM1420
|
3.1
|
32.3
|
1.0
|
|
CHB
|
D:HEM1420
|
3.4
|
34.4
|
1.0
|
|
CHD
|
D:HEM1420
|
3.4
|
32.2
|
1.0
|
|
CHA
|
D:HEM1420
|
3.4
|
31.1
|
1.0
|
|
CHC
|
D:HEM1420
|
3.4
|
31.2
|
1.0
|
|
CB
|
D:CYS52
|
3.6
|
31.9
|
1.0
|
|
CG
|
D:HIS65
|
4.1
|
28.4
|
1.0
|
|
ND1
|
D:HIS65
|
4.1
|
26.9
|
1.0
|
|
CA
|
D:CYS52
|
4.3
|
31.1
|
1.0
|
|
C2C
|
D:HEM1420
|
4.3
|
29.1
|
1.0
|
|
C2D
|
D:HEM1420
|
4.3
|
31.0
|
1.0
|
|
C3C
|
D:HEM1420
|
4.3
|
29.9
|
1.0
|
|
C3D
|
D:HEM1420
|
4.3
|
31.3
|
1.0
|
|
C2B
|
D:HEM1420
|
4.3
|
33.0
|
1.0
|
|
C3A
|
D:HEM1420
|
4.3
|
33.4
|
1.0
|
|
C2A
|
D:HEM1420
|
4.3
|
32.0
|
1.0
|
|
C3B
|
D:HEM1420
|
4.3
|
32.4
|
1.0
|
|
NH1
|
D:ARG266
|
4.7
|
23.4
|
1.0
|
|
N
|
D:THR53
|
4.8
|
33.9
|
1.0
|
|
C
|
D:CYS52
|
5.0
|
32.8
|
1.0
|
|
Iron binding site 5 out
of 6 in 1m54
Go back to
Iron Binding Sites List in 1m54
Iron binding site 5 out
of 6 in the Cystathionine-Beta Synthase: Reduced Vicinal Thiols
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Cystathionine-Beta Synthase: Reduced Vicinal Thiols within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe1520
b:44.6
occ:1.00
|
FE
|
E:HEM1520
|
0.0
|
44.6
|
1.0
|
|
ND
|
E:HEM1520
|
2.0
|
42.6
|
1.0
|
|
NE2
|
E:HIS65
|
2.0
|
30.3
|
1.0
|
|
NC
|
E:HEM1520
|
2.0
|
44.4
|
1.0
|
|
NB
|
E:HEM1520
|
2.0
|
45.5
|
1.0
|
|
NA
|
E:HEM1520
|
2.1
|
44.5
|
1.0
|
|
SG
|
E:CYS52
|
2.4
|
38.6
|
1.0
|
|
CD2
|
E:HIS65
|
2.9
|
31.8
|
1.0
|
|
CE1
|
E:HIS65
|
3.0
|
31.7
|
1.0
|
|
C1C
|
E:HEM1520
|
3.0
|
43.7
|
1.0
|
|
C1D
|
E:HEM1520
|
3.0
|
42.0
|
1.0
|
|
C4D
|
E:HEM1520
|
3.1
|
42.3
|
1.0
|
|
C1B
|
E:HEM1520
|
3.1
|
45.5
|
1.0
|
|
C4C
|
E:HEM1520
|
3.1
|
43.3
|
1.0
|
|
C4A
|
E:HEM1520
|
3.1
|
45.4
|
1.0
|
|
C4B
|
E:HEM1520
|
3.1
|
45.2
|
1.0
|
|
C1A
|
E:HEM1520
|
3.1
|
43.3
|
1.0
|
|
CHB
|
E:HEM1520
|
3.4
|
46.0
|
1.0
|
|
CHD
|
E:HEM1520
|
3.4
|
42.6
|
1.0
|
|
CHC
|
E:HEM1520
|
3.4
|
44.5
|
1.0
|
|
CHA
|
E:HEM1520
|
3.4
|
43.3
|
1.0
|
|
CB
|
E:CYS52
|
3.6
|
36.0
|
1.0
|
|
CG
|
E:HIS65
|
4.1
|
33.5
|
1.0
|
|
ND1
|
E:HIS65
|
4.1
|
32.5
|
1.0
|
|
C2D
|
E:HEM1520
|
4.3
|
42.5
|
1.0
|
|
C3D
|
E:HEM1520
|
4.3
|
41.7
|
1.0
|
|
C2C
|
E:HEM1520
|
4.3
|
43.1
|
1.0
|
|
C3C
|
E:HEM1520
|
4.3
|
42.6
|
1.0
|
|
C2B
|
E:HEM1520
|
4.3
|
45.6
|
1.0
|
|
C3A
|
E:HEM1520
|
4.3
|
44.1
|
1.0
|
|
C3B
|
E:HEM1520
|
4.3
|
46.1
|
1.0
|
|
C2A
|
E:HEM1520
|
4.3
|
43.2
|
1.0
|
|
CA
|
E:CYS52
|
4.5
|
33.8
|
1.0
|
|
NH1
|
E:ARG266
|
4.8
|
30.9
|
1.0
|
|
CB
|
E:TRP54
|
4.8
|
26.9
|
1.0
|
|
N
|
E:THR53
|
4.9
|
30.2
|
1.0
|
|
CG
|
E:PRO64
|
5.0
|
31.1
|
1.0
|
|
Iron binding site 6 out
of 6 in 1m54
Go back to
Iron Binding Sites List in 1m54
Iron binding site 6 out
of 6 in the Cystathionine-Beta Synthase: Reduced Vicinal Thiols
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Cystathionine-Beta Synthase: Reduced Vicinal Thiols within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe1620
b:38.5
occ:1.00
|
FE
|
F:HEM1620
|
0.0
|
38.5
|
1.0
|
|
ND
|
F:HEM1620
|
2.0
|
37.4
|
1.0
|
|
NC
|
F:HEM1620
|
2.0
|
36.6
|
1.0
|
|
NE2
|
F:HIS65
|
2.0
|
34.2
|
1.0
|
|
NB
|
F:HEM1620
|
2.0
|
36.9
|
1.0
|
|
NA
|
F:HEM1620
|
2.1
|
38.4
|
1.0
|
|
SG
|
F:CYS52
|
2.8
|
34.2
|
1.0
|
|
CD2
|
F:HIS65
|
3.0
|
36.2
|
1.0
|
|
C4D
|
F:HEM1620
|
3.0
|
37.1
|
1.0
|
|
CE1
|
F:HIS65
|
3.0
|
34.4
|
1.0
|
|
C1C
|
F:HEM1620
|
3.0
|
35.6
|
1.0
|
|
C1D
|
F:HEM1620
|
3.0
|
37.4
|
1.0
|
|
C1B
|
F:HEM1620
|
3.1
|
36.2
|
1.0
|
|
C1A
|
F:HEM1620
|
3.1
|
37.9
|
1.0
|
|
C4C
|
F:HEM1620
|
3.1
|
35.8
|
1.0
|
|
C4A
|
F:HEM1620
|
3.1
|
37.8
|
1.0
|
|
C4B
|
F:HEM1620
|
3.1
|
35.3
|
1.0
|
|
CHA
|
F:HEM1620
|
3.4
|
36.7
|
1.0
|
|
CHB
|
F:HEM1620
|
3.4
|
36.5
|
1.0
|
|
CHD
|
F:HEM1620
|
3.4
|
37.4
|
1.0
|
|
CHC
|
F:HEM1620
|
3.4
|
35.7
|
1.0
|
|
CB
|
F:CYS52
|
3.6
|
30.8
|
1.0
|
|
ND1
|
F:HIS65
|
4.1
|
35.9
|
1.0
|
|
CG
|
F:HIS65
|
4.1
|
36.6
|
1.0
|
|
C3D
|
F:HEM1620
|
4.3
|
37.1
|
1.0
|
|
C2D
|
F:HEM1620
|
4.3
|
36.9
|
1.0
|
|
C2C
|
F:HEM1620
|
4.3
|
34.8
|
1.0
|
|
C3C
|
F:HEM1620
|
4.3
|
33.8
|
1.0
|
|
C2A
|
F:HEM1620
|
4.3
|
38.0
|
1.0
|
|
C2B
|
F:HEM1620
|
4.3
|
35.3
|
1.0
|
|
C3B
|
F:HEM1620
|
4.3
|
34.8
|
1.0
|
|
C3A
|
F:HEM1620
|
4.3
|
38.2
|
1.0
|
|
CA
|
F:CYS52
|
4.5
|
28.1
|
1.0
|
|
CB
|
F:TRP54
|
4.8
|
25.5
|
1.0
|
|
N
|
F:TRP54
|
4.8
|
25.2
|
1.0
|
|
N
|
F:THR53
|
4.9
|
25.8
|
1.0
|
|
Reference:
S.Taoka,
B.W.Lepore,
O.Kabil,
S.Ojha,
D.Ringe,
R.Banerjee.
Human Cystathionine Beta-Synthase Is A Heme Sensor Protein. Evidence That the Redox Sensor Is Heme and Not the Vicinal Cysteines in the Cxxc Motif Seen in the Crystal Structure of the Truncated Enzyme Biochemistry V. 41 10454 2002.
ISSN: ISSN 0006-2960
PubMed: 12173932
DOI: 10.1021/BI026052D
Page generated: Sun Dec 13 14:22:57 2020
|
