Iron in PDB 5mms: Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant
Enzymatic activity of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant
All present enzymatic activity of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant:
4.2.1.22;
Protein crystallography data
The structure of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant, PDB code: 5mms
was solved by
J.B.Vicente,
H.G.Colaco,
F.Malagrino,
P.E.Santo,
A.Gutierres,
T.M.Bandeiras,
P.Leandro,
J.A.Brito,
A.Giuffre,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
76.35 /
2.80
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
86.174,
86.783,
97.786,
102.67,
103.07,
111.19
|
R / Rfree (%)
|
18.2 /
22.1
|
Other elements in 5mms:
The structure of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant
(pdb code 5mms). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant, PDB code: 5mms:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 5mms
Go back to
Iron Binding Sites List in 5mms
Iron binding site 1 out
of 6 in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1001
b:47.2
occ:1.00
|
FE
|
A:HEM1001
|
0.0
|
47.2
|
1.0
|
NC
|
A:HEM1001
|
1.9
|
46.1
|
1.0
|
NB
|
A:HEM1001
|
2.0
|
47.4
|
1.0
|
ND
|
A:HEM1001
|
2.0
|
46.9
|
1.0
|
NA
|
A:HEM1001
|
2.0
|
48.3
|
1.0
|
NE2
|
A:HIS65
|
2.2
|
46.3
|
1.0
|
SG
|
A:CYS52
|
2.4
|
43.3
|
1.0
|
C1D
|
A:HEM1001
|
3.0
|
46.6
|
1.0
|
C4B
|
A:HEM1001
|
3.0
|
47.4
|
1.0
|
C1C
|
A:HEM1001
|
3.0
|
46.0
|
1.0
|
C4C
|
A:HEM1001
|
3.0
|
45.7
|
1.0
|
C4D
|
A:HEM1001
|
3.0
|
47.7
|
1.0
|
C1B
|
A:HEM1001
|
3.0
|
48.5
|
1.0
|
C4A
|
A:HEM1001
|
3.0
|
49.0
|
1.0
|
C1A
|
A:HEM1001
|
3.0
|
48.8
|
1.0
|
CD2
|
A:HIS65
|
3.1
|
46.5
|
1.0
|
CE1
|
A:HIS65
|
3.2
|
46.1
|
1.0
|
CHC
|
A:HEM1001
|
3.3
|
47.2
|
1.0
|
CHD
|
A:HEM1001
|
3.4
|
46.4
|
1.0
|
CHA
|
A:HEM1001
|
3.4
|
48.8
|
1.0
|
CHB
|
A:HEM1001
|
3.4
|
49.5
|
1.0
|
CB
|
A:CYS52
|
3.6
|
40.3
|
1.0
|
C2C
|
A:HEM1001
|
4.2
|
45.9
|
1.0
|
C2A
|
A:HEM1001
|
4.2
|
50.1
|
1.0
|
C3C
|
A:HEM1001
|
4.2
|
45.7
|
1.0
|
C2D
|
A:HEM1001
|
4.2
|
47.0
|
1.0
|
C3A
|
A:HEM1001
|
4.2
|
50.3
|
1.0
|
CA
|
A:CYS52
|
4.2
|
40.8
|
1.0
|
C3D
|
A:HEM1001
|
4.2
|
47.8
|
1.0
|
CG
|
A:HIS65
|
4.3
|
46.8
|
1.0
|
C2B
|
A:HEM1001
|
4.3
|
48.9
|
1.0
|
C3B
|
A:HEM1001
|
4.3
|
48.5
|
1.0
|
ND1
|
A:HIS65
|
4.3
|
47.2
|
1.0
|
NH1
|
A:ARG266
|
4.4
|
36.6
|
1.0
|
CB
|
A:TRP54
|
4.9
|
42.1
|
1.0
|
C
|
A:CYS52
|
4.9
|
48.0
|
1.0
|
N
|
A:THR53
|
4.9
|
48.1
|
1.0
|
CD
|
A:PRO64
|
5.0
|
54.0
|
1.0
|
CG
|
A:PRO64
|
5.0
|
57.8
|
1.0
|
|
Iron binding site 2 out
of 6 in 5mms
Go back to
Iron Binding Sites List in 5mms
Iron binding site 2 out
of 6 in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1001
b:41.1
occ:1.00
|
FE
|
B:HEM1001
|
0.0
|
41.1
|
1.0
|
NC
|
B:HEM1001
|
1.9
|
40.0
|
1.0
|
ND
|
B:HEM1001
|
1.9
|
40.6
|
1.0
|
NA
|
B:HEM1001
|
2.0
|
42.6
|
1.0
|
NB
|
B:HEM1001
|
2.0
|
41.7
|
1.0
|
NE2
|
B:HIS65
|
2.2
|
48.8
|
1.0
|
SG
|
B:CYS52
|
2.5
|
44.0
|
1.0
|
C1D
|
B:HEM1001
|
2.9
|
40.1
|
1.0
|
C4C
|
B:HEM1001
|
2.9
|
39.4
|
1.0
|
C1C
|
B:HEM1001
|
3.0
|
39.9
|
1.0
|
C4D
|
B:HEM1001
|
3.0
|
41.3
|
1.0
|
C4B
|
B:HEM1001
|
3.0
|
41.8
|
1.0
|
C4A
|
B:HEM1001
|
3.0
|
43.5
|
1.0
|
C1B
|
B:HEM1001
|
3.0
|
43.2
|
1.0
|
C1A
|
B:HEM1001
|
3.0
|
42.8
|
1.0
|
CD2
|
B:HIS65
|
3.1
|
49.0
|
1.0
|
CE1
|
B:HIS65
|
3.2
|
48.6
|
1.0
|
CHD
|
B:HEM1001
|
3.3
|
40.0
|
1.0
|
CHC
|
B:HEM1001
|
3.3
|
41.4
|
1.0
|
CHA
|
B:HEM1001
|
3.4
|
42.6
|
1.0
|
CHB
|
B:HEM1001
|
3.4
|
44.2
|
1.0
|
CB
|
B:CYS52
|
3.5
|
40.5
|
1.0
|
C2D
|
B:HEM1001
|
4.2
|
40.3
|
1.0
|
C2C
|
B:HEM1001
|
4.2
|
39.8
|
1.0
|
C3C
|
B:HEM1001
|
4.2
|
39.3
|
1.0
|
C3D
|
B:HEM1001
|
4.2
|
41.1
|
1.0
|
CA
|
B:CYS52
|
4.2
|
40.7
|
1.0
|
C2A
|
B:HEM1001
|
4.2
|
44.4
|
1.0
|
CG
|
B:HIS65
|
4.2
|
47.9
|
1.0
|
C3A
|
B:HEM1001
|
4.3
|
44.8
|
1.0
|
C2B
|
B:HEM1001
|
4.3
|
43.7
|
1.0
|
C3B
|
B:HEM1001
|
4.3
|
43.1
|
1.0
|
ND1
|
B:HIS65
|
4.3
|
49.7
|
1.0
|
NH1
|
B:ARG266
|
4.4
|
23.8
|
1.0
|
CB
|
B:TRP54
|
4.9
|
39.1
|
1.0
|
N
|
B:THR53
|
5.0
|
41.6
|
1.0
|
C
|
B:CYS52
|
5.0
|
44.7
|
1.0
|
CD
|
B:PRO64
|
5.0
|
44.4
|
1.0
|
|
Iron binding site 3 out
of 6 in 5mms
Go back to
Iron Binding Sites List in 5mms
Iron binding site 3 out
of 6 in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe1001
b:32.4
occ:1.00
|
FE
|
C:HEM1001
|
0.0
|
32.4
|
1.0
|
NC
|
C:HEM1001
|
1.9
|
31.4
|
1.0
|
NB
|
C:HEM1001
|
2.0
|
33.1
|
1.0
|
NA
|
C:HEM1001
|
2.0
|
33.5
|
1.0
|
ND
|
C:HEM1001
|
2.0
|
31.9
|
1.0
|
NE2
|
C:HIS65
|
2.2
|
43.2
|
1.0
|
SG
|
C:CYS52
|
2.4
|
42.7
|
1.0
|
C1D
|
C:HEM1001
|
2.9
|
31.8
|
1.0
|
C4B
|
C:HEM1001
|
3.0
|
33.1
|
1.0
|
C1C
|
C:HEM1001
|
3.0
|
31.5
|
1.0
|
C4D
|
C:HEM1001
|
3.0
|
32.5
|
1.0
|
C1B
|
C:HEM1001
|
3.0
|
34.3
|
1.0
|
C4C
|
C:HEM1001
|
3.0
|
31.1
|
1.0
|
C4A
|
C:HEM1001
|
3.0
|
34.4
|
1.0
|
C1A
|
C:HEM1001
|
3.0
|
33.7
|
1.0
|
CD2
|
C:HIS65
|
3.1
|
43.6
|
1.0
|
CE1
|
C:HIS65
|
3.2
|
42.6
|
1.0
|
CHC
|
C:HEM1001
|
3.3
|
32.8
|
1.0
|
CHA
|
C:HEM1001
|
3.4
|
33.5
|
1.0
|
CHD
|
C:HEM1001
|
3.4
|
31.7
|
1.0
|
CHB
|
C:HEM1001
|
3.4
|
35.3
|
1.0
|
CB
|
C:CYS52
|
3.5
|
40.1
|
1.0
|
C2A
|
C:HEM1001
|
4.2
|
35.0
|
1.0
|
CA
|
C:CYS52
|
4.2
|
41.0
|
1.0
|
C2C
|
C:HEM1001
|
4.2
|
31.4
|
1.0
|
C3A
|
C:HEM1001
|
4.2
|
35.5
|
1.0
|
C2D
|
C:HEM1001
|
4.2
|
32.0
|
1.0
|
C3C
|
C:HEM1001
|
4.2
|
31.0
|
1.0
|
C3D
|
C:HEM1001
|
4.2
|
32.6
|
1.0
|
C2B
|
C:HEM1001
|
4.2
|
35.0
|
1.0
|
C3B
|
C:HEM1001
|
4.3
|
34.6
|
1.0
|
CG
|
C:HIS65
|
4.3
|
42.5
|
1.0
|
ND1
|
C:HIS65
|
4.3
|
43.6
|
1.0
|
NH1
|
C:ARG266
|
4.4
|
45.0
|
1.0
|
CB
|
C:TRP54
|
4.9
|
34.2
|
1.0
|
N
|
C:THR53
|
4.9
|
39.5
|
1.0
|
C
|
C:CYS52
|
4.9
|
43.1
|
1.0
|
CD
|
C:PRO64
|
5.0
|
40.8
|
1.0
|
N
|
C:TRP54
|
5.0
|
37.6
|
1.0
|
CG
|
C:PRO64
|
5.0
|
45.2
|
1.0
|
|
Iron binding site 4 out
of 6 in 5mms
Go back to
Iron Binding Sites List in 5mms
Iron binding site 4 out
of 6 in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1001
b:41.0
occ:1.00
|
FE
|
D:HEM1001
|
0.0
|
41.0
|
1.0
|
NC
|
D:HEM1001
|
1.9
|
40.1
|
1.0
|
NA
|
D:HEM1001
|
2.0
|
42.1
|
1.0
|
ND
|
D:HEM1001
|
2.0
|
40.5
|
1.0
|
NB
|
D:HEM1001
|
2.0
|
41.5
|
1.0
|
NE2
|
D:HIS65
|
2.2
|
51.4
|
1.0
|
SG
|
D:CYS52
|
2.5
|
49.6
|
1.0
|
C1C
|
D:HEM1001
|
2.9
|
40.2
|
1.0
|
C4B
|
D:HEM1001
|
2.9
|
41.7
|
1.0
|
C4C
|
D:HEM1001
|
3.0
|
39.6
|
1.0
|
C4D
|
D:HEM1001
|
3.0
|
41.0
|
1.0
|
C1D
|
D:HEM1001
|
3.0
|
40.1
|
1.0
|
C1A
|
D:HEM1001
|
3.0
|
42.1
|
1.0
|
CD2
|
D:HIS65
|
3.0
|
51.8
|
1.0
|
C1B
|
D:HEM1001
|
3.0
|
42.8
|
1.0
|
C4A
|
D:HEM1001
|
3.0
|
42.8
|
1.0
|
CE1
|
D:HIS65
|
3.2
|
51.1
|
1.0
|
CHC
|
D:HEM1001
|
3.2
|
41.6
|
1.0
|
CHD
|
D:HEM1001
|
3.3
|
40.1
|
1.0
|
CHA
|
D:HEM1001
|
3.4
|
42.1
|
1.0
|
CHB
|
D:HEM1001
|
3.4
|
43.4
|
1.0
|
CB
|
D:CYS52
|
3.6
|
46.5
|
1.0
|
C2C
|
D:HEM1001
|
4.1
|
40.1
|
1.0
|
C3C
|
D:HEM1001
|
4.2
|
39.6
|
1.0
|
CG
|
D:HIS65
|
4.2
|
50.7
|
1.0
|
C2A
|
D:HEM1001
|
4.2
|
43.7
|
1.0
|
ND1
|
D:HIS65
|
4.3
|
51.8
|
1.0
|
C3B
|
D:HEM1001
|
4.3
|
43.0
|
1.0
|
C2B
|
D:HEM1001
|
4.3
|
43.2
|
1.0
|
C3A
|
D:HEM1001
|
4.3
|
44.0
|
1.0
|
C2D
|
D:HEM1001
|
4.3
|
40.3
|
1.0
|
C3D
|
D:HEM1001
|
4.3
|
41.0
|
1.0
|
CA
|
D:CYS52
|
4.4
|
46.9
|
1.0
|
NH1
|
D:ARG266
|
4.8
|
42.4
|
1.0
|
CB
|
D:TRP54
|
4.9
|
41.4
|
1.0
|
CD
|
D:PRO64
|
4.9
|
45.6
|
1.0
|
CG
|
D:PRO64
|
5.0
|
49.8
|
1.0
|
N
|
D:THR53
|
5.0
|
45.9
|
1.0
|
|
Iron binding site 5 out
of 6 in 5mms
Go back to
Iron Binding Sites List in 5mms
Iron binding site 5 out
of 6 in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe502
b:42.3
occ:1.00
|
FE
|
E:HEM502
|
0.0
|
42.3
|
1.0
|
NA
|
E:HEM502
|
1.9
|
43.7
|
1.0
|
ND
|
E:HEM502
|
2.0
|
41.5
|
1.0
|
NC
|
E:HEM502
|
2.0
|
41.2
|
1.0
|
NB
|
E:HEM502
|
2.0
|
43.2
|
1.0
|
NE2
|
E:HIS65
|
2.2
|
49.8
|
1.0
|
SG
|
E:CYS52
|
2.4
|
47.2
|
1.0
|
CE1
|
E:HIS65
|
2.9
|
49.3
|
1.0
|
C4D
|
E:HEM502
|
3.0
|
42.0
|
1.0
|
C1A
|
E:HEM502
|
3.0
|
43.8
|
1.0
|
C1D
|
E:HEM502
|
3.0
|
41.0
|
1.0
|
C4A
|
E:HEM502
|
3.0
|
44.8
|
1.0
|
C4C
|
E:HEM502
|
3.0
|
40.6
|
1.0
|
C1B
|
E:HEM502
|
3.0
|
44.8
|
1.0
|
C4B
|
E:HEM502
|
3.1
|
43.4
|
1.0
|
C1C
|
E:HEM502
|
3.1
|
41.3
|
1.0
|
CD2
|
E:HIS65
|
3.3
|
49.8
|
1.0
|
CHA
|
E:HEM502
|
3.3
|
43.4
|
1.0
|
CHD
|
E:HEM502
|
3.4
|
41.0
|
1.0
|
CHB
|
E:HEM502
|
3.4
|
45.7
|
1.0
|
CHC
|
E:HEM502
|
3.5
|
42.9
|
1.0
|
CB
|
E:CYS52
|
3.6
|
43.7
|
1.0
|
ND1
|
E:HIS65
|
4.1
|
49.5
|
1.0
|
C2A
|
E:HEM502
|
4.2
|
45.4
|
1.0
|
CA
|
E:CYS52
|
4.2
|
45.1
|
1.0
|
C3A
|
E:HEM502
|
4.2
|
46.0
|
1.0
|
C3C
|
E:HEM502
|
4.2
|
40.4
|
1.0
|
C2C
|
E:HEM502
|
4.2
|
41.0
|
1.0
|
C2D
|
E:HEM502
|
4.3
|
41.1
|
1.0
|
C3D
|
E:HEM502
|
4.3
|
41.8
|
1.0
|
CG
|
E:HIS65
|
4.3
|
48.5
|
1.0
|
C2B
|
E:HEM502
|
4.3
|
45.6
|
1.0
|
C3B
|
E:HEM502
|
4.4
|
45.0
|
1.0
|
NH1
|
E:ARG266
|
4.7
|
21.9
|
1.0
|
N
|
E:THR53
|
4.8
|
43.9
|
1.0
|
C
|
E:CYS52
|
4.9
|
46.9
|
1.0
|
CD
|
E:PRO64
|
4.9
|
47.2
|
1.0
|
CG
|
E:PRO64
|
5.0
|
51.2
|
1.0
|
|
Iron binding site 6 out
of 6 in 5mms
Go back to
Iron Binding Sites List in 5mms
Iron binding site 6 out
of 6 in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe502
b:39.4
occ:1.00
|
FE
|
F:HEM502
|
0.0
|
39.4
|
1.0
|
NB
|
F:HEM502
|
1.9
|
39.9
|
1.0
|
NC
|
F:HEM502
|
1.9
|
38.2
|
1.0
|
NA
|
F:HEM502
|
2.0
|
40.8
|
1.0
|
ND
|
F:HEM502
|
2.0
|
38.9
|
1.0
|
NE2
|
F:HIS65
|
2.3
|
44.5
|
1.0
|
SG
|
F:CYS52
|
2.7
|
47.6
|
1.0
|
C4B
|
F:HEM502
|
2.9
|
40.0
|
1.0
|
C1B
|
F:HEM502
|
3.0
|
41.3
|
1.0
|
C1C
|
F:HEM502
|
3.0
|
38.1
|
1.0
|
C1D
|
F:HEM502
|
3.0
|
38.5
|
1.0
|
C4A
|
F:HEM502
|
3.0
|
41.7
|
1.0
|
C4C
|
F:HEM502
|
3.0
|
37.6
|
1.0
|
C4D
|
F:HEM502
|
3.0
|
39.7
|
1.0
|
C1A
|
F:HEM502
|
3.0
|
41.1
|
1.0
|
CD2
|
F:HIS65
|
3.2
|
44.9
|
1.0
|
CHC
|
F:HEM502
|
3.3
|
39.6
|
1.0
|
CE1
|
F:HIS65
|
3.3
|
44.2
|
1.0
|
CHB
|
F:HEM502
|
3.4
|
42.4
|
1.0
|
CHD
|
F:HEM502
|
3.4
|
38.3
|
1.0
|
CHA
|
F:HEM502
|
3.4
|
40.9
|
1.0
|
CB
|
F:CYS52
|
3.6
|
43.8
|
1.0
|
C2C
|
F:HEM502
|
4.2
|
38.0
|
1.0
|
C2A
|
F:HEM502
|
4.2
|
42.5
|
1.0
|
C3A
|
F:HEM502
|
4.2
|
43.0
|
1.0
|
C2B
|
F:HEM502
|
4.2
|
41.9
|
1.0
|
C3C
|
F:HEM502
|
4.2
|
37.5
|
1.0
|
CA
|
F:CYS52
|
4.2
|
44.0
|
1.0
|
C3B
|
F:HEM502
|
4.2
|
41.3
|
1.0
|
C2D
|
F:HEM502
|
4.3
|
38.9
|
1.0
|
C3D
|
F:HEM502
|
4.3
|
39.8
|
1.0
|
CG
|
F:HIS65
|
4.3
|
44.8
|
1.0
|
NH1
|
F:ARG266
|
4.4
|
35.5
|
1.0
|
ND1
|
F:HIS65
|
4.4
|
45.5
|
1.0
|
CB
|
F:TRP54
|
4.8
|
42.0
|
1.0
|
N
|
F:THR53
|
4.9
|
47.3
|
1.0
|
C
|
F:CYS52
|
4.9
|
49.8
|
1.0
|
N
|
F:TRP54
|
5.0
|
44.8
|
1.0
|
CD
|
F:PRO64
|
5.0
|
47.3
|
1.0
|
|
Reference:
J.B.Vicente,
H.G.Colaco,
F.Malagrino,
P.E.Santo,
A.Gutierres,
T.M.Bandeiras,
P.Leandro,
J.A.Brito,
A.Giuffre.
A Clinically Relevant Variant of the Human Hydrogen Sulfide-Synthesizing Enzyme Cystathionine Beta-Synthase: Increased Co Reactivity As A Novel Molecular Mechanism of Pathogenicity? Oxid Med Cell Longev V.2017 40321 2017.
ISSN: ISSN 1942-0994
PubMed: 28421128
DOI: 10.1155/2017/8940321
Page generated: Tue Aug 6 06:01:41 2024
|