Iron in PDB 4r33: X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound
Protein crystallography data
The structure of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound, PDB code: 4r33
was solved by
Y.Nicolet,
L.Zeppieri,
P.Amara,
J.-C.Fontecilla-Camps,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.23 /
1.78
|
Space group
|
P 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.720,
47.230,
114.360,
90.00,
108.71,
90.00
|
R / Rfree (%)
|
15.9 /
18.1
|
Other elements in 4r33:
The structure of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound
(pdb code 4r33). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound, PDB code: 4r33:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 4r33
Go back to
Iron Binding Sites List in 4r33
Iron binding site 1 out
of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:31.1
occ:1.00
|
FE1
|
A:SF4502
|
0.0
|
31.1
|
1.0
|
S4
|
A:SF4502
|
2.3
|
33.3
|
1.0
|
S3
|
A:SF4502
|
2.3
|
31.7
|
1.0
|
SG
|
A:CYS95
|
2.3
|
32.3
|
1.0
|
S2
|
A:SF4502
|
2.3
|
34.5
|
1.0
|
FE2
|
A:SF4502
|
2.7
|
32.4
|
1.0
|
FE3
|
A:SF4502
|
2.7
|
32.4
|
1.0
|
FE4
|
A:SF4502
|
2.8
|
31.0
|
1.0
|
CB
|
A:CYS95
|
3.4
|
30.2
|
1.0
|
S1
|
A:SF4502
|
3.9
|
33.2
|
1.0
|
N
|
A:SAH501
|
4.0
|
28.7
|
1.0
|
CB
|
A:SER97
|
4.2
|
41.9
|
1.0
|
N
|
A:GLU143
|
4.3
|
30.0
|
1.0
|
CA
|
A:GLY142
|
4.5
|
26.9
|
1.0
|
O
|
A:SAH501
|
4.6
|
35.1
|
1.0
|
CB
|
A:MET104
|
4.7
|
31.5
|
1.0
|
SG
|
A:CYS99
|
4.8
|
35.4
|
1.0
|
N
|
A:SER97
|
4.8
|
35.1
|
1.0
|
O
|
A:MET104
|
4.8
|
32.2
|
1.0
|
CA
|
A:CYS95
|
4.8
|
33.2
|
1.0
|
C
|
A:MET104
|
4.8
|
32.3
|
1.0
|
SG
|
A:CYS102
|
4.9
|
32.9
|
1.0
|
CA
|
A:SER97
|
4.9
|
39.2
|
1.0
|
C
|
A:SER97
|
4.9
|
38.2
|
1.0
|
C
|
A:GLY142
|
4.9
|
28.9
|
1.0
|
O
|
A:SER97
|
4.9
|
36.1
|
1.0
|
N
|
A:ARG105
|
5.0
|
35.8
|
1.0
|
|
Iron binding site 2 out
of 8 in 4r33
Go back to
Iron Binding Sites List in 4r33
Iron binding site 2 out
of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:32.4
occ:1.00
|
FE2
|
A:SF4502
|
0.0
|
32.4
|
1.0
|
S4
|
A:SF4502
|
2.3
|
33.3
|
1.0
|
S3
|
A:SF4502
|
2.3
|
31.7
|
1.0
|
S1
|
A:SF4502
|
2.3
|
33.2
|
1.0
|
SG
|
A:CYS102
|
2.4
|
32.9
|
1.0
|
FE3
|
A:SF4502
|
2.6
|
32.4
|
1.0
|
FE1
|
A:SF4502
|
2.7
|
31.1
|
1.0
|
FE4
|
A:SF4502
|
2.8
|
31.0
|
1.0
|
CB
|
A:CYS102
|
3.2
|
31.8
|
1.0
|
S2
|
A:SF4502
|
3.9
|
34.5
|
1.0
|
NE2
|
A:GLN363
|
4.0
|
34.2
|
1.0
|
CB
|
A:MET104
|
4.1
|
31.5
|
1.0
|
CB
|
A:CYS99
|
4.5
|
34.0
|
1.0
|
SG
|
A:CYS99
|
4.6
|
35.4
|
1.0
|
O
|
A:SAH501
|
4.6
|
35.1
|
1.0
|
N
|
A:ARG105
|
4.6
|
35.8
|
1.0
|
CA
|
A:CYS102
|
4.7
|
32.7
|
1.0
|
C
|
A:MET104
|
4.7
|
32.3
|
1.0
|
N
|
A:SAH501
|
4.8
|
28.7
|
1.0
|
CA
|
A:MET104
|
4.8
|
31.2
|
1.0
|
N
|
A:MET104
|
4.8
|
31.6
|
1.0
|
CG
|
A:SAH501
|
4.8
|
28.4
|
1.0
|
SG
|
A:CYS95
|
4.9
|
32.3
|
1.0
|
CD
|
A:GLN363
|
4.9
|
32.8
|
1.0
|
CG
|
A:GLN363
|
4.9
|
32.0
|
1.0
|
|
Iron binding site 3 out
of 8 in 4r33
Go back to
Iron Binding Sites List in 4r33
Iron binding site 3 out
of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:32.4
occ:1.00
|
FE3
|
A:SF4502
|
0.0
|
32.4
|
1.0
|
S2
|
A:SF4502
|
2.3
|
34.5
|
1.0
|
SG
|
A:CYS99
|
2.3
|
35.4
|
1.0
|
S4
|
A:SF4502
|
2.3
|
33.3
|
1.0
|
S1
|
A:SF4502
|
2.3
|
33.2
|
1.0
|
FE2
|
A:SF4502
|
2.6
|
32.4
|
1.0
|
FE1
|
A:SF4502
|
2.7
|
31.1
|
1.0
|
FE4
|
A:SF4502
|
2.7
|
31.0
|
1.0
|
CB
|
A:CYS99
|
3.2
|
34.0
|
1.0
|
NZ
|
A:LYS224
|
3.7
|
29.7
|
1.0
|
S3
|
A:SF4502
|
3.8
|
31.7
|
1.0
|
O
|
A:SAH501
|
3.8
|
35.1
|
1.0
|
CD
|
A:LYS224
|
3.8
|
33.9
|
1.0
|
N
|
A:CYS99
|
4.1
|
35.6
|
1.0
|
CA
|
A:CYS99
|
4.3
|
35.6
|
1.0
|
CE
|
A:LYS224
|
4.3
|
33.0
|
1.0
|
CB
|
A:SER97
|
4.5
|
41.9
|
1.0
|
CB
|
A:CYS102
|
4.7
|
31.8
|
1.0
|
SG
|
A:CYS95
|
4.7
|
32.3
|
1.0
|
SG
|
A:CYS102
|
4.7
|
32.9
|
1.0
|
O
|
A:HOH676
|
4.8
|
30.0
|
1.0
|
N
|
A:SAH501
|
4.9
|
28.7
|
1.0
|
|
Iron binding site 4 out
of 8 in 4r33
Go back to
Iron Binding Sites List in 4r33
Iron binding site 4 out
of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:31.0
occ:1.00
|
FE4
|
A:SF4502
|
0.0
|
31.0
|
1.0
|
O
|
A:SAH501
|
2.0
|
35.1
|
1.0
|
S3
|
A:SF4502
|
2.3
|
31.7
|
1.0
|
S1
|
A:SF4502
|
2.3
|
33.2
|
1.0
|
S2
|
A:SF4502
|
2.3
|
34.5
|
1.0
|
N
|
A:SAH501
|
2.3
|
28.7
|
1.0
|
FE3
|
A:SF4502
|
2.7
|
32.4
|
1.0
|
FE1
|
A:SF4502
|
2.8
|
31.1
|
1.0
|
FE2
|
A:SF4502
|
2.8
|
32.4
|
1.0
|
C
|
A:SAH501
|
2.9
|
34.3
|
1.0
|
CA
|
A:SAH501
|
3.1
|
28.9
|
1.0
|
CG
|
A:SAH501
|
3.2
|
28.4
|
1.0
|
CB
|
A:SAH501
|
3.7
|
25.6
|
1.0
|
NZ
|
A:LYS224
|
3.9
|
29.7
|
1.0
|
S4
|
A:SF4502
|
4.0
|
33.3
|
1.0
|
OXT
|
A:SAH501
|
4.1
|
33.8
|
1.0
|
SD
|
A:SAH501
|
4.6
|
43.2
|
1.0
|
CD
|
A:LYS224
|
4.7
|
33.9
|
1.0
|
SG
|
A:CYS95
|
4.7
|
32.3
|
1.0
|
SG
|
A:CYS99
|
4.8
|
35.4
|
1.0
|
NE2
|
A:GLN363
|
4.9
|
34.2
|
1.0
|
N
|
A:GLU143
|
5.0
|
30.0
|
1.0
|
CE
|
A:LYS224
|
5.0
|
33.0
|
1.0
|
O
|
A:THR141
|
5.0
|
27.9
|
1.0
|
|
Iron binding site 5 out
of 8 in 4r33
Go back to
Iron Binding Sites List in 4r33
Iron binding site 5 out
of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe502
b:17.7
occ:1.00
|
FE1
|
B:SF4502
|
0.0
|
17.7
|
1.0
|
S4
|
B:SF4502
|
2.3
|
18.2
|
1.0
|
SG
|
B:CYS95
|
2.3
|
16.7
|
1.0
|
S3
|
B:SF4502
|
2.3
|
19.8
|
1.0
|
S2
|
B:SF4502
|
2.3
|
17.4
|
1.0
|
FE2
|
B:SF4502
|
2.7
|
17.6
|
1.0
|
FE3
|
B:SF4502
|
2.7
|
17.8
|
1.0
|
FE4
|
B:SF4502
|
2.8
|
17.0
|
1.0
|
CB
|
B:CYS95
|
3.4
|
17.6
|
1.0
|
S1
|
B:SF4502
|
3.9
|
18.7
|
1.0
|
N
|
B:SAH501
|
4.2
|
18.2
|
1.0
|
CB
|
B:SER97
|
4.3
|
21.6
|
1.0
|
N
|
B:GLU143
|
4.3
|
14.1
|
1.0
|
CA
|
B:GLY142
|
4.4
|
15.7
|
1.0
|
CB
|
B:MET104
|
4.7
|
18.3
|
1.0
|
SG
|
B:CYS99
|
4.8
|
19.7
|
1.0
|
O
|
B:MET104
|
4.8
|
21.4
|
1.0
|
N
|
B:SER97
|
4.8
|
18.2
|
1.0
|
SG
|
B:CYS102
|
4.8
|
19.0
|
1.0
|
CA
|
B:CYS95
|
4.8
|
19.1
|
1.0
|
C
|
B:MET104
|
4.8
|
19.3
|
1.0
|
O
|
B:SAH501
|
4.8
|
18.0
|
1.0
|
CA
|
B:SER97
|
4.9
|
19.0
|
1.0
|
C
|
B:SER97
|
4.9
|
20.7
|
1.0
|
C
|
B:GLY142
|
4.9
|
15.9
|
1.0
|
O
|
B:SER97
|
4.9
|
18.4
|
1.0
|
N
|
B:ARG105
|
5.0
|
22.3
|
1.0
|
|
Iron binding site 6 out
of 8 in 4r33
Go back to
Iron Binding Sites List in 4r33
Iron binding site 6 out
of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe502
b:17.6
occ:1.00
|
FE2
|
B:SF4502
|
0.0
|
17.6
|
1.0
|
S3
|
B:SF4502
|
2.3
|
19.8
|
1.0
|
S1
|
B:SF4502
|
2.3
|
18.7
|
1.0
|
S4
|
B:SF4502
|
2.3
|
18.2
|
1.0
|
SG
|
B:CYS102
|
2.3
|
19.0
|
1.0
|
FE3
|
B:SF4502
|
2.6
|
17.8
|
1.0
|
FE1
|
B:SF4502
|
2.7
|
17.7
|
1.0
|
FE4
|
B:SF4502
|
2.8
|
17.0
|
1.0
|
CB
|
B:CYS102
|
3.2
|
16.6
|
1.0
|
S2
|
B:SF4502
|
3.9
|
17.4
|
1.0
|
NE2
|
B:GLN363
|
4.1
|
19.8
|
1.0
|
CB
|
B:MET104
|
4.1
|
18.3
|
1.0
|
CB
|
B:CYS99
|
4.5
|
16.7
|
1.0
|
SG
|
B:CYS99
|
4.6
|
19.7
|
1.0
|
N
|
B:ARG105
|
4.7
|
22.3
|
1.0
|
CA
|
B:CYS102
|
4.7
|
17.1
|
1.0
|
CG
|
B:SAH501
|
4.7
|
17.0
|
1.0
|
N
|
B:MET104
|
4.8
|
19.5
|
1.0
|
C
|
B:MET104
|
4.8
|
19.3
|
1.0
|
CA
|
B:MET104
|
4.8
|
18.7
|
1.0
|
O
|
B:SAH501
|
4.8
|
18.0
|
1.0
|
N
|
B:SAH501
|
4.8
|
18.2
|
1.0
|
SG
|
B:CYS95
|
4.9
|
16.7
|
1.0
|
CD
|
B:GLN363
|
4.9
|
19.9
|
1.0
|
|
Iron binding site 7 out
of 8 in 4r33
Go back to
Iron Binding Sites List in 4r33
Iron binding site 7 out
of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe502
b:17.8
occ:1.00
|
FE3
|
B:SF4502
|
0.0
|
17.8
|
1.0
|
S2
|
B:SF4502
|
2.3
|
17.4
|
1.0
|
SG
|
B:CYS99
|
2.3
|
19.7
|
1.0
|
S4
|
B:SF4502
|
2.3
|
18.2
|
1.0
|
S1
|
B:SF4502
|
2.3
|
18.7
|
1.0
|
FE2
|
B:SF4502
|
2.6
|
17.6
|
1.0
|
FE1
|
B:SF4502
|
2.7
|
17.7
|
1.0
|
FE4
|
B:SF4502
|
2.8
|
17.0
|
1.0
|
CB
|
B:CYS99
|
3.2
|
16.7
|
1.0
|
NZ
|
B:LYS224
|
3.8
|
16.9
|
1.0
|
S3
|
B:SF4502
|
3.8
|
19.8
|
1.0
|
CD
|
B:LYS224
|
3.9
|
18.8
|
1.0
|
O
|
B:SAH501
|
4.0
|
18.0
|
1.0
|
N
|
B:CYS99
|
4.1
|
16.7
|
1.0
|
CA
|
B:CYS99
|
4.2
|
18.1
|
1.0
|
CE
|
B:LYS224
|
4.4
|
16.9
|
1.0
|
CB
|
B:SER97
|
4.5
|
21.6
|
1.0
|
CB
|
B:CYS102
|
4.6
|
16.6
|
1.0
|
SG
|
B:CYS102
|
4.7
|
19.0
|
1.0
|
SG
|
B:CYS95
|
4.7
|
16.7
|
1.0
|
O
|
B:HOH672
|
4.8
|
18.8
|
1.0
|
N
|
B:SAH501
|
4.9
|
18.2
|
1.0
|
O
|
B:HOH962
|
5.0
|
34.1
|
1.0
|
|
Iron binding site 8 out
of 8 in 4r33
Go back to
Iron Binding Sites List in 4r33
Iron binding site 8 out
of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan and S- Adenosyl-L-Homocysteine Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe502
b:17.0
occ:1.00
|
FE4
|
B:SF4502
|
0.0
|
17.0
|
1.0
|
O
|
B:SAH501
|
2.2
|
18.0
|
1.0
|
S1
|
B:SF4502
|
2.3
|
18.7
|
1.0
|
N
|
B:SAH501
|
2.3
|
18.2
|
1.0
|
S2
|
B:SF4502
|
2.3
|
17.4
|
1.0
|
S3
|
B:SF4502
|
2.4
|
19.8
|
1.0
|
FE3
|
B:SF4502
|
2.8
|
17.8
|
1.0
|
FE1
|
B:SF4502
|
2.8
|
17.7
|
1.0
|
FE2
|
B:SF4502
|
2.8
|
17.6
|
1.0
|
C
|
B:SAH501
|
3.0
|
19.6
|
1.0
|
CG
|
B:SAH501
|
3.1
|
17.0
|
1.0
|
CA
|
B:SAH501
|
3.1
|
15.7
|
1.0
|
CB
|
B:SAH501
|
3.7
|
16.4
|
1.0
|
O
|
B:HOH962
|
3.8
|
34.1
|
1.0
|
NZ
|
B:LYS224
|
4.0
|
16.9
|
1.0
|
S4
|
B:SF4502
|
4.0
|
18.2
|
1.0
|
OXT
|
B:SAH501
|
4.2
|
21.2
|
1.0
|
SD
|
B:SAH501
|
4.7
|
24.8
|
1.0
|
CD
|
B:LYS224
|
4.7
|
18.8
|
1.0
|
SG
|
B:CYS95
|
4.7
|
16.7
|
1.0
|
SG
|
B:CYS99
|
4.8
|
19.7
|
1.0
|
CA
|
B:GLY142
|
4.9
|
15.7
|
1.0
|
N
|
B:GLU143
|
4.9
|
14.1
|
1.0
|
O
|
B:THR141
|
5.0
|
14.9
|
1.0
|
|
Reference:
Y.Nicolet,
L.Zeppieri,
P.Amara,
J.C.Fontecilla-Camps.
Crystal Structure of Tryptophan Lyase (Nosl): Evidence For Radical Formation at the Amino Group of Tryptophan. Angew.Chem.Int.Ed.Engl. V. 53 11840 2014.
ISSN: ISSN 1433-7851
PubMed: 25196319
DOI: 10.1002/ANIE.201407320
Page generated: Mon Aug 5 09:09:58 2024
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