Iron in PDB 2yaj: Crystal Structure of Glycyl Radical Enzyme with Bound Substrate
Enzymatic activity of Crystal Structure of Glycyl Radical Enzyme with Bound Substrate
All present enzymatic activity of Crystal Structure of Glycyl Radical Enzyme with Bound Substrate:
4.1.1.83;
Protein crystallography data
The structure of Crystal Structure of Glycyl Radical Enzyme with Bound Substrate, PDB code: 2yaj
was solved by
B.M.Martins,
M.Blaser,
M.Feliks,
G.M.Ullmann,
T.Selmer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.16 /
1.81
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
133.049,
228.588,
148.226,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.8 /
24.4
|
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Iron atom in the Crystal Structure of Glycyl Radical Enzyme with Bound Substrate
(pdb code 2yaj). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the
Crystal Structure of Glycyl Radical Enzyme with Bound Substrate, PDB code: 2yaj:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 16 in 2yaj
Go back to
Iron Binding Sites List in 2yaj
Iron binding site 1 out
of 16 in the Crystal Structure of Glycyl Radical Enzyme with Bound Substrate
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 Glycyl Radical Enzyme with Bound Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe87
b:46.9
occ:1.00
|
FE1
|
B:SF487
|
0.0
|
46.9
|
1.0
|
S2
|
B:SF487
|
2.3
|
43.0
|
1.0
|
S3
|
B:SF487
|
2.3
|
42.2
|
1.0
|
S4
|
B:SF487
|
2.3
|
48.1
|
1.0
|
SG
|
B:CYS6
|
2.5
|
44.3
|
1.0
|
FE3
|
B:SF487
|
2.7
|
50.8
|
1.0
|
FE2
|
B:SF487
|
2.7
|
46.6
|
1.0
|
FE4
|
B:SF487
|
2.8
|
45.1
|
1.0
|
HB3
|
B:CYS6
|
3.0
|
36.9
|
1.0
|
HB2
|
B:ASN8
|
3.0
|
41.1
|
1.0
|
CB
|
B:CYS6
|
3.1
|
30.8
|
1.0
|
HB2
|
B:CYS6
|
3.1
|
36.9
|
1.0
|
HA
|
B:PHE39
|
3.6
|
58.3
|
1.0
|
HA
|
B:HIS3
|
3.7
|
49.6
|
1.0
|
HD21
|
B:ASN8
|
3.8
|
44.8
|
1.0
|
CB
|
B:ASN8
|
4.0
|
34.3
|
1.0
|
HD2
|
B:PHE39
|
4.0
|
63.8
|
1.0
|
S1
|
B:SF487
|
4.0
|
54.9
|
1.0
|
H
|
B:ASN8
|
4.1
|
39.1
|
1.0
|
HB3
|
B:ASN8
|
4.2
|
41.1
|
1.0
|
H
|
B:CYS36
|
4.6
|
71.5
|
1.0
|
H
|
B:LYS40
|
4.6
|
66.8
|
1.0
|
CA
|
B:PHE39
|
4.6
|
48.6
|
1.0
|
ND2
|
B:ASN8
|
4.6
|
37.4
|
1.0
|
CA
|
B:CYS6
|
4.6
|
28.4
|
1.0
|
H
|
B:TYR9
|
4.6
|
39.9
|
1.0
|
ND1
|
B:HIS3
|
4.6
|
33.7
|
1.0
|
CA
|
B:HIS3
|
4.7
|
41.5
|
1.0
|
CD2
|
B:PHE39
|
4.7
|
53.2
|
1.0
|
HB3
|
B:HIS3
|
4.7
|
47.0
|
1.0
|
CA
|
B:ASN8
|
4.7
|
34.3
|
1.0
|
HB2
|
B:PHE39
|
4.7
|
52.0
|
1.0
|
N
|
B:TYR9
|
4.8
|
33.3
|
1.0
|
N
|
B:ASN8
|
4.8
|
32.7
|
1.0
|
CG
|
B:ASN8
|
4.8
|
32.4
|
1.0
|
HB2
|
B:TYR9
|
4.8
|
41.8
|
1.0
|
C
|
B:ASN8
|
4.8
|
41.1
|
1.0
|
O
|
B:HIS3
|
4.9
|
36.0
|
1.0
|
HD13
|
B:LEU21
|
4.9
|
67.2
|
1.0
|
SG
|
B:CYS19
|
4.9
|
40.4
|
1.0
|
HA
|
B:CYS6
|
5.0
|
34.0
|
1.0
|
|
Iron binding site 2 out
of 16 in 2yaj
Go back to
Iron Binding Sites List in 2yaj
Iron binding site 2 out
of 16 in the Crystal Structure of Glycyl Radical Enzyme with Bound Substrate
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 Glycyl Radical Enzyme with Bound Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe87
b:46.6
occ:1.00
|
FE2
|
B:SF487
|
0.0
|
46.6
|
1.0
|
ND1
|
B:HIS3
|
2.0
|
33.7
|
1.0
|
S2
|
B:SF487
|
2.2
|
43.0
|
1.0
|
S3
|
B:SF487
|
2.3
|
42.2
|
1.0
|
S1
|
B:SF487
|
2.4
|
54.9
|
1.0
|
FE4
|
B:SF487
|
2.7
|
45.1
|
1.0
|
FE3
|
B:SF487
|
2.7
|
50.8
|
1.0
|
FE1
|
B:SF487
|
2.7
|
46.9
|
1.0
|
CE1
|
B:HIS3
|
2.9
|
46.0
|
1.0
|
HA
|
B:HIS3
|
2.9
|
49.6
|
1.0
|
HE1
|
B:HIS3
|
3.0
|
55.1
|
1.0
|
CG
|
B:HIS3
|
3.0
|
44.7
|
1.0
|
HB3
|
B:HIS3
|
3.2
|
47.0
|
1.0
|
CB
|
B:HIS3
|
3.4
|
39.2
|
1.0
|
CA
|
B:HIS3
|
3.6
|
41.5
|
1.0
|
HB2
|
B:CYS19
|
3.7
|
35.0
|
1.0
|
S4
|
B:SF487
|
3.9
|
48.1
|
1.0
|
H
|
B:CYS36
|
3.9
|
71.5
|
1.0
|
NE2
|
B:HIS3
|
4.0
|
45.0
|
1.0
|
CD2
|
B:HIS3
|
4.1
|
49.0
|
1.0
|
HG22
|
B:VAL26
|
4.2
|
31.8
|
1.0
|
HB3
|
B:CYS36
|
4.2
|
68.7
|
1.0
|
HA
|
B:ALA35
|
4.2
|
0.2
|
1.0
|
HG12
|
B:VAL26
|
4.2
|
51.3
|
1.0
|
N
|
B:HIS3
|
4.4
|
39.3
|
1.0
|
HB3
|
B:CYS6
|
4.4
|
36.9
|
1.0
|
HB2
|
B:HIS3
|
4.4
|
47.0
|
1.0
|
H
|
B:HIS3
|
4.4
|
47.1
|
1.0
|
CB
|
B:CYS19
|
4.6
|
29.2
|
1.0
|
HB2
|
B:CYS6
|
4.6
|
36.9
|
1.0
|
N
|
B:CYS36
|
4.7
|
59.6
|
1.0
|
SG
|
B:CYS19
|
4.7
|
40.4
|
1.0
|
HA
|
B:CYS19
|
4.7
|
43.8
|
1.0
|
HE2
|
B:HIS3
|
4.8
|
53.9
|
1.0
|
C
|
B:HIS3
|
4.8
|
32.4
|
1.0
|
CB
|
B:CYS6
|
4.9
|
30.8
|
1.0
|
SG
|
B:CYS36
|
4.9
|
50.5
|
1.0
|
CB
|
B:CYS36
|
5.0
|
57.3
|
1.0
|
HD2
|
B:HIS3
|
5.0
|
58.8
|
1.0
|
O
|
B:HIS3
|
5.0
|
36.0
|
1.0
|
|
Iron binding site 3 out
of 16 in 2yaj
Go back to
Iron Binding Sites List in 2yaj
Iron binding site 3 out
of 16 in the Crystal Structure of Glycyl Radical Enzyme with Bound Substrate
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 Glycyl Radical Enzyme with Bound Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe87
b:50.8
occ:1.00
|
FE3
|
B:SF487
|
0.0
|
50.8
|
1.0
|
S4
|
B:SF487
|
2.3
|
48.1
|
1.0
|
S1
|
B:SF487
|
2.3
|
54.9
|
1.0
|
S2
|
B:SF487
|
2.4
|
43.0
|
1.0
|
SG
|
B:CYS36
|
2.5
|
50.5
|
1.0
|
FE1
|
B:SF487
|
2.7
|
46.9
|
1.0
|
FE4
|
B:SF487
|
2.7
|
45.1
|
1.0
|
FE2
|
B:SF487
|
2.7
|
46.6
|
1.0
|
HB3
|
B:CYS36
|
3.0
|
68.7
|
1.0
|
H
|
B:CYS36
|
3.1
|
71.5
|
1.0
|
CB
|
B:CYS36
|
3.3
|
57.3
|
1.0
|
HB2
|
B:ASN38
|
3.8
|
70.1
|
1.0
|
N
|
B:CYS36
|
3.8
|
59.6
|
1.0
|
S3
|
B:SF487
|
3.9
|
42.2
|
1.0
|
CA
|
B:CYS36
|
4.1
|
56.8
|
1.0
|
HB2
|
B:CYS36
|
4.1
|
68.7
|
1.0
|
HA
|
B:PHE39
|
4.2
|
58.3
|
1.0
|
O
|
B:CYS36
|
4.3
|
79.8
|
1.0
|
H
|
B:ASN38
|
4.4
|
79.6
|
1.0
|
HD13
|
B:LEU21
|
4.4
|
67.2
|
1.0
|
HE1
|
B:HIS3
|
4.4
|
55.1
|
1.0
|
ND1
|
B:HIS3
|
4.4
|
33.7
|
1.0
|
C
|
B:CYS36
|
4.5
|
69.4
|
1.0
|
N
|
B:PHE39
|
4.5
|
44.3
|
1.0
|
CB
|
B:ASN38
|
4.6
|
58.5
|
1.0
|
HB3
|
B:ASN38
|
4.6
|
70.1
|
1.0
|
H
|
B:PHE39
|
4.6
|
53.0
|
1.0
|
HB2
|
B:PHE39
|
4.6
|
52.0
|
1.0
|
C
|
B:ASN38
|
4.7
|
53.7
|
1.0
|
HD21
|
B:ASN8
|
4.7
|
44.8
|
1.0
|
SG
|
B:CYS19
|
4.8
|
40.4
|
1.0
|
HA
|
B:ALA35
|
4.8
|
0.2
|
1.0
|
CE1
|
B:HIS3
|
4.8
|
46.0
|
1.0
|
CA
|
B:PHE39
|
4.8
|
48.6
|
1.0
|
SG
|
B:CYS6
|
4.9
|
44.3
|
1.0
|
HA
|
B:CYS36
|
5.0
|
68.1
|
1.0
|
N
|
B:ASN38
|
5.0
|
66.4
|
1.0
|
HB2
|
B:ASN8
|
5.0
|
41.1
|
1.0
|
HD2
|
B:PHE39
|
5.0
|
63.8
|
1.0
|
HB2
|
B:CYS19
|
5.0
|
35.0
|
1.0
|
|
Iron binding site 4 out
of 16 in 2yaj
Go back to
Iron Binding Sites List in 2yaj
Iron binding site 4 out
of 16 in the Crystal Structure of Glycyl Radical Enzyme with Bound Substrate
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 Glycyl Radical Enzyme with Bound Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe87
b:45.1
occ:1.00
|
FE4
|
B:SF487
|
0.0
|
45.1
|
1.0
|
S4
|
B:SF487
|
2.2
|
48.1
|
1.0
|
SG
|
B:CYS19
|
2.3
|
40.4
|
1.0
|
S3
|
B:SF487
|
2.3
|
42.2
|
1.0
|
S1
|
B:SF487
|
2.4
|
54.9
|
1.0
|
FE3
|
B:SF487
|
2.7
|
50.8
|
1.0
|
HB2
|
B:CYS19
|
2.7
|
35.0
|
1.0
|
FE2
|
B:SF487
|
2.7
|
46.6
|
1.0
|
FE1
|
B:SF487
|
2.8
|
46.9
|
1.0
|
CB
|
B:CYS19
|
3.0
|
29.2
|
1.0
|
HA
|
B:CYS19
|
3.5
|
43.8
|
1.0
|
CA
|
B:CYS19
|
3.8
|
36.6
|
1.0
|
HB3
|
B:CYS19
|
3.8
|
35.0
|
1.0
|
HB2
|
B:LEU21
|
3.9
|
62.2
|
1.0
|
S2
|
B:SF487
|
3.9
|
43.0
|
1.0
|
HB2
|
B:ASN8
|
4.0
|
41.1
|
1.0
|
H
|
B:LEU21
|
4.0
|
57.4
|
1.0
|
HD13
|
B:LEU21
|
4.2
|
67.2
|
1.0
|
HB3
|
B:ASN8
|
4.2
|
41.1
|
1.0
|
HG21
|
B:THR22
|
4.3
|
46.0
|
1.0
|
ND1
|
B:HIS3
|
4.3
|
33.7
|
1.0
|
H
|
B:ALA20
|
4.4
|
47.2
|
1.0
|
C
|
B:CYS19
|
4.5
|
39.2
|
1.0
|
H
|
B:THR22
|
4.5
|
44.3
|
1.0
|
CB
|
B:ASN8
|
4.5
|
34.3
|
1.0
|
HD21
|
B:ASN8
|
4.6
|
44.8
|
1.0
|
HG
|
B:LEU21
|
4.6
|
60.3
|
1.0
|
N
|
B:ALA20
|
4.7
|
39.4
|
1.0
|
CB
|
B:LEU21
|
4.8
|
51.9
|
1.0
|
N
|
B:LEU21
|
4.8
|
47.9
|
1.0
|
HE1
|
B:HIS3
|
4.8
|
55.1
|
1.0
|
SG
|
B:CYS36
|
4.8
|
50.5
|
1.0
|
HG12
|
B:VAL26
|
4.8
|
51.3
|
1.0
|
CE1
|
B:HIS3
|
5.0
|
46.0
|
1.0
|
CD1
|
B:LEU21
|
5.0
|
56.1
|
1.0
|
|
Iron binding site 5 out
of 16 in 2yaj
Go back to
Iron Binding Sites List in 2yaj
Iron binding site 5 out
of 16 in the Crystal Structure of Glycyl Radical Enzyme with Bound Substrate
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 Glycyl Radical Enzyme with Bound Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe88
b:33.4
occ:1.00
|
FE1
|
B:SF488
|
0.0
|
33.4
|
1.0
|
S2
|
B:SF488
|
2.3
|
28.8
|
1.0
|
S3
|
B:SF488
|
2.3
|
29.9
|
1.0
|
SG
|
B:CYS62
|
2.3
|
27.9
|
1.0
|
S4
|
B:SF488
|
2.4
|
33.4
|
1.0
|
FE3
|
B:SF488
|
2.7
|
31.2
|
1.0
|
FE4
|
B:SF488
|
2.7
|
34.0
|
1.0
|
FE2
|
B:SF488
|
2.8
|
33.0
|
1.0
|
HB2
|
B:CYS62
|
3.0
|
41.8
|
1.0
|
CB
|
B:CYS62
|
3.3
|
34.9
|
1.0
|
HH12
|
A:ARG61
|
3.3
|
25.7
|
1.0
|
HB2
|
B:ASN50
|
3.8
|
51.8
|
1.0
|
S1
|
B:SF488
|
3.8
|
30.8
|
1.0
|
H
|
B:GLY64
|
3.8
|
58.9
|
1.0
|
HA
|
B:CYS62
|
3.9
|
41.6
|
1.0
|
HA3
|
B:GLY64
|
4.0
|
68.3
|
1.0
|
HB3
|
B:CYS62
|
4.0
|
41.8
|
1.0
|
HH22
|
A:ARG61
|
4.1
|
25.6
|
1.0
|
NH1
|
A:ARG61
|
4.2
|
21.5
|
1.0
|
CA
|
B:CYS62
|
4.2
|
34.8
|
1.0
|
HB3
|
B:ASN50
|
4.2
|
51.8
|
1.0
|
HD21
|
B:ASN50
|
4.3
|
40.4
|
1.0
|
CB
|
B:ASN50
|
4.4
|
43.3
|
1.0
|
HB3
|
B:ALA71
|
4.5
|
41.8
|
1.0
|
N
|
B:GLY64
|
4.6
|
49.1
|
1.0
|
HH11
|
A:ARG61
|
4.7
|
25.7
|
1.0
|
H
|
B:THR63
|
4.7
|
38.9
|
1.0
|
SG
|
B:CYS45
|
4.7
|
29.1
|
1.0
|
HH2
|
A:TRP58
|
4.7
|
30.8
|
1.0
|
CA
|
B:GLY64
|
4.7
|
57.0
|
1.0
|
HB2
|
B:SER82
|
4.8
|
49.8
|
1.0
|
HB2
|
B:PHE51
|
4.8
|
32.4
|
1.0
|
SG
|
B:CYS80
|
4.8
|
33.2
|
1.0
|
NH2
|
A:ARG61
|
4.8
|
21.4
|
1.0
|
SG
|
B:CYS48
|
4.8
|
35.3
|
1.0
|
HB2
|
B:ALA71
|
4.9
|
41.8
|
1.0
|
HB3
|
B:CYS45
|
4.9
|
28.7
|
1.0
|
C
|
B:CYS62
|
4.9
|
40.7
|
1.0
|
CZ
|
A:ARG61
|
5.0
|
23.6
|
1.0
|
N
|
B:THR63
|
5.0
|
32.5
|
1.0
|
|
Iron binding site 6 out
of 16 in 2yaj
Go back to
Iron Binding Sites List in 2yaj
Iron binding site 6 out
of 16 in the Crystal Structure of Glycyl Radical Enzyme with Bound Substrate
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 Glycyl Radical Enzyme with Bound Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe88
b:33.0
occ:1.00
|
FE2
|
B:SF488
|
0.0
|
33.0
|
1.0
|
S1
|
B:SF488
|
2.3
|
30.8
|
1.0
|
SG
|
B:CYS80
|
2.3
|
33.2
|
1.0
|
S3
|
B:SF488
|
2.3
|
29.9
|
1.0
|
S4
|
B:SF488
|
2.4
|
33.4
|
1.0
|
FE4
|
B:SF488
|
2.7
|
34.0
|
1.0
|
FE3
|
B:SF488
|
2.7
|
31.2
|
1.0
|
FE1
|
B:SF488
|
2.8
|
33.4
|
1.0
|
HB3
|
B:CYS80
|
3.3
|
33.0
|
1.0
|
CB
|
B:CYS80
|
3.3
|
27.5
|
1.0
|
HB2
|
B:CYS80
|
3.5
|
33.0
|
1.0
|
HB2
|
B:SER82
|
3.7
|
49.8
|
1.0
|
HH2
|
A:TRP58
|
3.8
|
30.8
|
1.0
|
HA
|
B:TYR83
|
3.8
|
42.2
|
1.0
|
S2
|
B:SF488
|
3.9
|
28.8
|
1.0
|
H
|
B:TYR83
|
4.0
|
44.1
|
1.0
|
HB2
|
B:TYR83
|
4.0
|
37.0
|
1.0
|
N
|
B:TYR83
|
4.1
|
36.8
|
1.0
|
H
|
B:SER82
|
4.1
|
49.9
|
1.0
|
HZ2
|
A:TRP58
|
4.3
|
36.9
|
1.0
|
CA
|
B:TYR83
|
4.3
|
35.2
|
1.0
|
HD21
|
B:ASN50
|
4.5
|
40.4
|
1.0
|
C
|
B:SER82
|
4.5
|
37.5
|
1.0
|
CB
|
B:SER82
|
4.6
|
41.6
|
1.0
|
CH2
|
A:TRP58
|
4.6
|
25.7
|
1.0
|
HD1
|
B:TYR83
|
4.6
|
46.5
|
1.0
|
CB
|
B:TYR83
|
4.6
|
30.9
|
1.0
|
HH12
|
A:ARG61
|
4.7
|
25.7
|
1.0
|
CA
|
B:CYS80
|
4.7
|
26.2
|
1.0
|
SG
|
B:CYS45
|
4.7
|
29.1
|
1.0
|
HB2
|
B:ALA77
|
4.7
|
32.8
|
1.0
|
SG
|
B:CYS62
|
4.7
|
27.9
|
1.0
|
O
|
A:HOH2035
|
4.8
|
42.2
|
1.0
|
CZ2
|
A:TRP58
|
4.8
|
30.8
|
1.0
|
N
|
B:SER82
|
4.8
|
41.6
|
1.0
|
SG
|
B:CYS48
|
4.8
|
35.3
|
1.0
|
CA
|
B:SER82
|
4.9
|
30.2
|
1.0
|
HB3
|
B:SER82
|
5.0
|
49.8
|
1.0
|
|
Iron binding site 7 out
of 16 in 2yaj
Go back to
Iron Binding Sites List in 2yaj
Iron binding site 7 out
of 16 in the Crystal Structure of Glycyl Radical Enzyme with Bound Substrate
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 Glycyl Radical Enzyme with Bound Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe88
b:31.2
occ:1.00
|
FE3
|
B:SF488
|
0.0
|
31.2
|
1.0
|
SG
|
B:CYS45
|
2.2
|
29.1
|
1.0
|
S2
|
B:SF488
|
2.3
|
28.8
|
1.0
|
S1
|
B:SF488
|
2.3
|
30.8
|
1.0
|
S4
|
B:SF488
|
2.4
|
33.4
|
1.0
|
FE1
|
B:SF488
|
2.7
|
33.4
|
1.0
|
FE2
|
B:SF488
|
2.7
|
33.0
|
1.0
|
FE4
|
B:SF488
|
2.8
|
34.0
|
1.0
|
HB3
|
B:CYS45
|
3.1
|
28.7
|
1.0
|
HA
|
B:CYS45
|
3.2
|
30.6
|
1.0
|
CB
|
B:CYS45
|
3.2
|
24.0
|
1.0
|
CA
|
B:CYS45
|
3.7
|
25.6
|
1.0
|
S3
|
B:SF488
|
3.9
|
29.9
|
1.0
|
HB2
|
B:CYS45
|
4.1
|
28.7
|
1.0
|
HB2
|
B:ALA71
|
4.1
|
41.8
|
1.0
|
HB2
|
B:CYS48
|
4.4
|
40.7
|
1.0
|
HB3
|
B:ALA77
|
4.4
|
32.8
|
1.0
|
HB3
|
B:CYS48
|
4.4
|
40.7
|
1.0
|
HB2
|
B:PHE51
|
4.4
|
32.4
|
1.0
|
HZ2
|
A:TRP58
|
4.5
|
36.9
|
1.0
|
HB2
|
B:CYS62
|
4.5
|
41.8
|
1.0
|
N
|
B:CYS45
|
4.5
|
30.8
|
1.0
|
HB2
|
B:ALA77
|
4.6
|
32.8
|
1.0
|
HH12
|
A:ARG61
|
4.6
|
25.7
|
1.0
|
H
|
B:CYS45
|
4.6
|
36.9
|
1.0
|
HD1
|
B:TYR83
|
4.6
|
46.5
|
1.0
|
HB3
|
B:ALA71
|
4.7
|
41.8
|
1.0
|
CB
|
B:CYS48
|
4.7
|
34.0
|
1.0
|
SG
|
B:CYS80
|
4.7
|
33.2
|
1.0
|
SG
|
B:CYS48
|
4.7
|
35.3
|
1.0
|
HH2
|
A:TRP58
|
4.8
|
30.8
|
1.0
|
CB
|
B:ALA71
|
4.8
|
34.9
|
1.0
|
HD1
|
B:PHE51
|
4.8
|
36.5
|
1.0
|
HB2
|
B:CYS80
|
4.8
|
33.0
|
1.0
|
SG
|
B:CYS62
|
4.8
|
27.9
|
1.0
|
HB3
|
B:CYS80
|
4.9
|
33.0
|
1.0
|
C
|
B:CYS45
|
4.9
|
36.6
|
1.0
|
CB
|
B:ALA77
|
4.9
|
27.4
|
1.0
|
HB3
|
B:CYS75
|
4.9
|
34.6
|
1.0
|
O
|
B:HOH2053
|
4.9
|
30.1
|
1.0
|
HB1
|
B:ALA71
|
5.0
|
41.8
|
1.0
|
|
Iron binding site 8 out
of 16 in 2yaj
Go back to
Iron Binding Sites List in 2yaj
Iron binding site 8 out
of 16 in the Crystal Structure of Glycyl Radical Enzyme with Bound Substrate
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 Glycyl Radical Enzyme with Bound Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe88
b:34.0
occ:1.00
|
FE4
|
B:SF488
|
0.0
|
34.0
|
1.0
|
S1
|
B:SF488
|
2.3
|
30.8
|
1.0
|
S3
|
B:SF488
|
2.3
|
29.9
|
1.0
|
SG
|
B:CYS48
|
2.3
|
35.3
|
1.0
|
S2
|
B:SF488
|
2.4
|
28.8
|
1.0
|
FE2
|
B:SF488
|
2.7
|
33.0
|
1.0
|
FE1
|
B:SF488
|
2.7
|
33.4
|
1.0
|
FE3
|
B:SF488
|
2.8
|
31.2
|
1.0
|
HB2
|
B:ASN50
|
3.0
|
51.8
|
1.0
|
HA
|
B:TYR83
|
3.1
|
42.2
|
1.0
|
CB
|
B:CYS48
|
3.2
|
34.0
|
1.0
|
HB2
|
B:CYS48
|
3.2
|
40.7
|
1.0
|
HB3
|
B:CYS48
|
3.2
|
40.7
|
1.0
|
HD21
|
B:ASN50
|
3.2
|
40.4
|
1.0
|
HD1
|
B:TYR83
|
3.7
|
46.5
|
1.0
|
CB
|
B:ASN50
|
3.9
|
43.3
|
1.0
|
HA
|
B:CYS45
|
3.9
|
30.6
|
1.0
|
S4
|
B:SF488
|
4.0
|
33.4
|
1.0
|
CA
|
B:TYR83
|
4.0
|
35.2
|
1.0
|
ND2
|
B:ASN50
|
4.1
|
33.7
|
1.0
|
H
|
B:ASN50
|
4.1
|
49.1
|
1.0
|
H
|
B:LYS84
|
4.2
|
47.6
|
1.0
|
HB2
|
B:PHE51
|
4.3
|
32.4
|
1.0
|
HB2
|
B:TYR83
|
4.3
|
37.0
|
1.0
|
HB3
|
B:ASN50
|
4.3
|
51.8
|
1.0
|
CD1
|
B:TYR83
|
4.4
|
38.8
|
1.0
|
N
|
B:TYR83
|
4.5
|
36.8
|
1.0
|
CG
|
B:ASN50
|
4.6
|
44.4
|
1.0
|
CA
|
B:CYS48
|
4.6
|
38.6
|
1.0
|
CB
|
B:TYR83
|
4.7
|
30.9
|
1.0
|
H
|
B:PHE51
|
4.7
|
40.3
|
1.0
|
SG
|
B:CYS62
|
4.7
|
27.9
|
1.0
|
O
|
B:SER82
|
4.8
|
35.8
|
1.0
|
SG
|
B:CYS45
|
4.8
|
29.1
|
1.0
|
HB3
|
B:CYS45
|
4.8
|
28.7
|
1.0
|
SG
|
B:CYS80
|
4.8
|
33.2
|
1.0
|
HB2
|
B:SER82
|
4.8
|
49.8
|
1.0
|
N
|
B:ASN50
|
4.8
|
41.0
|
1.0
|
HB2
|
B:ALA77
|
4.8
|
32.8
|
1.0
|
C
|
B:SER82
|
4.8
|
37.5
|
1.0
|
CA
|
B:ASN50
|
4.8
|
35.8
|
1.0
|
N
|
B:PHE51
|
4.8
|
33.7
|
1.0
|
H
|
B:TYR83
|
4.8
|
44.1
|
1.0
|
CA
|
B:CYS45
|
4.9
|
25.6
|
1.0
|
N
|
B:LYS84
|
4.9
|
39.8
|
1.0
|
HD22
|
B:ASN50
|
4.9
|
40.4
|
1.0
|
HA
|
B:CYS48
|
4.9
|
46.2
|
1.0
|
C
|
B:ASN50
|
5.0
|
39.9
|
1.0
|
|
Iron binding site 9 out
of 16 in 2yaj
Go back to
Iron Binding Sites List in 2yaj
Iron binding site 9 out
of 16 in the Crystal Structure of Glycyl Radical Enzyme with Bound Substrate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Crystal Structure of Glycyl Radical Enzyme with Bound Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe87
b:43.9
occ:1.00
|
FE1
|
D:SF487
|
0.0
|
43.9
|
1.0
|
S3
|
D:SF487
|
2.2
|
41.1
|
1.0
|
S2
|
D:SF487
|
2.3
|
38.1
|
1.0
|
SG
|
D:CYS6
|
2.3
|
34.6
|
1.0
|
S4
|
D:SF487
|
2.5
|
46.7
|
1.0
|
FE4
|
D:SF487
|
2.7
|
42.8
|
1.0
|
FE3
|
D:SF487
|
2.7
|
49.7
|
1.0
|
FE2
|
D:SF487
|
2.8
|
50.5
|
1.0
|
HB3
|
D:CYS6
|
2.9
|
33.8
|
1.0
|
CB
|
D:CYS6
|
3.0
|
28.3
|
1.0
|
HB2
|
D:CYS6
|
3.1
|
33.8
|
1.0
|
HB2
|
D:ASN8
|
3.1
|
52.8
|
1.0
|
HA
|
D:PHE39
|
3.5
|
71.2
|
1.0
|
HD21
|
D:ASN8
|
3.5
|
52.9
|
1.0
|
HA
|
D:HIS3
|
3.8
|
58.5
|
1.0
|
HD1
|
D:PHE39
|
3.8
|
68.0
|
1.0
|
H
|
D:ASN8
|
4.0
|
52.0
|
1.0
|
S1
|
D:SF487
|
4.0
|
53.8
|
1.0
|
CB
|
D:ASN8
|
4.1
|
44.1
|
1.0
|
H
|
D:LYS40
|
4.4
|
63.8
|
1.0
|
ND2
|
D:ASN8
|
4.4
|
44.1
|
1.0
|
CA
|
D:PHE39
|
4.4
|
59.4
|
1.0
|
HB3
|
D:ASN8
|
4.5
|
52.8
|
1.0
|
CA
|
D:CYS6
|
4.5
|
31.2
|
1.0
|
ND1
|
D:HIS3
|
4.6
|
51.5
|
1.0
|
H
|
D:CYS36
|
4.6
|
89.5
|
1.0
|
CD1
|
D:PHE39
|
4.6
|
56.7
|
1.0
|
HB2
|
D:PHE39
|
4.7
|
74.0
|
1.0
|
N
|
D:ASN8
|
4.7
|
43.4
|
1.0
|
CA
|
D:HIS3
|
4.7
|
48.8
|
1.0
|
HB3
|
D:HIS3
|
4.7
|
61.8
|
1.0
|
CG
|
D:ASN8
|
4.8
|
45.5
|
1.0
|
CA
|
D:ASN8
|
4.8
|
43.1
|
1.0
|
H
|
D:TYR9
|
4.8
|
46.1
|
1.0
|
N
|
D:PHE39
|
4.8
|
57.7
|
1.0
|
O
|
D:HIS3
|
4.8
|
53.6
|
1.0
|
SG
|
D:CYS19
|
4.8
|
46.6
|
1.0
|
HD13
|
D:LEU21
|
4.9
|
71.0
|
1.0
|
HA
|
D:CYS6
|
4.9
|
37.4
|
1.0
|
C
|
D:ASN8
|
4.9
|
38.4
|
1.0
|
SG
|
D:CYS36
|
4.9
|
58.3
|
1.0
|
N
|
D:TYR9
|
4.9
|
38.5
|
1.0
|
C
|
D:CYS6
|
5.0
|
43.6
|
1.0
|
|
Iron binding site 10 out
of 16 in 2yaj
Go back to
Iron Binding Sites List in 2yaj
Iron binding site 10 out
of 16 in the Crystal Structure of Glycyl Radical Enzyme with Bound Substrate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Crystal Structure of Glycyl Radical Enzyme with Bound Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe87
b:50.5
occ:1.00
|
FE2
|
D:SF487
|
0.0
|
50.5
|
1.0
|
ND1
|
D:HIS3
|
1.8
|
51.5
|
1.0
|
S1
|
D:SF487
|
2.2
|
53.8
|
1.0
|
S4
|
D:SF487
|
2.3
|
46.7
|
1.0
|
S3
|
D:SF487
|
2.5
|
41.1
|
1.0
|
FE3
|
D:SF487
|
2.7
|
49.7
|
1.0
|
FE4
|
D:SF487
|
2.7
|
42.8
|
1.0
|
CE1
|
D:HIS3
|
2.7
|
49.7
|
1.0
|
HE1
|
D:HIS3
|
2.8
|
59.5
|
1.0
|
FE1
|
D:SF487
|
2.8
|
43.9
|
1.0
|
CG
|
D:HIS3
|
3.0
|
58.8
|
1.0
|
HA
|
D:HIS3
|
3.0
|
58.5
|
1.0
|
HB3
|
D:HIS3
|
3.3
|
61.8
|
1.0
|
CB
|
D:HIS3
|
3.5
|
51.6
|
1.0
|
CA
|
D:HIS3
|
3.7
|
48.8
|
1.0
|
HA
|
D:ALA35
|
3.7
|
69.4
|
1.0
|
NE2
|
D:HIS3
|
3.9
|
53.6
|
1.0
|
HB2
|
D:CYS19
|
3.9
|
44.7
|
1.0
|
CD2
|
D:HIS3
|
4.0
|
58.6
|
1.0
|
S2
|
D:SF487
|
4.0
|
38.1
|
1.0
|
H
|
D:CYS36
|
4.0
|
89.5
|
1.0
|
HB3
|
D:CYS6
|
4.4
|
33.8
|
1.0
|
HB3
|
D:CYS36
|
4.4
|
86.2
|
1.0
|
HB2
|
D:HIS3
|
4.4
|
61.8
|
1.0
|
N
|
D:HIS3
|
4.4
|
43.1
|
1.0
|
HB2
|
D:CYS6
|
4.5
|
33.8
|
1.0
|
H
|
D:HIS3
|
4.5
|
51.7
|
1.0
|
HG22
|
D:VAL26
|
4.5
|
54.8
|
1.0
|
N
|
D:CYS36
|
4.6
|
74.6
|
1.0
|
CA
|
D:ALA35
|
4.6
|
57.9
|
1.0
|
HE2
|
D:HIS3
|
4.6
|
64.2
|
1.0
|
HG12
|
D:VAL26
|
4.7
|
58.2
|
1.0
|
CB
|
D:CYS19
|
4.7
|
37.3
|
1.0
|
SG
|
D:CYS19
|
4.8
|
46.6
|
1.0
|
CB
|
D:CYS6
|
4.8
|
28.3
|
1.0
|
SG
|
D:CYS36
|
4.8
|
58.3
|
1.0
|
C
|
D:HIS3
|
4.9
|
43.3
|
1.0
|
HD2
|
D:HIS3
|
4.9
|
70.2
|
1.0
|
HB2
|
D:ALA35
|
4.9
|
66.4
|
1.0
|
SG
|
D:CYS6
|
5.0
|
34.6
|
1.0
|
O
|
D:GLU34
|
5.0
|
64.2
|
1.0
|
HD1
|
D:PHE39
|
5.0
|
68.0
|
1.0
|
|
Reference:
B.M.Martins,
M.Blaser,
M.Feliks,
G.M.Ullmann,
W.Buckel,
T.Selmer.
Structural Basis For A Kolbe-Type Decarboxylation Catalyzed By A Glycyl Radical Enzyme. J.Am.Chem.Soc. V. 133 14666 2011.
ISSN: ISSN 0002-7863
PubMed: 21823587
DOI: 10.1021/JA203344X
Page generated: Sun Aug 4 05:10:50 2024
|