Iron in PDB 8wvr: Complex Structure of the Azoxy Synthase Vlmb and Its Substrate
Protein crystallography data
The structure of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate, PDB code: 8wvr
was solved by
X.Zang,
J.H.Zhou,
D.Yiling,
S.Jingkun,
Z.Zhijie,
S.Zhuanglin,
Z.Guiyun,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.88 /
2.05
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.82,
95.18,
183.25,
90,
90,
90
|
R / Rfree (%)
|
19.5 /
24.1
|
Iron Binding Sites:
The binding sites of Iron atom in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate
(pdb code 8wvr). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Complex Structure of the Azoxy Synthase Vlmb and Its Substrate, PDB code: 8wvr:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 8wvr
Go back to
Iron Binding Sites List in 8wvr
Iron binding site 1 out
of 8 in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:24.3
occ:1.00
|
O
|
A:HOH596
|
1.8
|
24.8
|
1.0
|
OE2
|
A:GLU84
|
2.0
|
22.3
|
1.0
|
OE1
|
A:GLU114
|
2.2
|
23.0
|
1.0
|
ND1
|
A:HIS117
|
2.2
|
23.1
|
1.0
|
N1
|
A:IMD401
|
2.3
|
28.1
|
1.0
|
CE1
|
A:HIS117
|
2.9
|
23.1
|
1.0
|
CD
|
A:GLU84
|
3.0
|
24.2
|
1.0
|
C5
|
A:IMD401
|
3.1
|
29.8
|
1.0
|
CD
|
A:GLU114
|
3.2
|
21.7
|
1.0
|
C2
|
A:IMD401
|
3.3
|
30.5
|
1.0
|
CG
|
A:HIS117
|
3.3
|
25.5
|
1.0
|
FE
|
A:FE403
|
3.4
|
25.7
|
1.0
|
OE1
|
A:GLU84
|
3.5
|
31.2
|
1.0
|
OE2
|
A:GLU114
|
3.6
|
24.2
|
1.0
|
CB
|
A:HIS117
|
3.9
|
23.2
|
1.0
|
NE2
|
A:HIS117
|
4.1
|
25.2
|
1.0
|
CG
|
A:GLU84
|
4.3
|
24.9
|
1.0
|
C4
|
A:IMD401
|
4.3
|
28.3
|
1.0
|
CD2
|
A:HIS117
|
4.4
|
22.7
|
1.0
|
N3
|
A:IMD401
|
4.4
|
26.8
|
1.0
|
OE2
|
A:GLU180
|
4.4
|
27.9
|
1.0
|
CG
|
A:GLU114
|
4.5
|
19.4
|
1.0
|
OE1
|
A:GLU212
|
4.6
|
24.5
|
1.0
|
CA
|
A:GLU114
|
4.6
|
21.2
|
1.0
|
CE1
|
A:HIS215
|
4.7
|
23.4
|
1.0
|
ND1
|
A:HIS215
|
4.8
|
19.4
|
1.0
|
CB
|
A:GLU114
|
4.8
|
20.6
|
1.0
|
|
Iron binding site 2 out
of 8 in 8wvr
Go back to
Iron Binding Sites List in 8wvr
Iron binding site 2 out
of 8 in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe403
b:25.7
occ:1.00
|
OE2
|
A:GLU180
|
1.9
|
27.9
|
1.0
|
O
|
A:HOH596
|
2.0
|
24.8
|
1.0
|
ND1
|
A:HIS215
|
2.1
|
19.4
|
1.0
|
OE1
|
A:GLU212
|
2.1
|
24.5
|
1.0
|
OE2
|
A:GLU114
|
2.2
|
24.2
|
1.0
|
CD
|
A:GLU180
|
2.9
|
25.9
|
1.0
|
CE1
|
A:HIS215
|
2.9
|
23.4
|
1.0
|
CD
|
A:GLU114
|
3.1
|
21.7
|
1.0
|
CD
|
A:GLU212
|
3.1
|
27.3
|
1.0
|
CG
|
A:HIS215
|
3.2
|
23.2
|
1.0
|
OE1
|
A:GLU180
|
3.3
|
28.6
|
1.0
|
OE1
|
A:GLU114
|
3.4
|
23.0
|
1.0
|
FE
|
A:FE402
|
3.4
|
24.3
|
1.0
|
OE2
|
A:GLU212
|
3.5
|
34.4
|
1.0
|
CB
|
A:HIS215
|
3.7
|
23.8
|
1.0
|
NE2
|
A:GLN110
|
3.8
|
19.1
|
1.0
|
NE2
|
A:HIS215
|
4.1
|
20.4
|
1.0
|
CG
|
A:GLU180
|
4.2
|
25.7
|
1.0
|
CD2
|
A:HIS215
|
4.3
|
18.9
|
1.0
|
CG
|
A:GLU212
|
4.4
|
24.4
|
1.0
|
CG
|
A:GLU114
|
4.5
|
19.4
|
1.0
|
CA
|
A:GLU212
|
4.6
|
23.2
|
1.0
|
CE1
|
A:HIS117
|
4.6
|
23.1
|
1.0
|
C5
|
A:IMD401
|
4.6
|
29.8
|
1.0
|
CB
|
A:GLU212
|
4.6
|
24.2
|
1.0
|
N1
|
A:IMD401
|
4.7
|
28.1
|
1.0
|
CD
|
A:GLN110
|
4.7
|
26.2
|
1.0
|
ND1
|
A:HIS117
|
4.8
|
23.1
|
1.0
|
CG
|
A:GLN110
|
5.0
|
19.0
|
1.0
|
|
Iron binding site 3 out
of 8 in 8wvr
Go back to
Iron Binding Sites List in 8wvr
Iron binding site 3 out
of 8 in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe402
b:24.6
occ:1.00
|
O
|
B:HOH556
|
1.9
|
26.0
|
1.0
|
OE2
|
B:GLU84
|
2.0
|
22.6
|
1.0
|
OE1
|
B:GLU114
|
2.1
|
21.5
|
1.0
|
N1
|
B:IMD401
|
2.2
|
28.6
|
1.0
|
ND1
|
B:HIS117
|
2.3
|
22.9
|
1.0
|
CD
|
B:GLU84
|
3.0
|
24.5
|
1.0
|
C5
|
B:IMD401
|
3.1
|
28.7
|
1.0
|
CE1
|
B:HIS117
|
3.1
|
23.4
|
1.0
|
CD
|
B:GLU114
|
3.2
|
22.0
|
1.0
|
C2
|
B:IMD401
|
3.2
|
27.0
|
1.0
|
OE1
|
B:GLU84
|
3.3
|
30.9
|
1.0
|
FE
|
B:FE403
|
3.4
|
24.4
|
1.0
|
CG
|
B:HIS117
|
3.4
|
23.3
|
1.0
|
OE2
|
B:GLU114
|
3.5
|
23.4
|
1.0
|
CB
|
B:HIS117
|
3.9
|
22.6
|
1.0
|
C4
|
B:IMD401
|
4.2
|
28.1
|
1.0
|
N3
|
B:IMD401
|
4.3
|
31.5
|
1.0
|
NE2
|
B:HIS117
|
4.3
|
22.5
|
1.0
|
CG
|
B:GLU84
|
4.3
|
25.4
|
1.0
|
OE2
|
B:GLU180
|
4.4
|
28.4
|
1.0
|
OE1
|
B:GLU212
|
4.4
|
25.2
|
1.0
|
CD2
|
B:HIS117
|
4.5
|
23.4
|
1.0
|
CG
|
B:GLU114
|
4.5
|
22.0
|
1.0
|
CA
|
B:GLU114
|
4.6
|
21.1
|
1.0
|
CE1
|
B:HIS215
|
4.8
|
23.0
|
1.0
|
ND1
|
B:HIS215
|
4.8
|
22.5
|
1.0
|
CB
|
B:GLU114
|
4.8
|
19.8
|
1.0
|
CD
|
B:GLU212
|
4.9
|
27.1
|
1.0
|
|
Iron binding site 4 out
of 8 in 8wvr
Go back to
Iron Binding Sites List in 8wvr
Iron binding site 4 out
of 8 in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe403
b:24.4
occ:1.00
|
OE2
|
B:GLU180
|
1.9
|
28.4
|
1.0
|
O
|
B:HOH556
|
1.9
|
26.0
|
1.0
|
OE1
|
B:GLU212
|
2.0
|
25.2
|
1.0
|
OE2
|
B:GLU114
|
2.2
|
23.4
|
1.0
|
ND1
|
B:HIS215
|
2.2
|
22.5
|
1.0
|
CD
|
B:GLU180
|
2.9
|
27.0
|
1.0
|
CD
|
B:GLU212
|
3.0
|
27.1
|
1.0
|
CE1
|
B:HIS215
|
3.0
|
23.0
|
1.0
|
CD
|
B:GLU114
|
3.1
|
22.0
|
1.0
|
OE1
|
B:GLU180
|
3.2
|
26.1
|
1.0
|
CG
|
B:HIS215
|
3.3
|
22.9
|
1.0
|
OE2
|
B:GLU212
|
3.4
|
31.9
|
1.0
|
OE1
|
B:GLU114
|
3.4
|
21.5
|
1.0
|
FE
|
B:FE402
|
3.4
|
24.6
|
1.0
|
CB
|
B:HIS215
|
3.7
|
22.0
|
1.0
|
NE2
|
B:GLN110
|
3.8
|
20.9
|
1.0
|
CG
|
B:GLU180
|
4.2
|
23.6
|
1.0
|
NE2
|
B:HIS215
|
4.2
|
23.6
|
1.0
|
CD2
|
B:HIS215
|
4.3
|
20.2
|
1.0
|
CG
|
B:GLU212
|
4.4
|
23.0
|
1.0
|
CG
|
B:GLU114
|
4.5
|
22.0
|
1.0
|
CA
|
B:GLU212
|
4.6
|
22.7
|
1.0
|
C5
|
B:IMD401
|
4.6
|
28.7
|
1.0
|
N1
|
B:IMD401
|
4.6
|
28.6
|
1.0
|
CB
|
B:GLU212
|
4.7
|
23.9
|
1.0
|
CD
|
B:GLN110
|
4.7
|
23.5
|
1.0
|
CE1
|
B:HIS117
|
4.7
|
23.4
|
1.0
|
ND1
|
B:HIS117
|
4.8
|
22.9
|
1.0
|
CG
|
B:GLN110
|
4.9
|
21.8
|
1.0
|
|
Iron binding site 5 out
of 8 in 8wvr
Go back to
Iron Binding Sites List in 8wvr
Iron binding site 5 out
of 8 in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe403
b:22.6
occ:1.00
|
O
|
C:HOH590
|
2.0
|
24.4
|
1.0
|
OE2
|
C:GLU84
|
2.0
|
25.1
|
1.0
|
OE1
|
C:GLU114
|
2.1
|
21.8
|
1.0
|
ND1
|
C:HIS117
|
2.3
|
20.3
|
1.0
|
N1
|
C:IMD401
|
2.3
|
27.7
|
1.0
|
N08
|
C:XBN402
|
2.7
|
25.9
|
0.6
|
N07
|
C:XBN402
|
2.8
|
26.9
|
0.6
|
C5
|
C:IMD401
|
2.9
|
28.0
|
1.0
|
CD
|
C:GLU84
|
3.0
|
28.4
|
1.0
|
CE1
|
C:HIS117
|
3.1
|
21.2
|
1.0
|
CD
|
C:GLU114
|
3.2
|
21.9
|
1.0
|
OE1
|
C:GLU84
|
3.3
|
33.2
|
1.0
|
FE
|
C:FE404
|
3.4
|
23.1
|
1.0
|
CG
|
C:HIS117
|
3.4
|
21.6
|
1.0
|
C2
|
C:IMD401
|
3.5
|
26.9
|
1.0
|
C06
|
C:XBN402
|
3.5
|
27.5
|
0.6
|
OE2
|
C:GLU114
|
3.6
|
21.2
|
1.0
|
C09
|
C:XBN402
|
3.6
|
30.3
|
0.6
|
CB
|
C:HIS117
|
3.9
|
20.5
|
1.0
|
C4
|
C:IMD401
|
4.2
|
26.7
|
1.0
|
NE2
|
C:HIS117
|
4.3
|
21.1
|
1.0
|
CG
|
C:GLU84
|
4.4
|
24.6
|
1.0
|
OE2
|
C:GLU180
|
4.5
|
24.1
|
1.0
|
N3
|
C:IMD401
|
4.5
|
26.4
|
1.0
|
CD2
|
C:HIS117
|
4.5
|
19.4
|
1.0
|
C12
|
C:XBN402
|
4.5
|
34.3
|
0.6
|
O13
|
C:XBN402
|
4.5
|
39.0
|
0.6
|
CG
|
C:GLU114
|
4.5
|
20.1
|
1.0
|
OE1
|
C:GLU212
|
4.6
|
21.4
|
1.0
|
CA
|
C:GLU114
|
4.6
|
20.9
|
1.0
|
CB
|
C:GLU114
|
4.8
|
22.8
|
1.0
|
CE1
|
C:HIS215
|
4.8
|
23.5
|
1.0
|
ND1
|
C:HIS215
|
4.9
|
21.8
|
1.0
|
C10
|
C:XBN402
|
4.9
|
29.9
|
0.6
|
CD
|
C:GLU212
|
5.0
|
23.7
|
1.0
|
|
Iron binding site 6 out
of 8 in 8wvr
Go back to
Iron Binding Sites List in 8wvr
Iron binding site 6 out
of 8 in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe404
b:23.1
occ:1.00
|
O
|
C:HOH590
|
1.9
|
24.4
|
1.0
|
OE2
|
C:GLU180
|
1.9
|
24.1
|
1.0
|
OE1
|
C:GLU212
|
2.1
|
21.4
|
1.0
|
OE2
|
C:GLU114
|
2.2
|
21.2
|
1.0
|
ND1
|
C:HIS215
|
2.2
|
21.8
|
1.0
|
N07
|
C:XBN402
|
2.9
|
26.9
|
0.6
|
CD
|
C:GLU180
|
2.9
|
26.7
|
1.0
|
CE1
|
C:HIS215
|
3.0
|
23.5
|
1.0
|
CD
|
C:GLU114
|
3.1
|
21.9
|
1.0
|
CD
|
C:GLU212
|
3.1
|
23.7
|
1.0
|
OE1
|
C:GLU114
|
3.3
|
21.8
|
1.0
|
CG
|
C:HIS215
|
3.3
|
22.1
|
1.0
|
FE
|
C:FE403
|
3.4
|
22.6
|
1.0
|
OE1
|
C:GLU180
|
3.4
|
27.4
|
1.0
|
OE2
|
C:GLU212
|
3.5
|
33.1
|
1.0
|
C06
|
C:XBN402
|
3.7
|
27.5
|
0.6
|
CB
|
C:HIS215
|
3.7
|
20.1
|
1.0
|
NE2
|
C:GLN110
|
3.8
|
24.1
|
1.0
|
N08
|
C:XBN402
|
4.0
|
25.9
|
0.6
|
CG
|
C:GLU180
|
4.2
|
27.6
|
1.0
|
NE2
|
C:HIS215
|
4.2
|
20.2
|
1.0
|
CD2
|
C:HIS215
|
4.4
|
22.9
|
1.0
|
CG
|
C:GLU212
|
4.4
|
23.3
|
1.0
|
C09
|
C:XBN402
|
4.5
|
30.3
|
0.6
|
CG
|
C:GLU114
|
4.5
|
20.1
|
1.0
|
C5
|
C:IMD401
|
4.5
|
28.0
|
1.0
|
CA
|
C:GLU212
|
4.6
|
20.7
|
1.0
|
CB
|
C:GLU212
|
4.6
|
23.2
|
1.0
|
CD
|
C:GLN110
|
4.7
|
23.3
|
1.0
|
C05
|
C:XBN402
|
4.7
|
30.5
|
0.6
|
CE1
|
C:HIS117
|
4.7
|
21.2
|
1.0
|
ND1
|
C:HIS117
|
4.8
|
20.3
|
1.0
|
N1
|
C:IMD401
|
4.8
|
27.7
|
1.0
|
C10
|
C:XBN402
|
4.8
|
29.9
|
0.6
|
CG
|
C:GLN110
|
4.9
|
22.3
|
1.0
|
|
Iron binding site 7 out
of 8 in 8wvr
Go back to
Iron Binding Sites List in 8wvr
Iron binding site 7 out
of 8 in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe402
b:42.7
occ:1.00
|
O
|
D:HOH536
|
2.0
|
29.3
|
1.0
|
OE2
|
D:GLU84
|
2.0
|
42.4
|
1.0
|
OE1
|
D:GLU114
|
2.2
|
35.2
|
1.0
|
ND1
|
D:HIS117
|
2.3
|
36.3
|
1.0
|
N1
|
D:IMD401
|
2.8
|
44.1
|
1.0
|
C2
|
D:IMD401
|
2.9
|
43.5
|
1.0
|
CE1
|
D:HIS117
|
3.0
|
37.7
|
1.0
|
CD
|
D:GLU84
|
3.1
|
39.9
|
1.0
|
CD
|
D:GLU114
|
3.2
|
35.9
|
1.0
|
OE1
|
D:GLU84
|
3.4
|
42.4
|
1.0
|
FE
|
D:FE403
|
3.5
|
39.1
|
1.0
|
CG
|
D:HIS117
|
3.5
|
35.3
|
1.0
|
OE2
|
D:GLU114
|
3.6
|
36.3
|
1.0
|
CB
|
D:HIS117
|
4.0
|
32.7
|
1.0
|
C5
|
D:IMD401
|
4.1
|
48.1
|
1.0
|
N3
|
D:IMD401
|
4.2
|
46.5
|
1.0
|
NE2
|
D:HIS117
|
4.2
|
35.9
|
1.0
|
CG
|
D:GLU84
|
4.4
|
41.8
|
1.0
|
CD2
|
D:HIS117
|
4.5
|
34.4
|
1.0
|
OE2
|
D:GLU180
|
4.5
|
39.6
|
1.0
|
OE1
|
D:GLU212
|
4.5
|
42.2
|
1.0
|
CG
|
D:GLU114
|
4.6
|
34.7
|
1.0
|
CA
|
D:GLU114
|
4.6
|
31.5
|
1.0
|
C4
|
D:IMD401
|
4.8
|
49.1
|
1.0
|
CB
|
D:GLU114
|
4.8
|
31.2
|
1.0
|
ND1
|
D:HIS215
|
4.9
|
36.5
|
1.0
|
CE1
|
D:HIS215
|
4.9
|
34.1
|
1.0
|
|
Iron binding site 8 out
of 8 in 8wvr
Go back to
Iron Binding Sites List in 8wvr
Iron binding site 8 out
of 8 in the Complex Structure of the Azoxy Synthase Vlmb and Its Substrate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Complex Structure of the Azoxy Synthase Vlmb and Its Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe403
b:39.1
occ:1.00
|
O
|
D:HOH536
|
1.9
|
29.3
|
1.0
|
OE2
|
D:GLU180
|
2.0
|
39.6
|
1.0
|
OE1
|
D:GLU212
|
2.2
|
42.2
|
1.0
|
OE2
|
D:GLU114
|
2.3
|
36.3
|
1.0
|
ND1
|
D:HIS215
|
2.3
|
36.5
|
1.0
|
CD
|
D:GLU180
|
3.0
|
42.9
|
1.0
|
CE1
|
D:HIS215
|
3.1
|
34.1
|
1.0
|
CD
|
D:GLU114
|
3.2
|
35.9
|
1.0
|
CD
|
D:GLU212
|
3.2
|
43.6
|
1.0
|
CG
|
D:HIS215
|
3.3
|
35.3
|
1.0
|
OE1
|
D:GLU180
|
3.3
|
42.9
|
1.0
|
OE1
|
D:GLU114
|
3.5
|
35.2
|
1.0
|
FE
|
D:FE402
|
3.5
|
42.7
|
1.0
|
OE2
|
D:GLU212
|
3.6
|
50.7
|
1.0
|
CB
|
D:HIS215
|
3.7
|
36.4
|
1.0
|
NE2
|
D:GLN110
|
3.8
|
35.6
|
1.0
|
CG
|
D:GLU180
|
4.2
|
39.0
|
1.0
|
NE2
|
D:HIS215
|
4.3
|
35.1
|
1.0
|
CD2
|
D:HIS215
|
4.4
|
35.0
|
1.0
|
CG
|
D:GLU212
|
4.5
|
42.0
|
1.0
|
CG
|
D:GLU114
|
4.6
|
34.7
|
1.0
|
CA
|
D:GLU212
|
4.6
|
35.3
|
1.0
|
CD
|
D:GLN110
|
4.6
|
36.6
|
1.0
|
C2
|
D:IMD401
|
4.7
|
43.5
|
1.0
|
CB
|
D:GLU212
|
4.8
|
38.3
|
1.0
|
CE1
|
D:HIS117
|
4.8
|
37.7
|
1.0
|
CG
|
D:GLN110
|
4.8
|
32.5
|
1.0
|
ND1
|
D:HIS117
|
5.0
|
36.3
|
1.0
|
CE1
|
D:PHE175
|
5.0
|
37.4
|
1.0
|
|
Reference:
X.Zang,
J.H.Zhou,
D.Yiling,
S.Jingkun,
Z.Zhijie,
S.Zhuanglin,
Z.Guiyun.
A Conserved Enzymatic Route For Azoxy Bond Formation in Natural Product Biosynthesis To Be Published.
Page generated: Wed Nov 13 09:55:45 2024
|