Iron in PDB 6vp4: Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG
Enzymatic activity of Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG
All present enzymatic activity of Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG:
1.13.12.19;
1.14.20.7;
Protein crystallography data
The structure of Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG, PDB code: 6vp4
was solved by
K.M.Davis,
R.A.Copeland,
A.K.Boal,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.77 /
1.83
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.73,
78.807,
195.905,
90,
92.67,
90
|
R / Rfree (%)
|
17.5 /
19.7
|
Iron Binding Sites:
The binding sites of Iron atom in the Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG
(pdb code 6vp4). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG, PDB code: 6vp4:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6vp4
Go back to
Iron Binding Sites List in 6vp4
Iron binding site 1 out
of 4 in the Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:18.1
occ:1.00
|
O1
|
A:AKG402
|
2.1
|
20.2
|
1.0
|
NE2
|
A:HIS268
|
2.1
|
17.8
|
1.0
|
NE2
|
A:HIS189
|
2.1
|
17.1
|
1.0
|
OD1
|
A:ASP191
|
2.2
|
22.2
|
1.0
|
O5
|
A:AKG402
|
2.3
|
25.1
|
1.0
|
OD2
|
A:ASP191
|
2.8
|
21.8
|
1.0
|
CG
|
A:ASP191
|
2.8
|
21.6
|
1.0
|
C1
|
A:AKG402
|
2.9
|
22.0
|
1.0
|
CE1
|
A:HIS189
|
3.0
|
20.9
|
1.0
|
C2
|
A:AKG402
|
3.0
|
24.3
|
1.0
|
CE1
|
A:HIS268
|
3.1
|
18.3
|
1.0
|
CD2
|
A:HIS268
|
3.1
|
17.5
|
1.0
|
CD2
|
A:HIS189
|
3.2
|
18.8
|
1.0
|
O2
|
A:AKG402
|
4.1
|
22.7
|
1.0
|
ND1
|
A:HIS189
|
4.2
|
16.9
|
1.0
|
CD
|
A:ARG403
|
4.2
|
22.2
|
1.0
|
ND1
|
A:HIS268
|
4.2
|
17.6
|
1.0
|
CG
|
A:HIS268
|
4.2
|
16.6
|
1.0
|
CG
|
A:HIS189
|
4.3
|
16.7
|
1.0
|
CB
|
A:ASP191
|
4.3
|
19.2
|
1.0
|
C3
|
A:AKG402
|
4.5
|
22.9
|
1.0
|
CE1
|
A:PHE283
|
4.6
|
18.0
|
1.0
|
CZ
|
A:PHE283
|
4.6
|
18.7
|
1.0
|
NH2
|
A:ARG403
|
4.9
|
18.6
|
1.0
|
CG
|
A:ARG403
|
4.9
|
22.2
|
1.0
|
N
|
A:ASP191
|
5.0
|
19.2
|
1.0
|
|
Iron binding site 2 out
of 4 in 6vp4
Go back to
Iron Binding Sites List in 6vp4
Iron binding site 2 out
of 4 in the Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:15.7
occ:1.00
|
O2
|
B:AKG402
|
2.0
|
16.7
|
1.0
|
NE2
|
B:HIS268
|
2.1
|
16.9
|
1.0
|
NE2
|
B:HIS189
|
2.1
|
14.8
|
1.0
|
OD2
|
B:ASP191
|
2.3
|
21.5
|
1.0
|
O5
|
B:AKG402
|
2.4
|
21.2
|
1.0
|
OD1
|
B:ASP191
|
2.8
|
19.6
|
1.0
|
CG
|
B:ASP191
|
2.9
|
19.6
|
1.0
|
C1
|
B:AKG402
|
2.9
|
22.9
|
1.0
|
C2
|
B:AKG402
|
3.0
|
23.2
|
1.0
|
CE1
|
B:HIS189
|
3.0
|
16.7
|
1.0
|
CE1
|
B:HIS268
|
3.1
|
15.5
|
1.0
|
CD2
|
B:HIS268
|
3.1
|
16.3
|
1.0
|
CD2
|
B:HIS189
|
3.2
|
14.5
|
1.0
|
O1
|
B:AKG402
|
4.1
|
22.6
|
1.0
|
CD
|
B:ARG403
|
4.2
|
17.6
|
1.0
|
ND1
|
B:HIS189
|
4.2
|
14.9
|
1.0
|
ND1
|
B:HIS268
|
4.2
|
13.8
|
1.0
|
CG
|
B:HIS268
|
4.2
|
13.3
|
1.0
|
CG
|
B:HIS189
|
4.3
|
14.5
|
1.0
|
CB
|
B:ASP191
|
4.3
|
15.3
|
1.0
|
C3
|
B:AKG402
|
4.5
|
22.0
|
1.0
|
CE1
|
B:PHE283
|
4.6
|
16.3
|
1.0
|
CZ
|
B:PHE283
|
4.7
|
17.6
|
1.0
|
NH1
|
B:ARG403
|
4.9
|
17.7
|
1.0
|
CG
|
B:ARG403
|
4.9
|
15.4
|
1.0
|
N
|
B:ASP191
|
5.0
|
15.4
|
1.0
|
|
Iron binding site 3 out
of 4 in 6vp4
Go back to
Iron Binding Sites List in 6vp4
Iron binding site 3 out
of 4 in the Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:19.3
occ:1.00
|
O2
|
C:AKG402
|
2.1
|
23.7
|
1.0
|
NE2
|
C:HIS268
|
2.1
|
18.0
|
1.0
|
NE2
|
C:HIS189
|
2.2
|
18.3
|
1.0
|
OD2
|
C:ASP191
|
2.2
|
23.5
|
1.0
|
O5
|
C:AKG402
|
2.3
|
25.0
|
1.0
|
OD1
|
C:ASP191
|
2.7
|
21.3
|
1.0
|
CG
|
C:ASP191
|
2.8
|
21.0
|
1.0
|
C1
|
C:AKG402
|
2.9
|
26.7
|
1.0
|
C2
|
C:AKG402
|
3.0
|
26.1
|
1.0
|
CE1
|
C:HIS189
|
3.1
|
17.0
|
1.0
|
CE1
|
C:HIS268
|
3.1
|
20.4
|
1.0
|
CD2
|
C:HIS268
|
3.1
|
18.6
|
1.0
|
CD2
|
C:HIS189
|
3.2
|
17.7
|
1.0
|
O1
|
C:AKG402
|
4.1
|
24.6
|
1.0
|
ND1
|
C:HIS268
|
4.2
|
18.3
|
1.0
|
ND1
|
C:HIS189
|
4.2
|
16.0
|
1.0
|
CD
|
C:ARG403
|
4.2
|
20.2
|
1.0
|
CG
|
C:HIS268
|
4.3
|
19.2
|
1.0
|
CB
|
C:ASP191
|
4.3
|
18.5
|
1.0
|
CG
|
C:HIS189
|
4.3
|
17.2
|
1.0
|
C3
|
C:AKG402
|
4.5
|
24.7
|
1.0
|
CE1
|
C:PHE283
|
4.6
|
17.7
|
1.0
|
CZ
|
C:PHE283
|
4.6
|
20.7
|
1.0
|
N
|
C:ASP191
|
4.9
|
20.1
|
1.0
|
CG
|
C:ARG403
|
4.9
|
21.1
|
1.0
|
NH1
|
C:ARG403
|
5.0
|
20.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 6vp4
Go back to
Iron Binding Sites List in 6vp4
Iron binding site 4 out
of 4 in the Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:18.7
occ:1.00
|
OD2
|
D:ASP191
|
2.1
|
24.8
|
1.0
|
O1
|
D:AKG402
|
2.1
|
22.6
|
1.0
|
NE2
|
D:HIS189
|
2.1
|
17.8
|
1.0
|
NE2
|
D:HIS268
|
2.2
|
17.6
|
1.0
|
O5
|
D:AKG402
|
2.2
|
26.5
|
1.0
|
CG
|
D:ASP191
|
2.8
|
21.5
|
1.0
|
OD1
|
D:ASP191
|
2.8
|
24.4
|
1.0
|
C1
|
D:AKG402
|
2.9
|
26.6
|
1.0
|
C2
|
D:AKG402
|
3.0
|
27.8
|
1.0
|
CE1
|
D:HIS189
|
3.1
|
18.3
|
1.0
|
CD2
|
D:HIS268
|
3.1
|
17.8
|
1.0
|
CD2
|
D:HIS189
|
3.2
|
18.0
|
1.0
|
CE1
|
D:HIS268
|
3.2
|
18.1
|
1.0
|
O2
|
D:AKG402
|
4.1
|
25.8
|
1.0
|
ND1
|
D:HIS189
|
4.2
|
17.2
|
1.0
|
CB
|
D:ASP191
|
4.2
|
17.6
|
1.0
|
CG
|
D:HIS189
|
4.3
|
18.4
|
1.0
|
CG
|
D:HIS268
|
4.3
|
16.5
|
1.0
|
ND1
|
D:HIS268
|
4.3
|
17.1
|
1.0
|
CD
|
D:ARG403
|
4.3
|
21.6
|
1.0
|
C3
|
D:AKG402
|
4.4
|
25.4
|
1.0
|
CE2
|
D:PHE283
|
4.6
|
20.3
|
1.0
|
CZ
|
D:PHE283
|
4.7
|
18.4
|
1.0
|
NH2
|
D:ARG403
|
4.9
|
21.3
|
1.0
|
N
|
D:ASP191
|
5.0
|
21.7
|
1.0
|
|
Reference:
R.A.Copeland,
K.M.Davis,
T.K.C.Shoda,
E.J.Blaesi,
A.K.Boal,
C.Krebs,
J.M.Bollinger Jr..
An Iron(IV)-Oxo Intermediate Initiating L-Arginine Oxidation But Not Ethylene Production By the 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme To Be Published.
Page generated: Wed Aug 7 13:32:44 2024
|