Iron in PDB 1oii: Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Iron and Alphaketoglutarate
Protein crystallography data
The structure of Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Iron and Alphaketoglutarate, PDB code: 1oii
was solved by
I.Mueller,
A.Kahnert,
T.Pape,
T.Dierks,
W.Meyer-Klauke,
M.A.Kertesz,
I.Uson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.19
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.421,
147.329,
158.573,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.5 /
22
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Iron and Alphaketoglutarate
(pdb code 1oii). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Iron and Alphaketoglutarate, PDB code: 1oii:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1oii
Go back to
Iron Binding Sites List in 1oii
Iron binding site 1 out
of 4 in the Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Iron and Alphaketoglutarate
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 the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Iron and Alphaketoglutarate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1301
b:21.6
occ:0.70
|
O
|
A:HOH2053
|
1.9
|
29.4
|
1.0
|
O5
|
A:AKG1302
|
1.9
|
32.4
|
0.7
|
OD2
|
A:ASP110
|
2.0
|
28.6
|
1.0
|
O2
|
A:AKG1302
|
2.1
|
26.2
|
0.7
|
NE2
|
A:HIS264
|
2.1
|
27.0
|
1.0
|
NE2
|
A:HIS108
|
2.2
|
30.6
|
1.0
|
C2
|
A:AKG1302
|
2.6
|
33.8
|
0.7
|
C1
|
A:AKG1302
|
2.7
|
32.5
|
0.7
|
CE1
|
A:HIS264
|
3.1
|
29.8
|
1.0
|
CG
|
A:ASP110
|
3.1
|
29.3
|
1.0
|
CD2
|
A:HIS264
|
3.1
|
25.9
|
1.0
|
CE1
|
A:HIS108
|
3.1
|
32.8
|
1.0
|
CD2
|
A:HIS108
|
3.2
|
30.9
|
1.0
|
OD1
|
A:ASP110
|
3.6
|
31.9
|
1.0
|
O1
|
A:AKG1302
|
3.9
|
33.4
|
0.7
|
C3
|
A:AKG1302
|
4.1
|
35.0
|
0.7
|
ND1
|
A:HIS264
|
4.2
|
25.4
|
1.0
|
O
|
A:HOH2150
|
4.2
|
37.2
|
1.0
|
CG
|
A:HIS264
|
4.2
|
25.2
|
1.0
|
ND1
|
A:HIS108
|
4.3
|
29.1
|
1.0
|
CG
|
A:HIS108
|
4.3
|
30.3
|
1.0
|
CB
|
A:ASP110
|
4.4
|
28.7
|
1.0
|
C4
|
A:AKG1302
|
4.7
|
31.9
|
0.7
|
CZ2
|
A:TRP257
|
4.7
|
27.4
|
1.0
|
CA
|
A:ASP110
|
4.8
|
28.6
|
1.0
|
O
|
A:HOH2054
|
4.9
|
37.5
|
1.0
|
|
Iron binding site 2 out
of 4 in 1oii
Go back to
Iron Binding Sites List in 1oii
Iron binding site 2 out
of 4 in the Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Iron and Alphaketoglutarate
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 the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Iron and Alphaketoglutarate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1301
b:21.8
occ:0.70
|
O
|
B:HOH2155
|
1.9
|
29.8
|
1.0
|
OD2
|
B:ASP110
|
2.0
|
28.2
|
1.0
|
O5
|
B:AKG1302
|
2.0
|
26.6
|
0.7
|
O2
|
B:AKG1302
|
2.1
|
25.6
|
0.7
|
NE2
|
B:HIS264
|
2.1
|
27.5
|
1.0
|
NE2
|
B:HIS108
|
2.2
|
30.1
|
1.0
|
C2
|
B:AKG1302
|
2.7
|
28.6
|
0.7
|
C1
|
B:AKG1302
|
2.8
|
27.2
|
0.7
|
CE1
|
B:HIS264
|
3.1
|
29.7
|
1.0
|
CG
|
B:ASP110
|
3.1
|
29.2
|
1.0
|
CD2
|
B:HIS264
|
3.1
|
25.8
|
1.0
|
CE1
|
B:HIS108
|
3.2
|
32.7
|
1.0
|
CD2
|
B:HIS108
|
3.2
|
30.2
|
1.0
|
OD1
|
B:ASP110
|
3.6
|
32.0
|
1.0
|
O1
|
B:AKG1302
|
4.0
|
27.1
|
0.7
|
C3
|
B:AKG1302
|
4.2
|
30.7
|
0.7
|
ND1
|
B:HIS264
|
4.2
|
25.1
|
1.0
|
CG
|
B:HIS264
|
4.3
|
25.0
|
1.0
|
ND1
|
B:HIS108
|
4.3
|
29.0
|
1.0
|
CG
|
B:HIS108
|
4.3
|
30.2
|
1.0
|
CB
|
B:ASP110
|
4.5
|
28.8
|
1.0
|
C4
|
B:AKG1302
|
4.7
|
28.1
|
0.7
|
CZ2
|
B:TRP257
|
4.7
|
27.2
|
1.0
|
CA
|
B:ASP110
|
4.9
|
28.6
|
1.0
|
O
|
B:HOH2055
|
4.9
|
35.5
|
1.0
|
|
Iron binding site 3 out
of 4 in 1oii
Go back to
Iron Binding Sites List in 1oii
Iron binding site 3 out
of 4 in the Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Iron and Alphaketoglutarate
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 the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Iron and Alphaketoglutarate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe1300
b:22.3
occ:0.70
|
O5
|
C:AKG1301
|
1.9
|
27.6
|
0.7
|
O
|
C:HOH2149
|
1.9
|
30.9
|
1.0
|
OD2
|
C:ASP110
|
2.0
|
28.6
|
1.0
|
O2
|
C:AKG1301
|
2.1
|
26.4
|
0.7
|
NE2
|
C:HIS264
|
2.1
|
27.9
|
1.0
|
NE2
|
C:HIS108
|
2.2
|
30.7
|
1.0
|
C2
|
C:AKG1301
|
2.7
|
30.8
|
0.7
|
C1
|
C:AKG1301
|
2.8
|
30.3
|
0.7
|
CE1
|
C:HIS264
|
3.1
|
30.2
|
1.0
|
CD2
|
C:HIS264
|
3.1
|
25.8
|
1.0
|
CE1
|
C:HIS108
|
3.1
|
32.5
|
1.0
|
CG
|
C:ASP110
|
3.2
|
29.5
|
1.0
|
CD2
|
C:HIS108
|
3.3
|
30.3
|
1.0
|
OD1
|
C:ASP110
|
3.5
|
32.3
|
1.0
|
O1
|
C:AKG1301
|
4.0
|
33.3
|
0.7
|
C3
|
C:AKG1301
|
4.1
|
25.2
|
0.7
|
ND1
|
C:HIS264
|
4.2
|
24.6
|
1.0
|
CG
|
C:HIS264
|
4.2
|
24.4
|
1.0
|
ND1
|
C:HIS108
|
4.3
|
28.8
|
1.0
|
CG
|
C:HIS108
|
4.4
|
30.6
|
1.0
|
CB
|
C:ASP110
|
4.5
|
28.6
|
1.0
|
CZ2
|
C:TRP257
|
4.6
|
27.6
|
1.0
|
C4
|
C:AKG1301
|
4.7
|
25.8
|
0.7
|
CA
|
C:ASP110
|
4.8
|
28.7
|
1.0
|
O
|
C:HOH2049
|
4.9
|
39.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 1oii
Go back to
Iron Binding Sites List in 1oii
Iron binding site 4 out
of 4 in the Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Iron and Alphaketoglutarate
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 the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Iron and Alphaketoglutarate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1300
b:22.9
occ:0.70
|
O2
|
D:AKG1301
|
2.0
|
28.8
|
0.7
|
O5
|
D:AKG1301
|
2.0
|
24.9
|
0.7
|
OD2
|
D:ASP110
|
2.1
|
29.3
|
1.0
|
O
|
D:HOH2115
|
2.1
|
31.7
|
1.0
|
NE2
|
D:HIS264
|
2.1
|
28.2
|
1.0
|
NE2
|
D:HIS108
|
2.2
|
30.9
|
1.0
|
C2
|
D:AKG1301
|
2.7
|
32.8
|
0.7
|
C1
|
D:AKG1301
|
2.7
|
30.0
|
0.7
|
CE1
|
D:HIS264
|
3.1
|
29.8
|
1.0
|
CE1
|
D:HIS108
|
3.1
|
32.7
|
1.0
|
CD2
|
D:HIS264
|
3.1
|
26.2
|
1.0
|
CG
|
D:ASP110
|
3.2
|
29.3
|
1.0
|
CD2
|
D:HIS108
|
3.2
|
30.3
|
1.0
|
OD1
|
D:ASP110
|
3.6
|
31.9
|
1.0
|
O1
|
D:AKG1301
|
3.9
|
29.6
|
0.7
|
O
|
D:HOH2116
|
4.0
|
40.0
|
1.0
|
ND1
|
D:HIS264
|
4.2
|
25.6
|
1.0
|
C3
|
D:AKG1301
|
4.2
|
30.6
|
0.7
|
CG
|
D:HIS264
|
4.2
|
24.6
|
1.0
|
ND1
|
D:HIS108
|
4.2
|
29.1
|
1.0
|
CG
|
D:HIS108
|
4.3
|
30.5
|
1.0
|
CB
|
D:ASP110
|
4.5
|
29.2
|
1.0
|
CZ2
|
D:TRP257
|
4.7
|
27.5
|
1.0
|
C4
|
D:AKG1301
|
4.7
|
27.5
|
0.7
|
CA
|
D:ASP110
|
4.8
|
29.2
|
1.0
|
O
|
D:HOH2038
|
5.0
|
39.1
|
1.0
|
|
Reference:
I.Mueller,
A.Kahnert,
T.Pape,
G.M.Sheldrick,
W.Meyer-Klaucke,
T.Dierks,
M.A.Kertesz,
I.Uson.
Crystal Structure of the Alkylsulfatase Atsk: Insights Into the Catalytic Mechanism of the Fe(II) Alpha-Ketoglutarate-Dependent Dioxygenase Superfamily Biochemistry V. 42 3075 2004.
ISSN: ISSN 0006-2960
PubMed: 15023059
DOI: 10.1021/BI035752V
Page generated: Sat Aug 3 12:30:20 2024
|