Sodium in PDB 1oij: Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate
Protein crystallography data
The structure of Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate, PDB code: 1oij
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)
|
38.92 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.447,
144.876,
160.692,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.1 /
21.5
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate
(pdb code 1oij). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate, PDB code: 1oij:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 1oij
Go back to
Sodium Binding Sites List in 1oij
Sodium 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 Alphaketoglutarate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1301
b:34.0
occ:0.70
|
OD1
|
A:ASP110
|
2.1
|
38.2
|
1.0
|
O5
|
A:AKG1302
|
2.2
|
48.1
|
0.7
|
NE2
|
A:HIS264
|
2.3
|
31.7
|
1.0
|
O2
|
A:AKG1302
|
2.4
|
53.1
|
0.7
|
NE2
|
A:HIS108
|
2.4
|
34.7
|
1.0
|
CE1
|
A:HIS264
|
2.9
|
30.9
|
1.0
|
C2
|
A:AKG1302
|
3.0
|
50.8
|
0.7
|
C1
|
A:AKG1302
|
3.1
|
53.7
|
0.7
|
CG
|
A:ASP110
|
3.2
|
37.5
|
1.0
|
CD2
|
A:HIS108
|
3.3
|
32.8
|
1.0
|
CE1
|
A:HIS108
|
3.4
|
34.3
|
1.0
|
CD2
|
A:HIS264
|
3.5
|
27.6
|
1.0
|
OD2
|
A:ASP110
|
3.7
|
38.2
|
1.0
|
NH1
|
A:ARG279
|
4.0
|
68.9
|
1.0
|
O
|
A:HOH2168
|
4.0
|
49.5
|
1.0
|
ND1
|
A:HIS264
|
4.1
|
32.7
|
1.0
|
O1
|
A:AKG1302
|
4.3
|
56.7
|
0.7
|
CG
|
A:HIS264
|
4.4
|
28.6
|
1.0
|
C3
|
A:AKG1302
|
4.4
|
45.3
|
0.7
|
ND1
|
A:HIS108
|
4.5
|
32.5
|
1.0
|
CG
|
A:HIS108
|
4.5
|
31.2
|
1.0
|
CB
|
A:ASP110
|
4.5
|
31.1
|
1.0
|
C4
|
A:AKG1302
|
4.7
|
38.6
|
0.7
|
CA
|
A:ASP110
|
4.7
|
31.3
|
1.0
|
CZ2
|
A:TRP257
|
4.9
|
29.8
|
1.0
|
CZ
|
A:ARG279
|
4.9
|
65.4
|
1.0
|
|
Sodium binding site 2 out
of 4 in 1oij
Go back to
Sodium Binding Sites List in 1oij
Sodium 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 Alphaketoglutarate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1301
b:37.5
occ:0.70
|
OD1
|
B:ASP110
|
2.2
|
38.3
|
1.0
|
O5
|
B:AKG1302
|
2.2
|
55.1
|
0.7
|
NE2
|
B:HIS264
|
2.4
|
32.5
|
1.0
|
NE2
|
B:HIS108
|
2.5
|
35.1
|
1.0
|
O2
|
B:AKG1302
|
2.5
|
51.9
|
0.7
|
CE1
|
B:HIS264
|
3.0
|
30.8
|
1.0
|
C2
|
B:AKG1302
|
3.1
|
52.0
|
0.7
|
C1
|
B:AKG1302
|
3.1
|
52.6
|
0.7
|
CD2
|
B:HIS108
|
3.4
|
32.5
|
1.0
|
CG
|
B:ASP110
|
3.4
|
37.4
|
1.0
|
CE1
|
B:HIS108
|
3.5
|
34.5
|
1.0
|
CD2
|
B:HIS264
|
3.6
|
27.7
|
1.0
|
OD2
|
B:ASP110
|
3.9
|
38.3
|
1.0
|
NH1
|
B:ARG279
|
4.0
|
69.5
|
1.0
|
ND1
|
B:HIS264
|
4.2
|
32.2
|
1.0
|
O
|
B:HOH2075
|
4.3
|
37.7
|
1.0
|
O1
|
B:AKG1302
|
4.3
|
56.5
|
0.7
|
C3
|
B:AKG1302
|
4.5
|
44.2
|
0.7
|
CG
|
B:HIS264
|
4.5
|
28.4
|
1.0
|
CB
|
B:ASP110
|
4.5
|
31.1
|
1.0
|
CG
|
B:HIS108
|
4.5
|
30.9
|
1.0
|
ND1
|
B:HIS108
|
4.6
|
32.1
|
1.0
|
CA
|
B:ASP110
|
4.8
|
31.4
|
1.0
|
CZ
|
B:ARG279
|
4.8
|
64.6
|
1.0
|
C4
|
B:AKG1302
|
4.8
|
36.3
|
0.7
|
CZ2
|
B:TRP257
|
4.9
|
29.8
|
1.0
|
|
Sodium binding site 3 out
of 4 in 1oij
Go back to
Sodium Binding Sites List in 1oij
Sodium 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 Alphaketoglutarate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na1300
b:32.0
occ:1.00
|
O5
|
C:AKG1301
|
2.1
|
59.8
|
1.0
|
NE2
|
C:HIS264
|
2.2
|
31.8
|
1.0
|
OD1
|
C:ASP110
|
2.2
|
37.8
|
1.0
|
O2
|
C:AKG1301
|
2.4
|
48.6
|
1.0
|
NE2
|
C:HIS108
|
2.5
|
35.3
|
1.0
|
CE1
|
C:HIS264
|
2.9
|
30.8
|
1.0
|
C2
|
C:AKG1301
|
2.9
|
56.8
|
1.0
|
C1
|
C:AKG1301
|
3.0
|
57.2
|
1.0
|
CD2
|
C:HIS264
|
3.3
|
27.6
|
1.0
|
CG
|
C:ASP110
|
3.4
|
37.2
|
1.0
|
CE1
|
C:HIS108
|
3.4
|
33.8
|
1.0
|
CD2
|
C:HIS108
|
3.5
|
32.0
|
1.0
|
OD2
|
C:ASP110
|
3.8
|
38.2
|
1.0
|
NH1
|
C:ARG279
|
3.8
|
63.0
|
1.0
|
ND1
|
C:HIS264
|
4.1
|
32.7
|
1.0
|
O1
|
C:AKG1301
|
4.2
|
63.8
|
1.0
|
C3
|
C:AKG1301
|
4.3
|
51.6
|
1.0
|
CG
|
C:HIS264
|
4.3
|
28.7
|
1.0
|
ND1
|
C:HIS108
|
4.5
|
32.3
|
1.0
|
CZ
|
C:ARG279
|
4.5
|
66.8
|
1.0
|
O
|
C:HOH2070
|
4.6
|
35.8
|
1.0
|
CG
|
C:HIS108
|
4.6
|
31.0
|
1.0
|
CB
|
C:ASP110
|
4.6
|
30.9
|
1.0
|
C4
|
C:AKG1301
|
4.6
|
45.2
|
1.0
|
NH2
|
C:ARG279
|
4.6
|
64.0
|
1.0
|
CZ2
|
C:TRP257
|
4.8
|
29.1
|
1.0
|
CA
|
C:ASP110
|
4.9
|
31.3
|
1.0
|
|
Sodium binding site 4 out
of 4 in 1oij
Go back to
Sodium Binding Sites List in 1oij
Sodium 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 Alphaketoglutarate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na1300
b:33.5
occ:0.80
|
O5
|
D:AKG1301
|
2.2
|
52.5
|
0.8
|
NE2
|
D:HIS264
|
2.2
|
32.0
|
1.0
|
OD1
|
D:ASP110
|
2.2
|
37.5
|
1.0
|
O2
|
D:AKG1301
|
2.3
|
42.3
|
0.8
|
NE2
|
D:HIS108
|
2.5
|
34.9
|
1.0
|
CE1
|
D:HIS264
|
2.8
|
31.2
|
1.0
|
C2
|
D:AKG1301
|
3.0
|
48.7
|
0.8
|
C1
|
D:AKG1301
|
3.0
|
53.1
|
0.8
|
CG
|
D:ASP110
|
3.4
|
36.9
|
1.0
|
CD2
|
D:HIS264
|
3.4
|
27.0
|
1.0
|
CE1
|
D:HIS108
|
3.4
|
34.1
|
1.0
|
CD2
|
D:HIS108
|
3.4
|
32.0
|
1.0
|
OD2
|
D:ASP110
|
3.8
|
38.0
|
1.0
|
ND1
|
D:HIS264
|
4.0
|
32.4
|
1.0
|
O1
|
D:AKG1301
|
4.2
|
56.6
|
0.8
|
CG
|
D:HIS264
|
4.3
|
28.2
|
1.0
|
C3
|
D:AKG1301
|
4.4
|
46.8
|
0.8
|
ND1
|
D:HIS108
|
4.5
|
32.5
|
1.0
|
CG
|
D:HIS108
|
4.6
|
31.4
|
1.0
|
CB
|
D:ASP110
|
4.6
|
31.4
|
1.0
|
O
|
D:HOH2070
|
4.6
|
36.6
|
1.0
|
C4
|
D:AKG1301
|
4.8
|
37.0
|
0.8
|
CZ2
|
D:TRP257
|
4.8
|
29.1
|
1.0
|
CA
|
D:ASP110
|
4.8
|
31.2
|
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: Sun Oct 6 21:11:56 2024
|