Sodium in PDB 7qte: Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate
Protein crystallography data
The structure of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate, PDB code: 7qte
was solved by
P.Lukat,
M.Daum,
A.Bechthold,
O.Einsle,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
51.24 /
1.81
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
116.077,
142.91,
109.072,
90,
90,
90
|
R / Rfree (%)
|
15.3 /
17.6
|
Other elements in 7qte:
The structure of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate
(pdb code 7qte). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the
Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate, PDB code: 7qte:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 7qte
Go back to
Sodium Binding Sites List in 7qte
Sodium binding site 1 out
of 3 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate
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 Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na304
b:24.5
occ:1.00
|
OD2
|
B:ASP280
|
2.6
|
28.0
|
1.0
|
O
|
B:ASN198
|
2.7
|
13.0
|
1.0
|
O
|
B:HOH482
|
2.8
|
25.6
|
1.0
|
HB2
|
B:ASP280
|
2.8
|
23.3
|
1.0
|
HB2
|
B:ASP201
|
3.0
|
15.3
|
1.0
|
HB2
|
B:ALA202
|
3.1
|
17.3
|
1.0
|
HB3
|
B:ASN198
|
3.4
|
17.4
|
1.0
|
HA
|
B:ASN198
|
3.5
|
15.7
|
1.0
|
CG
|
B:ASP280
|
3.5
|
26.2
|
1.0
|
H
|
B:ALA202
|
3.5
|
16.9
|
1.0
|
CB
|
B:ASP280
|
3.6
|
19.5
|
1.0
|
C
|
B:ASN198
|
3.6
|
15.1
|
1.0
|
HB3
|
B:ASP201
|
3.8
|
15.3
|
1.0
|
CB
|
B:ASP201
|
3.8
|
12.8
|
1.0
|
HD22
|
B:ASN198
|
3.9
|
24.8
|
1.0
|
H
|
B:ASP280
|
3.9
|
23.1
|
1.0
|
N
|
B:ALA202
|
3.9
|
14.1
|
1.0
|
CA
|
B:ASN198
|
3.9
|
13.1
|
1.0
|
CB
|
B:ALA202
|
4.0
|
14.4
|
1.0
|
HB3
|
B:ASP280
|
4.1
|
23.3
|
1.0
|
CB
|
B:ASN198
|
4.1
|
14.5
|
1.0
|
HA
|
B:ALA202
|
4.3
|
14.9
|
1.0
|
CA
|
B:ALA202
|
4.3
|
12.4
|
1.0
|
HB3
|
B:ALA202
|
4.4
|
17.3
|
1.0
|
C
|
B:ASP201
|
4.6
|
13.0
|
1.0
|
N
|
B:ASP280
|
4.6
|
19.3
|
1.0
|
HB1
|
B:ALA202
|
4.6
|
17.3
|
1.0
|
ND2
|
B:ASN198
|
4.6
|
20.7
|
1.0
|
OD2
|
B:ASP201
|
4.7
|
16.6
|
1.0
|
CZ3
|
B:TRP281
|
4.7
|
23.8
|
1.0
|
OD1
|
B:ASP280
|
4.7
|
27.4
|
1.0
|
CA
|
B:ASP280
|
4.7
|
19.3
|
1.0
|
CA
|
B:ASP201
|
4.8
|
14.8
|
1.0
|
HZ3
|
B:TRP281
|
4.8
|
28.6
|
1.0
|
N
|
B:GLU199
|
4.8
|
12.3
|
1.0
|
CG
|
B:ASP201
|
4.8
|
18.6
|
1.0
|
CE3
|
B:TRP281
|
4.8
|
35.4
|
1.0
|
HB2
|
B:ASN198
|
4.8
|
17.4
|
1.0
|
HA
|
B:GLU199
|
4.9
|
16.4
|
1.0
|
CH2
|
B:TRP281
|
4.9
|
26.6
|
1.0
|
H
|
B:ASP201
|
4.9
|
18.5
|
1.0
|
CG
|
B:ASN198
|
5.0
|
18.1
|
1.0
|
|
Sodium binding site 2 out
of 3 in 7qte
Go back to
Sodium Binding Sites List in 7qte
Sodium binding site 2 out
of 3 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate
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 Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na305
b:47.9
occ:1.00
|
O
|
B:HOH713
|
2.5
|
46.3
|
1.0
|
O
|
B:HOH720
|
2.6
|
53.4
|
1.0
|
O
|
B:HOH697
|
2.6
|
47.3
|
1.0
|
O
|
B:ARG66
|
2.9
|
27.3
|
1.0
|
HB3
|
B:ARG66
|
3.2
|
31.5
|
1.0
|
O
|
B:GLY69
|
3.3
|
26.4
|
1.0
|
HG2
|
B:ARG66
|
3.4
|
38.2
|
1.0
|
HA
|
B:ARG66
|
3.5
|
33.2
|
1.0
|
C
|
B:GLY69
|
3.5
|
24.3
|
1.0
|
HA2
|
B:GLY69
|
3.7
|
31.9
|
1.0
|
C
|
B:ARG66
|
3.8
|
24.8
|
1.0
|
CB
|
B:ARG66
|
3.8
|
26.3
|
1.0
|
HA
|
B:GLU70
|
3.9
|
27.2
|
1.0
|
CA
|
B:ARG66
|
3.9
|
27.7
|
1.0
|
CA
|
B:GLY69
|
4.0
|
26.6
|
1.0
|
H
|
B:GLY69
|
4.1
|
31.8
|
1.0
|
CG
|
B:ARG66
|
4.1
|
31.8
|
1.0
|
N
|
B:GLU70
|
4.1
|
22.6
|
1.0
|
O
|
B:HOH668
|
4.2
|
54.1
|
1.0
|
N
|
B:GLY69
|
4.4
|
26.4
|
1.0
|
HD3
|
B:ARG66
|
4.5
|
38.3
|
1.0
|
CA
|
B:GLU70
|
4.5
|
22.7
|
1.0
|
H
|
B:GLU70
|
4.7
|
27.1
|
1.0
|
HB2
|
B:ARG66
|
4.7
|
31.5
|
1.0
|
O
|
B:HOH681
|
4.8
|
42.5
|
1.0
|
HG3
|
B:ARG66
|
4.8
|
38.2
|
1.0
|
CD
|
B:ARG66
|
4.9
|
31.9
|
1.0
|
O
|
B:HOH769
|
4.9
|
49.4
|
1.0
|
O
|
B:HOH601
|
4.9
|
29.4
|
1.0
|
HA3
|
B:GLY69
|
4.9
|
31.9
|
1.0
|
|
Sodium binding site 3 out
of 3 in 7qte
Go back to
Sodium Binding Sites List in 7qte
Sodium binding site 3 out
of 3 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate
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 Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na306
b:54.2
occ:1.00
|
O
|
B:HOH707
|
2.5
|
27.0
|
1.0
|
HB
|
B:THR258
|
2.6
|
30.9
|
1.0
|
O
|
B:THR258
|
2.9
|
18.2
|
1.0
|
HG
|
B:SER260
|
3.0
|
33.4
|
1.0
|
OD2
|
A:ASP32
|
3.1
|
41.3
|
1.0
|
O
|
A:HOH697
|
3.1
|
37.0
|
1.0
|
O
|
B:HOH672
|
3.1
|
37.0
|
1.0
|
HB3
|
A:ASP32
|
3.3
|
33.8
|
1.0
|
OG
|
B:SER260
|
3.4
|
27.8
|
1.0
|
CB
|
B:THR258
|
3.6
|
25.7
|
1.0
|
CG
|
A:ASP32
|
3.8
|
40.4
|
1.0
|
HB2
|
B:SER260
|
3.9
|
23.8
|
1.0
|
HG22
|
B:THR258
|
3.9
|
34.8
|
1.0
|
C
|
B:THR258
|
3.9
|
19.1
|
1.0
|
H
|
B:THR258
|
4.0
|
24.4
|
1.0
|
CB
|
A:ASP32
|
4.0
|
28.1
|
1.0
|
O
|
B:HOH454
|
4.1
|
17.7
|
1.0
|
CG2
|
B:THR258
|
4.2
|
29.0
|
1.0
|
HB3
|
B:PRO175
|
4.2
|
22.4
|
1.0
|
CA
|
B:THR258
|
4.2
|
18.9
|
1.0
|
CB
|
B:SER260
|
4.2
|
19.8
|
1.0
|
HB2
|
A:ASP32
|
4.3
|
33.8
|
1.0
|
O
|
A:HOH543
|
4.3
|
23.6
|
1.0
|
HG21
|
B:THR258
|
4.3
|
34.8
|
1.0
|
HG3
|
B:PRO175
|
4.4
|
28.5
|
1.0
|
N
|
B:THR258
|
4.5
|
20.3
|
1.0
|
OG1
|
B:THR258
|
4.5
|
23.9
|
1.0
|
HG1
|
B:THR258
|
4.6
|
28.7
|
1.0
|
OD1
|
A:ASP32
|
4.8
|
32.8
|
1.0
|
O
|
B:HOH427
|
4.8
|
38.9
|
1.0
|
O
|
B:HOH449
|
4.8
|
31.5
|
1.0
|
HB3
|
B:SER260
|
4.8
|
23.8
|
1.0
|
HH21
|
B:ARG172
|
4.8
|
19.9
|
1.0
|
H
|
B:SER260
|
5.0
|
18.2
|
1.0
|
|
Reference:
P.Lukat,
M.Daum,
D.Zechel,
A.Bechthold,
O.Einsle.
Structural Investigations on the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygense PLAO1 From Streptomyces Sp. TU6071 To Be Published.
Page generated: Wed Oct 9 08:23:48 2024
|