Magnesium in PDB 6xpu: Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Idp
Enzymatic activity of Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Idp
All present enzymatic activity of Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Idp:
2.7.4.6;
Protein crystallography data
The structure of Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Idp, PDB code: 6xpu
was solved by
S.Nguyen,
J.B.Bruning,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.27 /
1.90
|
Space group
|
P 21 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.900,
70.307,
119.133,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.8 /
22.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Idp
(pdb code 6xpu). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the
Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Idp, PDB code: 6xpu:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 6xpu
Go back to
Magnesium Binding Sites List in 6xpu
Magnesium binding site 1 out
of 3 in the Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Idp
![](/pictures/MG/pdb/xp/6xpu-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/xp/6xpu-MG-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Idp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg201
b:37.4
occ:1.00
|
O
|
A:HOH315
|
2.1
|
30.3
|
1.0
|
O
|
A:HOH319
|
2.1
|
32.8
|
1.0
|
O2A
|
A:IDP202
|
2.2
|
26.8
|
0.9
|
O
|
A:HOH521
|
2.2
|
30.9
|
1.0
|
O
|
A:HOH466
|
2.4
|
31.4
|
1.0
|
O
|
A:HOH475
|
2.5
|
34.3
|
1.0
|
O2B
|
A:IDP202
|
3.4
|
26.7
|
0.9
|
PA
|
A:IDP202
|
3.7
|
27.4
|
0.9
|
O
|
A:HOH384
|
4.0
|
27.4
|
1.0
|
O
|
A:HOH310
|
4.0
|
34.3
|
1.0
|
O
|
A:HOH323
|
4.1
|
22.9
|
1.0
|
OD2
|
A:ASP120
|
4.2
|
35.5
|
1.0
|
O1A
|
A:IDP202
|
4.4
|
27.6
|
0.9
|
PB
|
A:IDP202
|
4.6
|
26.8
|
0.9
|
O5'
|
A:IDP202
|
4.6
|
26.1
|
0.9
|
O3A
|
A:IDP202
|
4.6
|
26.0
|
0.9
|
C5'
|
A:IDP202
|
4.6
|
23.2
|
0.9
|
CG
|
A:ASP120
|
4.7
|
26.3
|
1.0
|
O
|
A:HOH352
|
4.8
|
35.0
|
1.0
|
O
|
A:HOH498
|
4.8
|
39.0
|
1.0
|
CD1
|
A:LEU54
|
4.8
|
28.2
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 6xpu
Go back to
Magnesium Binding Sites List in 6xpu
Magnesium binding site 2 out
of 3 in the Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Idp
![](/pictures/MG/pdb/xp/6xpu-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/xp/6xpu-MG-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Idp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg201
b:26.0
occ:1.00
|
O2A
|
B:IDP202
|
2.0
|
26.9
|
1.0
|
O
|
B:HOH449
|
2.1
|
26.6
|
1.0
|
O
|
B:HOH310
|
2.1
|
29.4
|
1.0
|
O
|
B:HOH375
|
2.2
|
23.9
|
1.0
|
O
|
B:HOH328
|
2.2
|
23.9
|
1.0
|
O
|
B:HOH407
|
2.2
|
24.6
|
1.0
|
PA
|
B:IDP202
|
3.5
|
25.2
|
1.0
|
O2B
|
B:IDP202
|
3.6
|
24.8
|
1.0
|
OD2
|
B:ASP53
|
3.7
|
33.8
|
1.0
|
O
|
B:HOH320
|
4.0
|
33.4
|
1.0
|
O
|
B:HOH397
|
4.1
|
22.1
|
1.0
|
O1A
|
B:IDP202
|
4.1
|
26.8
|
1.0
|
O
|
B:HOH334
|
4.2
|
31.6
|
1.0
|
O
|
B:HOH471
|
4.2
|
29.8
|
1.0
|
OD2
|
B:ASP120
|
4.2
|
35.1
|
1.0
|
O
|
B:HOH360
|
4.2
|
23.2
|
1.0
|
OD1
|
B:ASP53
|
4.4
|
32.1
|
1.0
|
O3A
|
B:IDP202
|
4.4
|
26.9
|
1.0
|
CG
|
B:ASP53
|
4.4
|
30.9
|
1.0
|
O5'
|
B:IDP202
|
4.5
|
23.2
|
1.0
|
PB
|
B:IDP202
|
4.5
|
24.1
|
1.0
|
C5'
|
B:IDP202
|
4.6
|
20.4
|
1.0
|
CD1
|
B:LEU54
|
4.7
|
26.5
|
1.0
|
CG
|
B:ASP120
|
4.8
|
25.6
|
1.0
|
O
|
B:HOH509
|
4.9
|
30.8
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 6xpu
Go back to
Magnesium Binding Sites List in 6xpu
Magnesium binding site 3 out
of 3 in the Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Idp
![](/pictures/MG/pdb/xp/6xpu-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/xp/6xpu-MG-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Idp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg201
b:35.5
occ:1.00
|
O
|
C:HOH347
|
2.1
|
31.1
|
1.0
|
O
|
C:HOH405
|
2.1
|
34.2
|
1.0
|
O1A
|
C:IDP202
|
2.1
|
30.4
|
0.9
|
O
|
C:HOH351
|
2.1
|
29.5
|
1.0
|
O
|
C:HOH324
|
2.3
|
35.1
|
1.0
|
O
|
C:HOH465
|
2.5
|
34.6
|
1.0
|
O1B
|
C:IDP202
|
3.3
|
26.8
|
0.9
|
PA
|
C:IDP202
|
3.6
|
31.2
|
0.9
|
O
|
C:HOH338
|
4.0
|
26.5
|
1.0
|
OD2
|
C:ASP53
|
4.0
|
43.7
|
1.0
|
O
|
C:HOH344
|
4.1
|
35.8
|
1.0
|
O2A
|
C:IDP202
|
4.2
|
28.9
|
0.9
|
O
|
C:HOH339
|
4.3
|
28.4
|
1.0
|
PB
|
C:IDP202
|
4.4
|
28.5
|
0.9
|
O3A
|
C:IDP202
|
4.4
|
32.2
|
0.9
|
OD2
|
C:ASP120
|
4.5
|
36.9
|
1.0
|
O
|
C:HOH392
|
4.5
|
38.6
|
1.0
|
O5'
|
C:IDP202
|
4.5
|
28.5
|
0.9
|
C5'
|
C:IDP202
|
4.6
|
28.3
|
0.9
|
OD1
|
C:ASP53
|
4.7
|
39.9
|
1.0
|
O
|
C:HOH477
|
4.7
|
34.7
|
1.0
|
CG
|
C:ASP120
|
4.7
|
30.1
|
1.0
|
CG
|
C:ASP53
|
4.8
|
41.2
|
1.0
|
CD1
|
C:LEU54
|
4.9
|
31.4
|
1.0
|
O3B
|
C:IDP202
|
5.0
|
27.3
|
0.9
|
|
Reference:
S.Nguyen,
B.Jovcevski,
T.L.Pukala,
J.B.Bruning.
Nucleoside Selectivity of Aspergillus Fumigatus Nucleoside-Diphosphate Kinase. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 33089641
DOI: 10.1111/FEBS.15607
Page generated: Tue Dec 15 01:43:10 2020
|