Magnesium in PDB 5qjk: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060
Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060
All present enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060:
2.7.7.96;
3.6.1.13;
3.6.1.58;
Protein crystallography data
The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060, PDB code: 5qjk
was solved by
Y.Dubianok,
P.Collins,
T.Krojer,
N.Wright,
C.Strain-Damerell,
N.Burgess-Brown,
C.Bountra,
C.H.Arrowsmith,
A.Edwards,
K.Huber,
F.Von Delft,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
78.39 /
1.65
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.961,
59.772,
80.215,
79.30,
81.69,
75.95
|
R / Rfree (%)
|
20.7 /
23.7
|
Other elements in 5qjk:
The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060 also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060
(pdb code 5qjk). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060, PDB code: 5qjk:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 5qjk
Go back to
Magnesium Binding Sites List in 5qjk
Magnesium binding site 1 out
of 8 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg301
b:24.8
occ:1.00
|
OE2
|
A:GLU116
|
2.1
|
23.2
|
1.0
|
O
|
A:ALA96
|
2.1
|
20.6
|
1.0
|
O
|
A:HOH432
|
2.1
|
21.9
|
1.0
|
O
|
A:HOH448
|
2.2
|
23.0
|
1.0
|
O
|
A:HOH428
|
2.2
|
25.8
|
1.0
|
O
|
A:HOH462
|
2.2
|
22.5
|
1.0
|
CD
|
A:GLU116
|
3.1
|
24.0
|
1.0
|
C
|
A:ALA96
|
3.3
|
19.5
|
1.0
|
MG
|
A:MG302
|
3.4
|
52.5
|
1.0
|
OE1
|
A:GLU116
|
3.4
|
23.1
|
1.0
|
OE2
|
A:GLU166
|
3.9
|
44.1
|
1.0
|
OE2
|
A:GLU112
|
4.0
|
30.0
|
1.0
|
CA
|
A:GLY97
|
4.1
|
20.0
|
1.0
|
N
|
A:GLY97
|
4.1
|
20.0
|
1.0
|
N
|
A:ALA96
|
4.2
|
18.2
|
1.0
|
NH2
|
A:ARG84
|
4.2
|
24.2
|
1.0
|
CA
|
A:ALA96
|
4.2
|
17.6
|
1.0
|
O
|
A:HOH471
|
4.3
|
47.9
|
1.0
|
O
|
A:HOH416
|
4.3
|
20.8
|
1.0
|
NE2
|
A:GLN82
|
4.4
|
25.0
|
1.0
|
OE1
|
A:GLN82
|
4.4
|
26.3
|
1.0
|
O
|
A:HOH470
|
4.4
|
28.1
|
1.0
|
CG
|
A:GLU116
|
4.5
|
23.1
|
1.0
|
O
|
A:HOH469
|
4.5
|
23.1
|
0.9
|
CB
|
A:ALA96
|
4.7
|
16.3
|
1.0
|
CD
|
A:GLN82
|
4.8
|
29.7
|
1.0
|
O
|
A:HOH463
|
4.8
|
31.4
|
1.0
|
CD
|
A:GLU112
|
4.8
|
28.9
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 5qjk
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Magnesium Binding Sites List in 5qjk
Magnesium binding site 2 out
of 8 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg302
b:52.5
occ:1.00
|
O
|
A:HOH407
|
1.9
|
34.6
|
1.0
|
O
|
A:HOH448
|
2.0
|
23.0
|
1.0
|
OE2
|
A:GLU112
|
2.2
|
30.0
|
1.0
|
O
|
A:HOH415
|
2.4
|
46.4
|
1.0
|
OE2
|
A:GLU166
|
2.5
|
44.1
|
1.0
|
OE2
|
A:GLU116
|
2.6
|
23.2
|
1.0
|
CD
|
A:GLU112
|
3.0
|
28.9
|
1.0
|
CD
|
A:GLU166
|
3.1
|
62.6
|
1.0
|
OE1
|
A:GLU112
|
3.2
|
31.4
|
1.0
|
OE1
|
A:GLU166
|
3.2
|
51.5
|
1.0
|
MG
|
A:MG301
|
3.4
|
24.8
|
1.0
|
CD
|
A:GLU116
|
3.6
|
24.0
|
1.0
|
CG
|
A:GLU116
|
3.8
|
23.1
|
1.0
|
O
|
A:HOH428
|
3.9
|
25.8
|
1.0
|
O
|
A:ALA96
|
4.0
|
20.6
|
1.0
|
O
|
A:HOH471
|
4.0
|
47.9
|
1.0
|
OE2
|
A:GLU115
|
4.2
|
34.1
|
1.0
|
CG
|
A:GLU166
|
4.4
|
56.6
|
1.0
|
CG
|
A:GLU112
|
4.5
|
26.9
|
1.0
|
OE1
|
A:GLU116
|
4.7
|
23.1
|
1.0
|
O
|
A:HOH463
|
4.7
|
31.4
|
1.0
|
CA
|
A:GLY97
|
4.9
|
20.0
|
1.0
|
CB
|
A:GLU112
|
5.0
|
26.5
|
1.0
|
C
|
A:ALA96
|
5.0
|
19.5
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 5qjk
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Magnesium Binding Sites List in 5qjk
Magnesium binding site 3 out
of 8 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg302
b:27.1
occ:1.00
|
O
|
B:ALA96
|
2.0
|
24.6
|
1.0
|
OE2
|
B:GLU116
|
2.1
|
28.5
|
1.0
|
O
|
B:HOH438
|
2.1
|
28.0
|
1.0
|
O
|
B:HOH418
|
2.1
|
27.6
|
1.0
|
O
|
B:HOH450
|
2.1
|
25.9
|
1.0
|
O
|
B:HOH414
|
2.2
|
27.1
|
1.0
|
CD
|
B:GLU116
|
3.1
|
29.5
|
1.0
|
C
|
B:ALA96
|
3.2
|
21.1
|
1.0
|
OE1
|
B:GLU116
|
3.4
|
28.1
|
1.0
|
OE2
|
B:GLU166
|
3.9
|
48.0
|
1.0
|
CA
|
B:GLY97
|
4.1
|
22.2
|
1.0
|
N
|
B:GLY97
|
4.1
|
23.5
|
1.0
|
OE2
|
B:GLU112
|
4.1
|
34.2
|
1.0
|
NH2
|
B:ARG84
|
4.2
|
26.9
|
1.0
|
O
|
B:HOH425
|
4.2
|
25.8
|
1.0
|
N
|
B:ALA96
|
4.2
|
22.4
|
1.0
|
CA
|
B:ALA96
|
4.2
|
23.2
|
1.0
|
NE2
|
B:GLN82
|
4.4
|
32.2
|
1.0
|
O
|
B:HOH467
|
4.4
|
34.4
|
0.9
|
OE1
|
B:GLN82
|
4.4
|
34.4
|
1.0
|
CG
|
B:GLU116
|
4.5
|
28.6
|
1.0
|
O
|
B:HOH470
|
4.5
|
40.8
|
1.0
|
O
|
B:HOH468
|
4.7
|
23.5
|
0.9
|
CD
|
B:GLU166
|
4.7
|
65.8
|
1.0
|
CB
|
B:ALA96
|
4.7
|
24.9
|
1.0
|
CD
|
B:GLN82
|
4.8
|
36.2
|
1.0
|
MG
|
B:MG303
|
4.8
|
65.3
|
1.0
|
CD
|
B:GLU112
|
4.9
|
36.2
|
1.0
|
O
|
B:HOH404
|
4.9
|
40.8
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 5qjk
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Magnesium Binding Sites List in 5qjk
Magnesium binding site 4 out
of 8 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg303
b:65.3
occ:1.00
|
O
|
B:HOH411
|
1.6
|
41.8
|
1.0
|
OE1
|
B:GLU166
|
2.1
|
66.3
|
1.0
|
O
|
B:HOH404
|
2.3
|
40.8
|
1.0
|
CD
|
B:GLU166
|
2.9
|
65.8
|
1.0
|
O
|
B:HOH438
|
3.0
|
28.0
|
1.0
|
OE2
|
B:GLU166
|
3.1
|
48.0
|
1.0
|
OE2
|
B:GLU112
|
3.3
|
34.2
|
1.0
|
OE1
|
B:GLU112
|
3.5
|
36.5
|
1.0
|
OE2
|
B:GLU115
|
3.8
|
40.1
|
1.0
|
CD
|
B:GLU112
|
3.8
|
36.2
|
1.0
|
O
|
B:HOH467
|
4.3
|
34.4
|
0.9
|
OE2
|
B:GLU116
|
4.3
|
28.5
|
1.0
|
CG
|
B:GLU166
|
4.3
|
59.9
|
1.0
|
MG
|
B:MG302
|
4.8
|
27.1
|
1.0
|
O
|
B:HOH414
|
5.0
|
27.1
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 5qjk
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Magnesium Binding Sites List in 5qjk
Magnesium binding site 5 out
of 8 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg302
b:38.2
occ:1.00
|
MG
|
C:MG303
|
2.1
|
29.0
|
1.0
|
OE2
|
C:GLU116
|
2.8
|
27.3
|
1.0
|
O
|
C:ALA96
|
3.0
|
25.0
|
1.0
|
O
|
C:HOH460
|
3.0
|
25.5
|
1.0
|
O
|
C:HOH412
|
3.0
|
29.8
|
1.0
|
O
|
C:HOH461
|
3.1
|
41.8
|
1.0
|
OE2
|
C:GLU166
|
3.2
|
56.7
|
1.0
|
OE2
|
C:GLU112
|
3.2
|
31.7
|
1.0
|
O
|
C:HOH429
|
3.2
|
51.0
|
1.0
|
CA
|
C:GLY97
|
3.6
|
28.2
|
1.0
|
OE1
|
C:GLU112
|
3.6
|
40.9
|
1.0
|
O
|
C:HOH403
|
3.7
|
44.1
|
1.0
|
CD
|
C:GLU112
|
3.7
|
33.9
|
1.0
|
C
|
C:ALA96
|
4.0
|
25.9
|
1.0
|
CD
|
C:GLU116
|
4.1
|
29.2
|
1.0
|
CD
|
C:GLU166
|
4.1
|
65.5
|
1.0
|
O
|
C:HOH424
|
4.2
|
24.8
|
1.0
|
N
|
C:GLY97
|
4.3
|
25.3
|
1.0
|
O
|
C:HOH469
|
4.5
|
27.9
|
1.0
|
OE1
|
C:GLU166
|
4.7
|
67.9
|
1.0
|
C
|
C:GLY97
|
4.8
|
28.7
|
1.0
|
OE1
|
C:GLU116
|
4.9
|
32.6
|
1.0
|
CG
|
C:GLU116
|
5.0
|
27.4
|
1.0
|
N
|
C:LEU98
|
5.0
|
29.8
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 5qjk
Go back to
Magnesium Binding Sites List in 5qjk
Magnesium binding site 6 out
of 8 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg303
b:29.0
occ:1.00
|
O
|
C:HOH460
|
2.0
|
25.5
|
1.0
|
OE2
|
C:GLU116
|
2.0
|
27.3
|
1.0
|
O
|
C:HOH424
|
2.1
|
24.8
|
1.0
|
MG
|
C:MG302
|
2.1
|
38.2
|
1.0
|
O
|
C:ALA96
|
2.1
|
25.0
|
1.0
|
O
|
C:HOH412
|
2.2
|
29.8
|
1.0
|
CD
|
C:GLU116
|
3.1
|
29.2
|
1.0
|
C
|
C:ALA96
|
3.3
|
25.9
|
1.0
|
OE1
|
C:GLU116
|
3.5
|
32.6
|
1.0
|
OE2
|
C:GLU166
|
3.8
|
56.7
|
1.0
|
OE2
|
C:GLU112
|
4.1
|
31.7
|
1.0
|
CA
|
C:GLY97
|
4.1
|
28.2
|
1.0
|
N
|
C:GLY97
|
4.2
|
25.3
|
1.0
|
N
|
C:ALA96
|
4.2
|
21.8
|
1.0
|
CA
|
C:ALA96
|
4.2
|
22.0
|
1.0
|
O
|
C:HOH417
|
4.2
|
25.0
|
0.9
|
NH2
|
C:ARG84
|
4.2
|
28.2
|
1.0
|
NE2
|
C:GLN82
|
4.4
|
30.7
|
1.0
|
OE1
|
C:GLN82
|
4.5
|
30.0
|
1.0
|
O
|
C:HOH473
|
4.5
|
32.2
|
0.9
|
O
|
C:HOH461
|
4.5
|
41.8
|
1.0
|
CG
|
C:GLU116
|
4.5
|
27.4
|
1.0
|
O
|
C:HOH469
|
4.7
|
27.9
|
1.0
|
CB
|
C:ALA96
|
4.7
|
21.8
|
1.0
|
O
|
C:HOH403
|
4.8
|
44.1
|
1.0
|
CD
|
C:GLU112
|
4.8
|
33.9
|
1.0
|
CD
|
C:GLN82
|
4.9
|
35.5
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 5qjk
Go back to
Magnesium Binding Sites List in 5qjk
Magnesium binding site 7 out
of 8 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg301
b:27.5
occ:1.00
|
O
|
D:HOH429
|
1.9
|
30.7
|
0.9
|
OE2
|
D:GLU116
|
2.0
|
28.1
|
1.0
|
O
|
D:HOH409
|
2.0
|
25.3
|
1.0
|
O
|
D:HOH434
|
2.1
|
28.1
|
1.0
|
O
|
D:ALA96
|
2.2
|
28.4
|
1.0
|
MG
|
D:MG302
|
2.2
|
44.2
|
1.0
|
O
|
D:HOH436
|
2.3
|
33.6
|
1.0
|
CD
|
D:GLU116
|
3.1
|
34.5
|
1.0
|
C
|
D:ALA96
|
3.3
|
27.9
|
1.0
|
OE1
|
D:GLU116
|
3.4
|
31.9
|
1.0
|
OE2
|
D:GLU112
|
4.2
|
39.5
|
1.0
|
N
|
D:GLY97
|
4.2
|
28.1
|
1.0
|
N
|
D:ALA96
|
4.2
|
25.1
|
1.0
|
CA
|
D:GLY97
|
4.2
|
28.4
|
1.0
|
CA
|
D:ALA96
|
4.2
|
26.6
|
1.0
|
NH2
|
D:ARG84
|
4.3
|
29.8
|
1.0
|
O
|
D:HOH416
|
4.4
|
26.2
|
0.9
|
CG
|
D:GLU116
|
4.4
|
32.3
|
1.0
|
NE2
|
D:GLN82
|
4.4
|
32.9
|
1.0
|
OE1
|
D:GLN82
|
4.5
|
30.3
|
1.0
|
O
|
D:HOH445
|
4.6
|
29.4
|
0.9
|
OE2
|
D:GLU166
|
4.6
|
71.2
|
1.0
|
O
|
D:HOH442
|
4.7
|
26.8
|
0.9
|
O
|
D:HOH405
|
4.7
|
45.5
|
1.0
|
CB
|
D:ALA96
|
4.7
|
27.1
|
1.0
|
CD
|
D:GLU112
|
4.7
|
41.4
|
1.0
|
CD
|
D:GLN82
|
4.9
|
32.5
|
1.0
|
CG
|
D:GLU112
|
5.0
|
46.6
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 5qjk
Go back to
Magnesium Binding Sites List in 5qjk
Magnesium binding site 8 out
of 8 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg302
b:44.2
occ:1.00
|
O
|
D:HOH436
|
1.4
|
33.6
|
1.0
|
MG
|
D:MG301
|
2.2
|
27.5
|
1.0
|
OE2
|
D:GLU112
|
2.6
|
39.5
|
1.0
|
OE2
|
D:GLU116
|
2.6
|
28.1
|
1.0
|
O
|
D:ALA96
|
2.7
|
28.4
|
1.0
|
CD
|
D:GLU112
|
3.2
|
41.4
|
1.0
|
O
|
D:HOH429
|
3.2
|
30.7
|
0.9
|
O
|
D:HOH430
|
3.2
|
50.3
|
1.0
|
O
|
D:HOH405
|
3.3
|
45.5
|
1.0
|
O
|
D:HOH434
|
3.3
|
28.1
|
1.0
|
OE2
|
D:GLU166
|
3.3
|
71.2
|
1.0
|
CA
|
D:GLY97
|
3.4
|
28.4
|
1.0
|
OE1
|
D:GLU112
|
3.6
|
45.4
|
1.0
|
C
|
D:ALA96
|
3.7
|
27.9
|
1.0
|
CD
|
D:GLU116
|
3.8
|
34.5
|
1.0
|
N
|
D:GLY97
|
4.0
|
28.1
|
1.0
|
CG
|
D:GLU112
|
4.0
|
46.6
|
1.0
|
O
|
D:HOH409
|
4.2
|
25.3
|
1.0
|
CD
|
D:GLU166
|
4.4
|
72.8
|
1.0
|
OE1
|
D:GLU116
|
4.6
|
31.9
|
1.0
|
CG
|
D:GLU116
|
4.6
|
32.3
|
1.0
|
C
|
D:GLY97
|
4.7
|
27.4
|
1.0
|
OE1
|
D:GLU166
|
4.8
|
73.9
|
1.0
|
N
|
D:LEU98
|
4.9
|
30.2
|
1.0
|
|
Reference:
Y.Dubianok,
P.Collins,
T.Krojer,
N.Wright,
C.Strain-Damerell,
N.Burgess-Brown,
C.Bountra,
C.H.Arrowsmith,
A.Edwards,
K.Huber,
F.Von Delft.
Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) To Be Published.
Page generated: Mon Sep 30 02:18:47 2024
|