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Magnesium in PDB 5qj8: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829

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 Z2856434829:
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 Z2856434829, PDB code: 5qj8 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) 77.81 / 1.76
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.530, 59.990, 79.650, 79.56, 81.09, 75.49
R / Rfree (%) 23.5 / 27.8

Other elements in 5qj8:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829 also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Chlorine (Cl) 1 atom

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 Z2856434829 (pdb code 5qj8). 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 Z2856434829, PDB code: 5qj8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qj8

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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 Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:28.1
occ:1.00
 O A:ALA96 2.0 25.6 1.0
O A:HOH436 2.1 23.2 1.0
O A:HOH451 2.1 24.1 1.0
O A:HOH422 2.1 26.2 1.0
O A:HOH423 2.1 28.5 1.0
OE2 A:GLU116 2.1 26.9 1.0
C A:ALA96 3.1 25.1 1.0
CD A:GLU116 3.1 31.9 1.0
OE1 A:GLU116 3.4 29.5 1.0
MG A:MG302 3.5 65.6 1.0
N A:GLY97 4.0 27.8 1.0
OE2 A:GLU166 4.0 56.1 1.0
CA A:GLY97 4.0 28.9 1.0
OE2 A:GLU112 4.0 38.1 1.0
CA A:ALA96 4.1 23.4 1.0
O A:HOH441 4.1 31.0 1.0
N A:ALA96 4.1 22.6 1.0
NH2 A:ARG84 4.2 29.3 1.0
O A:HOH463 4.3 29.5 1.0
O A:HOH420 4.3 25.8 1.0
NE2 A:GLN82 4.4 30.4 1.0
O A:HOH458 4.4 36.2 1.0
CG A:GLU116 4.4 30.6 1.0
OE1 A:GLN82 4.5 29.5 1.0
CB A:ALA96 4.5 23.2 1.0
CD A:GLN82 4.8 34.0 1.0
CD A:GLU112 4.9 32.2 1.0
O A:HOH470 4.9 54.2 1.0

Magnesium binding site 2 out of 8 in 5qj8

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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 Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:65.6
occ:1.00
 O A:HOH405 2.0 44.9 1.0
OE2 A:GLU112 2.0 38.1 1.0
O A:HOH436 2.1 23.2 1.0
O A:HOH419 2.5 53.2 1.0
OE2 A:GLU166 2.6 56.1 1.0
OE2 A:GLU116 2.8 26.9 1.0
CD A:GLU112 2.9 32.2 1.0
OE1 A:GLU112 3.0 31.2 1.0
CD A:GLU166 3.3 65.4 1.0
OE1 A:GLU166 3.5 58.0 1.0
MG A:MG301 3.5 28.1 1.0
CD A:GLU116 3.7 31.9 1.0
CG A:GLU116 3.9 30.6 1.0
O A:ALA96 3.9 25.6 1.0
OE2 A:GLU115 4.0 36.1 1.0
O A:HOH423 4.0 28.5 1.0
O A:HOH458 4.1 36.2 1.0
CG A:GLU112 4.3 29.7 1.0
CG A:GLU166 4.5 60.9 1.0
CA A:GLY97 4.6 28.9 1.0
CB A:GLU112 4.8 27.6 1.0
OE1 A:GLU116 4.9 29.5 1.0
O A:HOH403 4.9 42.5 1.0
C A:ALA96 4.9 25.1 1.0

Magnesium binding site 3 out of 8 in 5qj8

Go back to Magnesium Binding Sites List in 5qj8
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 Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:34.5
occ:1.00
 O B:ALA96 2.0 32.9 1.0
O B:HOH422 2.0 40.1 1.0
OE2 B:GLU116 2.1 41.0 1.0
O B:HOH410 2.1 31.6 1.0
O B:HOH440 2.2 27.6 1.0
O B:HOH441 2.4 33.5 1.0
CD B:GLU116 3.1 40.6 1.0
C B:ALA96 3.2 28.1 1.0
OE1 B:GLU116 3.4 32.5 1.0
OE2 B:GLU166 4.0 61.8 1.0
MG B:MG304 4.0 71.6 1.0
N B:GLY97 4.1 31.0 1.0
N B:ALA96 4.1 27.5 1.0
O B:HOH427 4.1 32.5 1.0
CA B:ALA96 4.1 29.3 1.0
OE1 B:GLN82 4.1 40.5 1.0
CA B:GLY97 4.1 31.9 1.0
OE2 B:GLU112 4.2 44.0 1.0
NE2 B:GLN82 4.2 37.6 1.0
NH2 B:ARG84 4.4 29.7 1.0
CG B:GLU116 4.4 36.6 1.0
CB B:ALA96 4.5 31.3 1.0
O B:HOH463 4.6 38.7 1.0
CD B:GLN82 4.6 44.1 1.0
CD B:GLU166 5.0 78.1 1.0

Magnesium binding site 4 out of 8 in 5qj8

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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 Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:71.6
occ:1.00
 OE2 B:GLU112 1.7 44.0 1.0
O B:HOH458 2.4 46.5 1.0
O B:HOH405 2.6 64.0 1.0
OE2 B:GLU166 2.7 61.8 1.0
OE2 B:GLU116 2.8 41.0 1.0
CD B:GLU112 2.8 38.9 1.0
O B:HOH441 2.9 33.5 1.0
OE1 B:GLU112 3.2 38.2 1.0
CG B:GLU116 3.3 36.6 1.0
OE2 B:GLU115 3.4 55.1 1.0
CD B:GLU116 3.4 40.6 1.0
CD B:GLU166 3.6 78.1 1.0
OE1 B:GLU166 3.7 77.2 1.0
MG B:MG303 4.0 34.5 1.0
CG B:GLU112 4.1 36.4 1.0
O B:ALA96 4.1 32.9 1.0
CB B:GLU115 4.3 40.3 1.0
CB B:GLU112 4.4 36.8 1.0
CA B:GLU112 4.4 33.3 1.0
CD B:GLU115 4.5 51.0 1.0
O B:GLU112 4.5 32.9 1.0
OE1 B:GLU116 4.6 32.5 1.0
O B:HOH422 4.7 40.1 1.0
CB B:GLU116 4.8 34.6 1.0
C B:GLU112 4.9 29.6 1.0
C B:ALA96 5.0 28.1 1.0
CG B:GLU166 5.0 73.2 1.0
CG B:GLU115 5.0 46.6 1.0
N B:GLU116 5.0 38.0 1.0

Magnesium binding site 5 out of 8 in 5qj8

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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 Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:71.0
occ:1.00
 O C:HOH410 1.8 44.5 1.0
O C:HOH404 2.1 46.9 1.0
OE2 C:GLU166 2.3 62.5 1.0
OE2 C:GLU112 2.5 36.5 1.0
O C:HOH444 2.7 66.1 1.0
O C:HOH435 3.0 59.4 1.0
CD C:GLU166 3.2 65.8 1.0
CD C:GLU112 3.2 43.8 1.0
OE1 C:GLU112 3.2 52.6 1.0
OE2 C:GLU116 3.4 35.6 1.0
OE1 C:GLU166 3.5 58.6 1.0
MG C:MG303 3.7 35.0 1.0
O C:ALA96 4.0 31.5 1.0
O C:HOH403 4.1 39.7 1.0
CA C:GLY97 4.4 35.7 1.0
CD C:GLU116 4.4 33.3 1.0
OE2 C:GLU115 4.4 46.5 1.0
CG C:GLU166 4.5 59.7 1.0
O C:HOH460 4.5 64.6 1.0
O C:HOH442 4.7 30.0 1.0
CG C:GLU116 4.7 32.8 1.0
CG C:GLU112 4.7 39.5 1.0
C C:ALA96 4.9 35.8 1.0
N C:GLY97 5.0 34.5 1.0

Magnesium binding site 6 out of 8 in 5qj8

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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 Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:35.0
occ:1.00
 OE2 C:GLU116 1.9 35.6 1.0
O C:HOH442 2.0 30.0 1.0
O C:HOH410 2.0 44.5 1.0
O C:HOH416 2.1 31.1 1.0
O C:ALA96 2.1 31.5 1.0
O C:HOH403 2.2 39.7 1.0
CD C:GLU116 3.1 33.3 1.0
C C:ALA96 3.3 35.8 1.0
OE2 C:GLU166 3.3 62.5 1.0
OE1 C:GLU116 3.4 39.3 1.0
MG C:MG302 3.7 71.0 1.0
NH2 C:ARG84 4.2 35.4 1.0
N C:GLY97 4.2 34.5 1.0
CA C:ALA96 4.2 32.2 1.0
CA C:GLY97 4.2 35.7 1.0
N C:ALA96 4.2 30.2 1.0
OE1 C:GLN82 4.3 32.3 1.0
NE2 C:GLN82 4.3 40.6 1.0
CG C:GLU116 4.4 32.8 1.0
OE2 C:GLU112 4.5 36.5 1.0
CD C:GLU166 4.5 65.8 1.0
CB C:ALA96 4.5 31.5 1.0
CD C:GLN82 4.8 36.9 1.0
O C:HOH404 4.9 46.9 1.0
NH1 C:ARG84 5.0 34.3 1.0
CZ C:ARG84 5.0 38.3 1.0

Magnesium binding site 7 out of 8 in 5qj8

Go back to Magnesium Binding Sites List in 5qj8
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 Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:40.7
occ:1.00
 OE2 D:GLU116 2.0 51.8 1.0
O D:HOH411 2.1 31.3 1.0
O D:HOH415 2.1 33.3 1.0
MG D:MG302 2.2 46.8 1.0
O D:HOH427 2.7 45.7 1.0
O D:ALA96 3.1 45.4 1.0
CD D:GLU116 3.2 60.1 1.0
NE2 D:GLN82 3.5 48.9 1.0
OE1 D:GLU116 3.6 52.0 1.0
OE2 D:GLU112 3.8 63.7 1.0
OE2 D:GLU166 3.9 97.8 1.0
NH2 D:ARG84 4.0 45.5 1.0
OE1 D:GLN82 4.1 56.8 1.0
C D:ALA96 4.2 52.9 1.0
CD D:GLN82 4.3 55.0 1.0
CG D:GLU116 4.4 56.0 1.0
CD D:GLU166 4.7 88.0 1.0
N D:ALA96 4.8 50.6 1.0
O D:HOH406 4.8 61.2 1.0
NH1 D:ARG84 4.8 42.9 1.0
CD D:GLU112 4.9 60.7 1.0
CZ D:ARG84 4.9 48.0 1.0
CA D:GLY97 4.9 53.7 1.0
CA D:ALA96 5.0 52.1 1.0
O D:HOH409 5.0 43.9 1.0

Magnesium binding site 8 out of 8 in 5qj8

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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 Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:46.8
occ:1.00
 OE2 D:GLU112 2.1 63.7 1.0
O D:HOH427 2.2 45.7 1.0
MG D:MG301 2.2 40.7 1.0
O D:HOH415 2.7 33.3 1.0
O D:HOH409 2.8 43.9 1.0
OE2 D:GLU116 2.9 51.8 1.0
OE2 D:GLU166 3.0 97.8 1.0
O D:ALA96 3.1 45.4 1.0
CD D:GLU112 3.3 60.7 1.0
CA D:GLY97 3.6 53.7 1.0
O D:HOH406 3.8 61.2 1.0
CD D:GLU116 4.0 60.1 1.0
C D:ALA96 4.0 52.9 1.0
OE1 D:GLU112 4.1 61.4 1.0
O D:HOH411 4.1 31.3 1.0
CG D:GLU112 4.1 58.9 1.0
CD D:GLU166 4.1 88.0 1.0
N D:GLY97 4.3 49.3 1.0
OE1 D:GLU116 4.7 52.0 1.0
C D:GLY97 4.8 58.6 1.0
N D:LEU98 4.9 56.8 1.0
CG D:GLU166 4.9 79.5 1.0
OE1 D:GLU166 5.0 87.3 1.0
CG D:GLU116 5.0 56.0 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 02:11:14 2024

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