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Magnesium in PDB 5qj6: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1614545742

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1614545742

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 Z1614545742:
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 Z1614545742, PDB code: 5qj6 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) 78.30 / 1.65
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.250, 59.780, 80.090, 79.42, 81.68, 75.64
R / Rfree (%) 21.2 / 24.9

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 Z1614545742 (pdb code 5qj6). 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 Z1614545742, PDB code: 5qj6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qj6

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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 Z1614545742


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 Z1614545742 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:27.3
occ:1.00
 OE2 A:GLU116 2.0 24.4 1.0
O A:ALA96 2.1 21.8 1.0
O A:HOH441 2.1 22.1 1.0
O A:HOH411 2.1 23.7 1.0
O A:HOH414 2.2 26.2 1.0
O A:HOH453 2.2 22.5 1.0
CD A:GLU116 3.0 25.8 1.0
C A:ALA96 3.2 22.0 1.0
OE1 A:GLU116 3.4 25.2 1.0
MG A:MG302 3.4 60.3 1.0
OE2 A:GLU166 3.8 58.1 1.0
OE2 A:GLU112 4.0 31.7 1.0
N A:GLY97 4.1 21.6 1.0
O A:HOH444 4.1 28.9 1.0
CA A:GLY97 4.1 22.7 1.0
N A:ALA96 4.2 19.7 1.0
CA A:ALA96 4.2 20.3 1.0
NH2 A:ARG84 4.3 23.9 1.0
O A:HOH465 4.3 54.9 1.0
O A:HOH427 4.3 20.1 1.0
NE2 A:GLN82 4.4 29.2 1.0
CG A:GLU116 4.4 25.6 1.0
O A:HOH462 4.4 28.0 1.0
OE1 A:GLN82 4.5 25.4 1.0
O A:HOH458 4.5 34.8 1.0
CB A:ALA96 4.7 17.6 1.0
CD A:GLU112 4.8 29.9 1.0
CD A:GLN82 4.8 33.8 1.0

Magnesium binding site 2 out of 8 in 5qj6

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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 Z1614545742


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 Z1614545742 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:60.3
occ:1.00
 O A:HOH409 1.9 38.6 1.0
O A:HOH441 2.1 22.1 1.0
OE2 A:GLU112 2.2 31.7 1.0
OE2 A:GLU166 2.5 58.1 1.0
O A:HOH415 2.5 46.1 1.0
OE2 A:GLU116 2.7 24.4 1.0
CD A:GLU166 3.1 76.7 1.0
CD A:GLU112 3.1 29.9 1.0
OE1 A:GLU166 3.2 64.7 1.0
OE1 A:GLU112 3.3 32.3 1.0
MG A:MG301 3.4 27.3 1.0
CD A:GLU116 3.6 25.8 1.0
CG A:GLU116 3.8 25.6 1.0
O A:HOH414 4.0 26.2 1.0
O A:ALA96 4.1 21.8 1.0
OE2 A:GLU115 4.1 37.1 1.0
O A:HOH465 4.2 54.9 1.0
CG A:GLU166 4.4 65.8 1.0
O A:HOH458 4.4 34.8 1.0
CG A:GLU112 4.5 26.4 1.0
OE1 A:GLU116 4.7 25.2 1.0
CA A:GLY97 4.9 22.7 1.0
CB A:GLU112 4.9 26.5 1.0

Magnesium binding site 3 out of 8 in 5qj6

Go back to Magnesium Binding Sites List in 5qj6
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 Z1614545742


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 Z1614545742 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:32.3
occ:1.00
 OE2 B:GLU116 2.0 36.0 1.0
O B:ALA96 2.0 26.8 1.0
O B:HOH406 2.1 29.2 1.0
O B:HOH407 2.2 31.8 1.0
O B:HOH449 2.2 30.7 1.0
O B:HOH448 2.2 27.1 1.0
CD B:GLU116 3.0 37.0 1.0
C B:ALA96 3.2 22.6 1.0
OE1 B:GLU116 3.3 31.1 1.0
OE2 B:GLU166 3.8 47.6 1.0
MG B:MG303 3.9 0.3 1.0
N B:GLY97 4.1 25.0 1.0
CA B:GLY97 4.1 24.6 1.0
N B:ALA96 4.1 23.8 1.0
OE2 B:GLU112 4.1 41.2 1.0
CA B:ALA96 4.2 24.0 1.0
O B:HOH427 4.2 27.6 1.0
NE2 B:GLN82 4.3 34.1 1.0
O B:HOH417 4.3 35.6 1.0
NH2 B:ARG84 4.3 26.8 1.0
CG B:GLU116 4.3 33.1 1.0
OE1 B:GLN82 4.4 33.8 1.0
O B:HOH468 4.4 40.4 1.0
O B:HOH472 4.5 38.1 1.0
CD B:GLU166 4.7 70.4 1.0
CB B:ALA96 4.7 26.1 1.0
CD B:GLN82 4.7 42.9 1.0
O B:HOH416 4.9 61.8 1.0
CD B:GLU112 5.0 36.6 1.0

Magnesium binding site 4 out of 8 in 5qj6

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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 Z1614545742


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 Z1614545742 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:0.3
occ:1.00
 O B:HOH451 1.8 51.2 1.0
O B:HOH416 2.0 61.8 1.0
O B:HOH449 2.2 30.7 1.0
OE2 B:GLU112 2.4 41.2 1.0
OE2 B:GLU166 2.8 47.6 1.0
OE1 B:GLU166 3.0 72.9 1.0
OE1 B:GLU112 3.1 34.0 1.0
CD B:GLU112 3.1 36.6 1.0
CD B:GLU166 3.3 70.4 1.0
OE2 B:GLU116 3.5 36.0 1.0
O B:HOH468 3.7 40.4 1.0
OE2 B:GLU115 3.8 44.5 1.0
MG B:MG302 3.9 32.3 1.0
O B:ALA96 4.4 26.8 1.0
CD B:GLU116 4.4 37.0 1.0
O B:HOH407 4.5 31.8 1.0
CG B:GLU116 4.6 33.1 1.0
CG B:GLU112 4.6 34.6 1.0
CG B:GLU166 4.7 61.1 1.0
CA B:GLY97 4.7 24.6 1.0

Magnesium binding site 5 out of 8 in 5qj6

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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 Z1614545742


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 Z1614545742 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:65.6
occ:1.00
 O C:HOH448 1.9 31.9 1.0
OE2 C:GLU112 2.1 34.0 1.0
O C:HOH407 2.1 52.4 1.0
O C:HOH451 2.2 53.8 1.0
OE2 C:GLU166 2.4 58.1 1.0
OE2 C:GLU116 2.5 33.6 1.0
MG C:MG303 3.1 31.7 1.0
CD C:GLU112 3.1 37.6 1.0
OE1 C:GLU112 3.3 42.9 1.0
CD C:GLU166 3.3 68.7 1.0
CD C:GLU116 3.5 32.3 1.0
O C:ALA96 3.5 26.4 1.0
O C:HOH424 3.5 49.0 1.0
OE1 C:GLU166 3.6 78.9 1.0
O C:HOH416 3.8 33.9 1.0
CG C:GLU116 3.9 29.1 1.0
OE2 C:GLU115 4.4 42.3 1.0
CA C:GLY97 4.4 32.5 1.0
CG C:GLU112 4.5 33.0 1.0
C C:ALA96 4.5 28.9 1.0
O C:HOH457 4.5 27.3 1.0
OE1 C:GLU116 4.6 36.9 1.0
CG C:GLU166 4.6 56.8 1.0
N C:GLY97 4.9 30.7 1.0
O C:HOH423 4.9 27.1 1.0
CB C:GLU112 5.0 31.6 1.0

Magnesium binding site 6 out of 8 in 5qj6

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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 Z1614545742


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 Z1614545742 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:31.7
occ:1.00
 OE2 C:GLU116 1.9 33.6 1.0
O C:HOH448 2.1 31.9 1.0
O C:HOH457 2.1 27.3 1.0
O C:ALA96 2.1 26.4 1.0
O C:HOH423 2.1 27.1 1.0
O C:HOH416 2.2 33.9 1.0
CD C:GLU116 3.0 32.3 1.0
MG C:MG302 3.1 65.6 1.0
C C:ALA96 3.3 28.9 1.0
OE1 C:GLU116 3.4 36.9 1.0
OE2 C:GLU166 3.7 58.1 1.0
OE2 C:GLU112 4.2 34.0 1.0
N C:ALA96 4.2 24.9 1.0
N C:GLY97 4.2 30.7 1.0
O C:HOH415 4.2 29.8 1.0
CA C:ALA96 4.2 22.9 1.0
CA C:GLY97 4.2 32.5 1.0
NH2 C:ARG84 4.3 31.5 1.0
NE2 C:GLN82 4.4 34.7 1.0
CG C:GLU116 4.4 29.1 1.0
OE1 C:GLN82 4.4 35.1 1.0
O C:HOH465 4.5 36.2 1.0
CB C:ALA96 4.6 23.4 1.0
O C:HOH407 4.8 52.4 1.0
CD C:GLN82 4.8 41.4 1.0
CD C:GLU166 4.9 68.7 1.0
CD C:GLU112 5.0 37.6 1.0

Magnesium binding site 7 out of 8 in 5qj6

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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 Z1614545742


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 Z1614545742 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:33.2
occ:1.00
 O D:HOH408 1.9 30.6 1.0
OE2 D:GLU116 1.9 31.5 1.0
O D:HOH404 2.1 28.4 1.0
MG D:MG302 2.2 38.8 1.0
O D:ALA96 2.2 32.3 1.0
O D:HOH436 2.6 44.4 1.0
CD D:GLU116 3.0 41.0 1.0
OE1 D:GLU116 3.3 37.5 1.0
C D:ALA96 3.4 33.4 1.0
OE2 D:GLU166 3.7 77.7 1.0
OE2 D:GLU112 3.7 52.2 1.0
N D:ALA96 4.2 32.6 1.0
O D:HOH428 4.2 32.8 1.0
NE2 D:GLN82 4.3 39.4 1.0
CA D:GLY97 4.3 36.0 1.0
CA D:ALA96 4.3 31.4 1.0
N D:GLY97 4.3 34.2 1.0
CG D:GLU116 4.3 37.6 1.0
NH2 D:ARG84 4.3 32.4 1.0
OE1 D:GLN82 4.4 35.6 1.0
CD D:GLU112 4.6 53.7 1.0
CB D:ALA96 4.8 32.8 1.0
CG D:GLU112 4.8 58.6 1.0
O D:HOH411 4.8 56.1 1.0
CD D:GLN82 4.8 42.9 1.0
CD D:GLU166 4.8 83.4 1.0
O D:HOH401 4.9 56.8 1.0

Magnesium binding site 8 out of 8 in 5qj6

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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 Z1614545742


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 Z1614545742 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:38.8
occ:1.00
 O D:HOH436 1.8 44.4 1.0
MG D:MG301 2.2 33.2 1.0
OE2 D:GLU112 2.4 52.2 1.0
O D:HOH411 2.7 56.1 1.0
OE2 D:GLU116 2.8 31.5 1.0
O D:ALA96 2.9 32.3 1.0
O D:HOH408 2.9 30.6 1.0
OE2 D:GLU166 3.0 77.7 1.0
CD D:GLU112 3.4 53.7 1.0
CA D:GLY97 3.5 36.0 1.0
O D:HOH401 3.7 56.8 1.0
C D:ALA96 3.9 33.4 1.0
OE1 D:GLU112 4.0 53.8 1.0
CD D:GLU116 4.0 41.0 1.0
CD D:GLU166 4.1 83.4 1.0
N D:GLY97 4.2 34.2 1.0
CG D:GLU112 4.2 58.6 1.0
O D:HOH404 4.2 28.4 1.0
O D:HOH428 4.3 32.8 1.0
C D:GLY97 4.8 36.6 1.0
OE1 D:GLU116 4.8 37.5 1.0
CG D:GLU116 4.9 37.6 1.0
CG D:GLU166 4.9 72.3 1.0
N D:LEU98 4.9 38.4 1.0
OE1 D:GLU166 5.0 80.7 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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