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Magnesium in PDB 5qji: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1899842917

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1899842917

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 Z1899842917:
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 Z1899842917, PDB code: 5qji 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) 77.65 / 1.69
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.980, 59.770, 79.380, 79.84, 81.43, 75.99
R / Rfree (%) 25.7 / 30.1

Other elements in 5qji:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1899842917 also contains other interesting chemical elements:

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 Z1899842917 (pdb code 5qji). 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 Z1899842917, PDB code: 5qji:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qji

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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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:39.2
occ:1.00
 O A:HOH424 1.9 38.4 1.0
OE2 A:GLU116 2.0 32.9 1.0
O A:HOH441 2.0 30.0 1.0
O A:ALA96 2.1 27.7 1.0
O A:HOH425 2.2 28.2 1.0
O A:HOH448 2.5 31.8 1.0
CD A:GLU116 3.0 33.4 1.0
MG A:MG302 3.3 61.2 1.0
C A:ALA96 3.3 27.1 1.0
OE1 A:GLU116 3.4 39.8 1.0
OE2 A:GLU166 3.8 72.5 1.0
OE2 A:GLU112 4.0 34.9 1.0
NE2 A:GLN82 4.2 37.7 1.0
N A:GLY97 4.2 28.4 1.0
CA A:GLY97 4.3 30.0 1.0
CA A:ALA96 4.3 24.4 1.0
CG A:GLU116 4.3 33.1 1.0
OE1 A:GLN82 4.3 38.2 1.0
O A:HOH444 4.3 34.1 0.7
N A:ALA96 4.4 24.3 1.0
NH2 A:ARG84 4.4 39.0 1.0
O A:HOH421 4.4 28.9 1.0
O A:HOH461 4.5 35.2 1.0
CD A:GLN82 4.6 37.3 1.0
O A:HOH456 4.7 40.7 1.0
O A:HOH466 4.8 49.2 1.0
CB A:ALA96 4.8 22.8 1.0
CD A:GLU112 4.8 36.0 1.0
O A:HOH411 4.9 47.6 1.0

Magnesium binding site 2 out of 8 in 5qji

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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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:61.2
occ:1.00
 O A:HOH411 2.0 47.6 1.0
O A:HOH441 2.1 30.0 1.0
OE2 A:GLU112 2.2 34.9 1.0
OE2 A:GLU166 2.2 72.5 1.0
OE2 A:GLU116 2.6 32.9 1.0
O A:HOH413 2.6 43.3 1.0
CD A:GLU166 3.1 74.8 1.0
CD A:GLU112 3.2 36.0 1.0
MG A:MG301 3.3 39.2 1.0
OE1 A:GLU112 3.3 35.1 1.0
OE1 A:GLU166 3.4 73.8 1.0
CD A:GLU116 3.6 33.4 1.0
O A:HOH424 3.8 38.4 1.0
CG A:GLU116 3.8 33.1 1.0
O A:ALA96 4.0 27.7 1.0
OE2 A:GLU115 4.1 45.1 1.0
O A:HOH456 4.4 40.7 1.0
CG A:GLU166 4.5 69.5 1.0
CG A:GLU112 4.6 35.4 1.0
OE1 A:GLU116 4.7 39.8 1.0
CA A:GLY97 4.9 30.0 1.0
C A:ALA96 5.0 27.1 1.0

Magnesium binding site 3 out of 8 in 5qji

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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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:39.5
occ:1.00
 O B:ALA96 1.9 33.7 1.0
O B:HOH433 1.9 39.0 1.0
OE2 B:GLU116 2.1 39.8 1.0
O B:HOH440 2.1 37.0 1.0
O B:HOH402 2.2 33.6 1.0
O B:HOH443 2.4 35.3 1.0
CD B:GLU116 3.0 41.5 1.0
C B:ALA96 3.0 30.3 1.0
OE1 B:GLU116 3.3 40.6 1.0
N B:ALA96 3.9 28.8 1.0
OE1 B:GLN82 3.9 45.5 1.0
N B:GLY97 3.9 32.1 1.0
CA B:ALA96 4.0 34.9 1.0
CA B:GLY97 4.0 33.5 1.0
O B:HOH422 4.0 34.4 1.0
OE2 B:GLU166 4.1 50.8 1.0
MG B:MG303 4.1 73.8 1.0
NE2 B:GLN82 4.1 42.5 1.0
OE2 B:GLU112 4.1 43.1 1.0
NH2 B:ARG84 4.2 39.9 1.0
CD B:GLN82 4.4 50.2 1.0
CG B:GLU116 4.4 37.3 1.0
CB B:ALA96 4.5 35.2 1.0
O B:HOH460 4.7 50.2 1.0

Magnesium binding site 4 out of 8 in 5qji

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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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:73.8
occ:1.00
 OE2 B:GLU112 1.9 43.1 1.0
O B:HOH412 2.0 62.2 1.0
O B:HOH427 2.6 44.0 1.0
OE2 B:GLU166 2.7 50.8 1.0
OE2 B:GLU116 2.9 39.8 1.0
CD B:GLU112 3.0 41.3 1.0
O B:HOH443 3.0 35.3 1.0
OE1 B:GLU166 3.1 71.9 1.0
CD B:GLU166 3.2 69.6 1.0
CG B:GLU116 3.4 37.3 1.0
OE1 B:GLU112 3.4 40.3 1.0
CD B:GLU116 3.5 41.5 1.0
OE2 B:GLU115 3.6 64.5 1.0
MG B:MG302 4.1 39.5 1.0
CB B:GLU115 4.2 49.4 1.0
CG B:GLU112 4.3 38.4 1.0
O B:ALA96 4.4 33.7 1.0
O B:HOH433 4.4 39.0 1.0
CB B:GLU112 4.5 37.2 1.0
CA B:GLU112 4.6 38.3 1.0
CD B:GLU115 4.6 60.3 1.0
OE1 B:GLU116 4.7 40.6 1.0
O B:GLU112 4.7 33.2 1.0
CG B:GLU166 4.7 72.9 1.0
CB B:GLU116 4.9 37.3 1.0
CG B:GLU115 5.0 56.5 1.0

Magnesium binding site 5 out of 8 in 5qji

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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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:47.5
occ:1.00
 O C:HOH408 1.4 70.2 1.0
O C:HOH404 2.1 45.6 1.0
OE2 C:GLU166 2.3 58.7 1.0
OE2 C:GLU112 2.4 43.3 1.0
MG C:MG303 2.8 39.1 1.0
O C:HOH461 2.8 53.6 1.0
OE2 C:GLU116 2.8 44.5 1.0
CD C:GLU112 3.3 52.9 1.0
O C:ALA96 3.5 35.1 1.0
CD C:GLU166 3.5 59.7 1.0
OE1 C:GLU112 3.6 60.1 1.0
O C:HOH422 3.6 41.4 1.0
O C:HOH432 3.8 29.5 1.0
O C:HOH446 3.9 54.6 1.0
CD C:GLU116 4.0 40.1 1.0
CA C:GLY97 4.1 42.6 1.0
OE1 C:GLU166 4.2 66.1 1.0
CG C:GLU116 4.5 38.1 1.0
C C:ALA96 4.5 37.9 1.0
CG C:GLU166 4.6 57.6 1.0
CG C:GLU112 4.7 47.5 1.0
O C:HOH467 4.7 62.4 1.0
O C:HOH424 4.8 35.2 1.0
N C:GLY97 4.8 37.4 1.0
OE2 C:GLU115 5.0 49.8 1.0
OE1 C:GLU116 5.0 42.5 1.0

Magnesium binding site 6 out of 8 in 5qji

Go back to Magnesium Binding Sites List in 5qji
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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:39.1
occ:1.00
 O C:HOH432 1.7 29.5 1.0
OE2 C:GLU116 1.9 44.5 1.0
O C:HOH408 2.0 70.2 1.0
O C:HOH424 2.0 35.2 1.0
O C:ALA96 2.2 35.1 1.0
O C:HOH422 2.2 41.4 1.0
MG C:MG302 2.8 47.5 1.0
CD C:GLU116 3.0 40.1 1.0
C C:ALA96 3.3 37.9 1.0
OE1 C:GLU116 3.4 42.5 1.0
OE2 C:GLU112 3.8 43.3 1.0
OE2 C:GLU166 3.8 58.7 1.0
N C:GLY97 4.2 37.4 1.0
CA C:GLY97 4.3 42.6 1.0
N C:ALA96 4.3 32.6 1.0
CA C:ALA96 4.3 32.9 1.0
CG C:GLU116 4.3 38.1 1.0
O C:HOH404 4.4 45.6 1.0
NE2 C:GLN82 4.4 46.8 1.0
NH2 C:ARG84 4.4 47.4 1.0
OE1 C:GLN82 4.4 38.0 1.0
CB C:ALA96 4.8 33.2 1.0
CD C:GLN82 4.8 40.0 1.0
CD C:GLU112 4.9 52.9 1.0
O C:HOH461 4.9 53.6 1.0
CD C:GLU166 4.9 59.7 1.0

Magnesium binding site 7 out of 8 in 5qji

Go back to Magnesium Binding Sites List in 5qji
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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:40.9
occ:1.00
 OE2 D:GLU116 2.2 44.9 1.0
O D:HOH409 2.3 30.0 1.0
MG D:MG302 2.3 47.4 1.0
O D:HOH412 2.5 31.0 1.0
O D:ALA96 3.3 46.5 1.0
O D:HOH423 3.3 44.0 1.0
CD D:GLU116 3.3 51.1 1.0
NE2 D:GLN82 3.5 47.0 1.0
OE2 D:GLU166 3.5 0.1 1.0
NH2 D:ARG84 3.7 44.1 1.0
OE1 D:GLU116 3.8 43.0 1.0
OE1 D:GLN82 4.0 49.9 1.0
CD D:GLN82 4.2 50.5 1.0
CD D:GLU166 4.4 0.3 1.0
NH1 D:ARG84 4.5 46.6 1.0
C D:ALA96 4.5 46.6 1.0
CG D:GLU116 4.5 49.0 1.0
CZ D:ARG84 4.5 51.7 1.0
OE2 D:GLU112 4.6 68.3 1.0
CG D:GLU166 4.7 93.5 1.0
CG1 D:VAL168 5.0 81.8 1.0

Magnesium binding site 8 out of 8 in 5qji

Go back to Magnesium Binding Sites List in 5qji
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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:47.4
occ:1.00
 MG D:MG301 2.3 40.9 1.0
OE2 D:GLU166 2.6 0.1 1.0
O D:HOH414 2.8 52.3 1.0
OE2 D:GLU116 2.9 44.9 1.0
O D:HOH412 2.9 31.0 1.0
O D:HOH423 3.2 44.0 1.0
OE2 D:GLU112 3.2 68.3 1.0
O D:ALA96 3.2 46.5 1.0
CD D:GLU112 3.6 65.8 1.0
OE1 D:GLU112 3.8 68.7 1.0
CD D:GLU166 3.8 0.3 1.0
CA D:GLY97 3.9 42.5 1.0
CD D:GLU116 4.1 51.1 1.0
O D:HOH409 4.2 30.0 1.0
C D:ALA96 4.3 46.6 1.0
CG D:GLU112 4.4 64.2 1.0
N D:GLY97 4.6 44.7 1.0
CG D:GLU166 4.6 93.5 1.0
OE1 D:GLU166 4.7 0.0 1.0
O D:HOH405 4.7 76.6 1.0
OE1 D:GLU116 4.8 43.0 1.0
CG D:GLU116 5.0 49.0 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 Dec 14 21:07:05 2020

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