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Magnesium in PDB 5qjx: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434778

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434778

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 Z2856434778:
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 Z2856434778, PDB code: 5qjx 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) 78.96 / 1.73
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.520, 59.520, 80.620, 79.68, 82.36, 76.36
R / Rfree (%) 22 / 25.6

Other elements in 5qjx:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434778 also contains other interesting chemical elements:

Fluorine (F) 3 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 Z2856434778 (pdb code 5qjx). 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 Z2856434778, PDB code: 5qjx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjx

Go back to Magnesium Binding Sites List in 5qjx
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 Z2856434778


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 Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:48.9
occ:1.00
 O A:HOH423 2.0 36.0 1.0
O A:ALA96 2.1 30.4 1.0
O A:HOH446 2.1 28.8 1.0
OE2 A:GLU116 2.2 39.8 1.0
O A:HOH440 2.3 31.1 1.0
O A:HOH424 2.6 40.3 1.0
C A:ALA96 3.2 27.1 1.0
MG A:MG302 3.2 74.2 1.0
CD A:GLU116 3.3 35.4 1.0
OE1 A:GLU116 3.7 34.1 1.0
OE2 A:GLU112 3.9 45.1 1.0
N A:ALA96 4.1 23.7 1.0
N A:GLY97 4.1 26.1 1.0
CA A:ALA96 4.2 25.9 1.0
CA A:GLY97 4.2 26.2 1.0
O A:HOH416 4.3 25.1 1.0
NH2 A:ARG84 4.3 30.9 1.0
OE1 A:GLN82 4.3 32.6 1.0
NE2 A:GLN82 4.4 33.8 1.0
O A:HOH461 4.5 38.6 1.0
O A:HOH460 4.5 50.9 1.0
CD A:GLU112 4.6 36.7 1.0
CG A:GLU116 4.6 32.0 1.0
CB A:ALA96 4.6 21.4 1.0
CD A:GLN82 4.7 38.8 1.0
OE1 A:GLU112 5.0 46.3 1.0

Magnesium binding site 2 out of 8 in 5qjx

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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 Z2856434778


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 Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:74.2
occ:1.00
 O A:HOH413 2.2 73.5 1.0
O A:HOH446 2.2 28.8 1.0
OE2 A:GLU116 2.6 39.8 1.0
OE2 A:GLU166 2.9 82.7 1.0
OE2 A:GLU112 3.0 45.1 1.0
O A:HOH424 3.2 40.3 1.0
CD A:GLU166 3.2 86.4 1.0
MG A:MG301 3.2 48.9 1.0
OE1 A:GLU166 3.3 91.7 1.0
O A:HOH402 3.4 56.8 1.0
CD A:GLU116 3.6 35.4 1.0
OE1 A:GLU112 3.8 46.3 1.0
CD A:GLU112 3.8 36.7 1.0
CG A:GLU116 3.9 32.0 1.0
O A:HOH460 4.1 50.9 1.0
O A:ALA96 4.3 30.4 1.0
CG A:GLU166 4.3 79.9 1.0
OE2 A:GLU115 4.7 54.7 1.0
OE1 A:GLU116 4.7 34.1 1.0
O A:HOH423 4.8 36.0 1.0
CB A:GLU166 4.9 72.1 1.0

Magnesium binding site 3 out of 8 in 5qjx

Go back to Magnesium Binding Sites List in 5qjx
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 Z2856434778


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 Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:54.5
occ:1.00
 O B:HOH416 1.9 35.9 1.0
OE2 B:GLU116 2.3 52.5 1.0
O B:ALA96 2.3 38.5 1.0
O B:HOH435 2.4 39.9 1.0
O B:HOH456 2.5 35.0 1.0
O B:HOH403 2.5 44.5 1.0
MG B:MG303 3.4 87.0 1.0
CD B:GLU116 3.4 46.4 1.0
C B:ALA96 3.4 31.9 1.0
OE1 B:GLU116 3.9 49.8 1.0
OE2 B:GLU166 4.0 71.1 1.0
O B:HOH436 4.0 30.4 1.0
NH2 B:ARG84 4.2 31.9 1.0
N B:ALA96 4.2 26.5 1.0
NE2 B:GLN82 4.3 39.3 1.0
CA B:ALA96 4.3 28.8 1.0
OE2 B:GLU112 4.3 48.1 1.0
OE1 B:GLN82 4.3 39.2 1.0
N B:GLY97 4.3 30.8 1.0
CA B:GLY97 4.4 35.3 1.0
CG B:GLU116 4.6 39.5 1.0
CB B:ALA96 4.6 30.0 1.0
CD B:GLN82 4.7 45.7 1.0
O B:HOH467 4.9 42.4 1.0

Magnesium binding site 4 out of 8 in 5qjx

Go back to Magnesium Binding Sites List in 5qjx
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 Z2856434778


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 Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:87.0
occ:1.00
 O B:HOH406 2.0 59.8 1.0
O B:HOH435 2.3 39.9 1.0
OE2 B:GLU112 2.4 48.1 1.0
OE2 B:GLU166 2.5 71.1 1.0
OE2 B:GLU116 2.7 52.5 1.0
O B:HOH432 2.8 59.5 1.0
CD B:GLU112 3.2 46.3 1.0
OE1 B:GLU112 3.3 55.4 1.0
CD B:GLU166 3.3 87.1 1.0
MG B:MG302 3.4 54.5 1.0
CD B:GLU116 3.5 46.4 1.0
OE1 B:GLU166 3.5 73.1 1.0
CG B:GLU116 3.7 39.5 1.0
O B:ALA96 3.8 38.5 1.0
O B:HOH403 4.0 44.5 1.0
OE2 B:GLU115 4.4 55.1 1.0
OE1 B:GLU116 4.6 49.8 1.0
CG B:GLU112 4.7 46.1 1.0
CG B:GLU166 4.7 83.9 1.0
O B:HOH416 4.9 35.9 1.0
C B:ALA96 4.9 31.9 1.0

Magnesium binding site 5 out of 8 in 5qjx

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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 Z2856434778


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 Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:55.8
occ:1.00
 O C:HOH415 2.4 66.4 1.0
MG C:MG303 2.6 55.9 1.0
OE2 C:GLU166 2.7 92.1 1.0
OE2 C:GLU112 2.8 43.1 1.0
O C:ALA96 2.9 36.6 1.0
O C:HOH457 3.2 60.3 1.0
OE2 C:GLU116 3.3 40.0 1.0
O C:HOH452 3.4 70.1 1.0
CD C:GLU112 3.4 49.2 1.0
O C:HOH409 3.5 47.0 1.0
OE1 C:GLU112 3.6 57.6 1.0
O C:HOH448 3.6 37.2 1.0
CA C:GLY97 3.7 44.0 1.0
CD C:GLU166 3.8 98.3 1.0
C C:ALA96 4.0 38.5 1.0
N C:GLY97 4.3 40.3 1.0
OE1 C:GLU166 4.3 0.7 1.0
O C:HOH411 4.3 34.3 1.0
O C:HOH442 4.4 65.4 1.0
CD C:GLU116 4.5 38.1 1.0
CG C:GLU112 4.7 45.8 1.0
C C:GLY97 5.0 45.0 1.0
CG C:GLU166 5.0 84.7 1.0

Magnesium binding site 6 out of 8 in 5qjx

Go back to Magnesium Binding Sites List in 5qjx
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 Z2856434778


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 Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:55.9
occ:1.00
 O C:HOH411 1.8 34.3 1.0
O C:HOH448 2.2 37.2 1.0
O C:ALA96 2.2 36.6 1.0
O C:HOH409 2.6 47.0 1.0
OE2 C:GLU116 2.6 40.0 1.0
MG C:MG302 2.6 55.8 1.0
C C:ALA96 3.3 38.5 1.0
CD C:GLU116 3.7 38.1 1.0
OE2 C:GLU166 3.8 92.1 1.0
NH2 C:ARG84 4.1 35.2 1.0
N C:ALA96 4.1 31.6 1.0
OE1 C:GLN82 4.1 45.1 1.0
CA C:ALA96 4.1 32.5 1.0
OE1 C:GLU116 4.1 51.1 1.0
OE2 C:GLU112 4.3 43.1 1.0
N C:GLY97 4.3 40.3 1.0
O C:HOH457 4.4 60.3 1.0
CA C:GLY97 4.4 44.0 1.0
NE2 C:GLN82 4.4 43.5 1.0
CB C:ALA96 4.4 32.0 1.0
CD C:GLN82 4.7 52.9 1.0
O C:HOH415 4.9 66.4 1.0
CG C:GLU116 4.9 34.0 1.0
CD C:GLU166 5.0 98.3 1.0
CZ C:ARG84 5.0 35.7 1.0

Magnesium binding site 7 out of 8 in 5qjx

Go back to Magnesium Binding Sites List in 5qjx
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 Z2856434778


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 Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:51.0
occ:1.00
 O D:HOH418 2.1 30.8 1.0
O D:HOH421 2.2 35.1 1.0
O D:HOH402 2.3 46.5 1.0
O D:ALA96 2.3 31.1 1.0
OE2 D:GLU116 2.4 43.6 1.0
MG D:MG302 3.3 59.8 1.0
C D:ALA96 3.4 31.3 1.0
CD D:GLU116 3.6 42.8 1.0
OE1 D:GLU116 4.0 46.2 1.0
OE2 D:GLU112 4.1 51.4 1.0
CA D:GLY97 4.1 35.5 1.0
NH2 D:ARG84 4.2 32.2 1.0
N D:ALA96 4.2 30.9 1.0
N D:GLY97 4.2 35.0 1.0
CA D:ALA96 4.3 26.8 1.0
NE2 D:GLN82 4.5 37.6 1.0
OE1 D:GLN82 4.5 35.4 1.0
CB D:ALA96 4.5 28.0 1.0
CD D:GLU112 4.7 52.1 1.0
CG D:GLU116 4.8 36.9 1.0
CD D:GLN82 4.9 44.0 1.0
NH1 D:ARG84 5.0 38.3 1.0

Magnesium binding site 8 out of 8 in 5qjx

Go back to Magnesium Binding Sites List in 5qjx
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 Z2856434778


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 Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:59.8
occ:1.00
 O D:HOH421 1.9 35.1 1.0
OE2 D:GLU112 2.6 51.4 1.0
O D:HOH403 2.6 66.1 1.0
O D:HOH419 2.8 52.5 1.0
OE2 D:GLU116 3.0 43.6 1.0
MG D:MG301 3.3 51.0 1.0
CD D:GLU112 3.7 52.1 1.0
OE1 D:GLU166 3.7 72.7 1.0
CD D:GLU166 3.8 70.2 1.0
OE2 D:GLU166 3.8 77.5 1.0
CD D:GLU116 3.9 42.8 1.0
CG D:GLU116 4.1 36.9 1.0
OE1 D:GLU112 4.2 51.2 1.0
O D:ALA96 4.2 31.1 1.0
CG D:GLU166 4.6 66.3 1.0
OE2 D:GLU115 4.7 46.9 1.0
CG D:GLU112 4.8 52.1 1.0
O D:HOH402 4.9 46.5 1.0
O D:HOH418 4.9 30.8 1.0
CA D:GLY97 5.0 35.5 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 02:23:13 2024

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