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Magnesium in PDB 5qju: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z906021418

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z906021418

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 Z906021418:
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 Z906021418, PDB code: 5qju 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) 78.31 / 1.77
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.918, 59.649, 80.054, 79.55, 81.88, 76.15
R / Rfree (%) 21 / 24.8

Other elements in 5qju:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z906021418 also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

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 Z906021418 (pdb code 5qju). 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 Z906021418, PDB code: 5qju:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qju

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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 Z906021418


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 Z906021418 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:31.9
occ:1.00
 OE2 A:GLU116 2.0 27.6 1.0
O A:HOH455 2.0 26.1 1.0
O A:ALA96 2.1 25.2 1.0
O A:HOH443 2.1 30.4 1.0
O A:HOH409 2.2 27.3 1.0
O A:HOH423 2.2 28.6 1.0
CD A:GLU116 3.1 26.9 1.0
C A:ALA96 3.2 26.3 1.0
OE1 A:GLU116 3.4 28.3 1.0
MG A:MG302 3.4 57.5 1.0
OE2 A:GLU166 3.8 74.7 1.0
OE2 A:GLU112 4.0 38.3 1.0
N A:GLY97 4.1 26.1 1.0
CA A:GLY97 4.1 26.0 1.0
N A:ALA96 4.2 22.1 1.0
O A:HOH454 4.2 29.6 0.8
CA A:ALA96 4.2 22.9 1.0
NE2 A:GLN82 4.3 26.4 1.0
NH2 A:ARG84 4.3 27.9 1.0
O A:HOH425 4.4 22.7 1.0
OE1 A:GLN82 4.4 28.2 1.0
CG A:GLU116 4.4 29.2 1.0
O B:HOH470 4.4 46.8 1.0
O A:HOH460 4.5 32.6 1.0
CB A:ALA96 4.7 21.1 1.0
CD A:GLN82 4.8 32.9 1.0
CD A:GLU112 4.8 36.0 1.0
O A:HOH470 4.9 52.2 1.0

Magnesium binding site 2 out of 8 in 5qju

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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 Z906021418


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 Z906021418 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:57.5
occ:1.00
 O A:HOH412 1.7 40.8 1.0
OE2 A:GLU112 2.1 38.3 1.0
OE2 A:GLU166 2.2 74.7 1.0
O A:HOH443 2.2 30.4 1.0
OE2 A:GLU116 2.5 27.6 1.0
O A:HOH408 2.6 46.4 1.0
CD A:GLU166 3.0 83.2 1.0
CD A:GLU112 3.1 36.0 1.0
OE1 A:GLU166 3.3 77.5 1.0
OE1 A:GLU112 3.3 38.4 1.0
CD A:GLU116 3.4 26.9 1.0
MG A:MG301 3.4 31.9 1.0
CG A:GLU116 3.5 29.2 1.0
O A:HOH423 4.0 28.6 1.0
O A:ALA96 4.0 25.2 1.0
OE2 A:GLU115 4.1 40.6 1.0
CG A:GLU166 4.4 76.2 1.0
OE1 A:GLU116 4.5 28.3 1.0
CG A:GLU112 4.5 31.8 1.0
O A:HOH460 4.8 32.6 1.0
CB A:GLU112 4.9 30.4 1.0
CB A:GLU115 5.0 30.8 1.0

Magnesium binding site 3 out of 8 in 5qju

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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 Z906021418


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 Z906021418 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:36.8
occ:1.00
 OE2 B:GLU116 2.1 36.9 1.0
O B:HOH425 2.1 31.1 1.0
O B:ALA96 2.1 30.7 1.0
O B:HOH450 2.1 27.6 1.0
O B:HOH413 2.1 32.4 1.0
O B:HOH439 2.2 35.5 1.0
CD B:GLU116 3.1 37.1 1.0
C B:ALA96 3.3 29.7 1.0
OE1 B:GLU116 3.4 37.1 1.0
MG B:MG303 3.6 96.8 1.0
OE2 B:GLU166 4.1 59.3 1.0
CA B:GLY97 4.1 30.6 1.0
N B:GLY97 4.1 29.0 1.0
NH2 B:ARG84 4.2 32.9 1.0
O B:HOH432 4.2 32.1 1.0
N B:ALA96 4.3 27.5 1.0
CA B:ALA96 4.3 28.3 1.0
OE2 B:GLU112 4.3 43.4 1.0
NE2 B:GLN82 4.3 35.8 1.0
OE1 B:GLN82 4.4 36.8 1.0
O A:HOH457 4.5 45.8 1.0
CG B:GLU116 4.5 34.4 1.0
O B:HOH466 4.5 41.2 1.0
CB B:ALA96 4.7 26.0 1.0
CD B:GLN82 4.7 41.2 1.0
CD B:GLU166 4.9 79.8 1.0

Magnesium binding site 4 out of 8 in 5qju

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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 Z906021418


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 Z906021418 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:96.8
occ:1.00
 O B:HOH414 1.8 50.8 1.0
OE2 B:GLU112 2.1 43.4 1.0
O B:HOH436 2.5 45.5 1.0
OE2 B:GLU166 2.6 59.3 1.0
OE2 B:GLU116 2.6 36.9 1.0
O B:HOH439 2.6 35.5 1.0
CD B:GLU112 3.1 40.2 1.0
OE1 B:GLU112 3.3 39.6 1.0
CD B:GLU166 3.3 79.8 1.0
OE1 B:GLU166 3.3 79.0 1.0
CD B:GLU116 3.4 37.1 1.0
CG B:GLU116 3.5 34.4 1.0
MG B:MG302 3.6 36.8 1.0
OE2 B:GLU115 3.8 48.2 1.0
O B:ALA96 4.1 30.7 1.0
O B:HOH425 4.2 31.1 1.0
CG B:GLU112 4.5 36.1 1.0
OE1 B:GLU116 4.6 37.1 1.0
CG B:GLU166 4.7 73.3 1.0
CB B:GLU115 4.8 41.8 1.0
O B:HOH466 4.9 41.2 1.0
CD B:GLU115 4.9 45.0 1.0
CB B:GLU112 4.9 35.7 1.0
CA B:GLY97 5.0 30.6 1.0

Magnesium binding site 5 out of 8 in 5qju

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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 Z906021418


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 Z906021418 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:44.2
occ:1.00
 MG C:MG303 2.0 36.7 1.0
OE2 C:GLU116 2.7 34.5 1.0
O C:ALA96 2.7 29.3 1.0
O C:HOH418 3.0 36.4 1.0
O C:HOH453 3.0 29.9 1.0
O C:HOH435 3.1 58.7 1.0
OE2 C:GLU112 3.2 38.8 1.0
O C:HOH404 3.3 47.4 1.0
O C:HOH446 3.3 45.8 1.0
OE2 C:GLU166 3.4 73.1 1.0
CA C:GLY97 3.6 34.2 1.0
OE1 C:GLU112 3.7 52.4 1.0
CD C:GLU112 3.7 42.4 1.0
C C:ALA96 3.8 30.6 1.0
CD C:GLU116 3.9 32.3 1.0
CD C:GLU166 4.0 78.7 1.0
O C:HOH434 4.0 28.3 1.0
N C:GLY97 4.2 29.5 1.0
OE1 C:GLU166 4.3 77.0 1.0
O C:HOH448 4.4 44.2 0.9
OE1 C:GLU116 4.6 41.6 1.0
O C:HOH464 4.6 68.9 1.0
CG C:GLU116 4.8 30.9 1.0
CG C:GLU112 4.9 34.5 1.0
O C:HOH458 4.9 43.9 0.9
C C:GLY97 5.0 34.0 1.0

Magnesium binding site 6 out of 8 in 5qju

Go back to Magnesium Binding Sites List in 5qju
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 Z906021418


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 Z906021418 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:36.7
occ:1.00
 MG C:MG302 2.0 44.2 1.0
OE2 C:GLU116 2.0 34.5 1.0
O C:HOH434 2.1 28.3 1.0
O C:HOH453 2.1 29.9 1.0
O C:HOH418 2.1 36.4 1.0
O C:ALA96 2.2 29.3 1.0
CD C:GLU116 3.1 32.3 1.0
OE1 C:GLU116 3.3 41.6 1.0
C C:ALA96 3.3 30.6 1.0
OE2 C:GLU166 3.8 73.1 1.0
N C:ALA96 4.2 27.8 1.0
OE2 C:GLU112 4.2 38.8 1.0
CA C:ALA96 4.2 26.4 1.0
N C:GLY97 4.3 29.5 1.0
O C:HOH414 4.3 32.2 0.9
NE2 C:GLN82 4.3 32.3 1.0
O C:HOH404 4.3 47.4 1.0
CA C:GLY97 4.3 34.2 1.0
O C:HOH448 4.3 44.2 0.9
OE1 C:GLN82 4.4 35.0 1.0
CG C:GLU116 4.4 30.9 1.0
NH2 C:ARG84 4.4 33.0 1.0
O C:HOH458 4.5 43.9 0.9
CB C:ALA96 4.7 26.3 1.0
O C:HOH446 4.8 45.8 1.0
CD C:GLU166 4.8 78.7 1.0
CD C:GLN82 4.8 41.6 1.0
CD C:GLU112 4.9 42.4 1.0
O C:HOH435 4.9 58.7 1.0

Magnesium binding site 7 out of 8 in 5qju

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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 Z906021418


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 Z906021418 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:35.1
occ:1.00
 O D:HOH405 2.0 29.9 0.9
O D:HOH421 2.0 27.8 1.0
OE2 D:GLU116 2.0 32.1 1.0
O D:HOH416 2.0 32.1 1.0
O D:ALA96 2.1 31.6 1.0
MG D:MG302 2.2 42.3 1.0
O D:HOH422 2.3 46.0 0.9
CD D:GLU116 3.1 37.8 1.0
C D:ALA96 3.3 32.5 1.0
OE1 D:GLU116 3.4 34.5 1.0
OE2 D:GLU112 3.7 49.7 1.0
OE2 D:GLU166 3.9 90.0 1.0
N D:GLY97 4.1 33.3 1.0
CA D:GLY97 4.2 35.6 1.0
N D:ALA96 4.2 31.6 1.0
CA D:ALA96 4.2 34.1 1.0
NH2 D:ARG84 4.3 36.3 1.0
O D:HOH408 4.4 30.9 0.9
NE2 D:GLN82 4.4 39.7 1.0
CG D:GLU116 4.4 32.9 1.0
OE1 D:GLN82 4.5 35.2 1.0
CD D:GLU112 4.5 49.1 1.0
O D:HOH428 4.6 43.6 1.0
CG D:GLU112 4.7 52.5 1.0
CB D:ALA96 4.7 34.1 1.0
CD D:GLN82 4.9 42.3 1.0
O D:HOH406 4.9 52.0 1.0
O D:HOH410 4.9 60.6 1.0

Magnesium binding site 8 out of 8 in 5qju

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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 Z906021418


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 Z906021418 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:42.3
occ:1.00
 MG D:MG301 2.2 35.1 1.0
OE2 D:GLU112 2.4 49.7 1.0
OE2 D:GLU166 2.7 90.0 1.0
O D:HOH405 2.7 29.9 0.9
OE2 D:GLU116 2.7 32.1 1.0
O D:HOH410 2.7 60.6 1.0
O D:ALA96 3.1 31.6 1.0
O D:HOH428 3.2 43.6 1.0
O D:HOH421 3.2 27.8 1.0
CD D:GLU112 3.3 49.1 1.0
O D:HOH422 3.5 46.0 0.9
O D:HOH406 3.7 52.0 1.0
CA D:GLY97 3.7 35.6 1.0
OE1 D:GLU112 3.9 47.8 1.0
CD D:GLU166 3.9 87.5 1.0
CD D:GLU116 3.9 37.8 1.0
C D:ALA96 4.1 32.5 1.0
O D:HOH416 4.2 32.1 1.0
CG D:GLU112 4.2 52.5 1.0
N D:GLY97 4.4 33.3 1.0
OE1 D:GLU166 4.7 78.9 1.0
OE1 D:GLU116 4.8 34.5 1.0
CG D:GLU116 4.8 32.9 1.0
CG D:GLU166 4.8 77.4 1.0
C D:GLY97 5.0 37.8 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 02:23:09 2024

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