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Magnesium in PDB 5qto: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641:
2.7.7.96; 3.6.1.13; 3.6.1.58;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641, PDB code: 5qto was solved by Y.Dubianok, T.Krojer, H.Kovacs, F.Moriaud, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.52 / 1.67
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.260, 59.871, 79.887, 79.47, 81.46, 75.59
R / Rfree (%) 22.9 / 26.2

Other elements in 5qto:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641 also contains other interesting chemical elements:

Fluorine (F) 20 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641 (pdb code 5qto). 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 -- Crystal Structure of NUDT5 in Complex with 1R-0641, PDB code: 5qto:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qto

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Magnesium binding site 1 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 -- Crystal Structure of NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:30.4
occ:1.00
 OE2 A:GLU116 2.0 30.6 1.0
O A:HOH427 2.0 24.9 1.0
O A:ALA96 2.1 25.0 1.0
O A:HOH408 2.1 24.0 1.0
O A:HOH458 2.2 27.2 1.0
O A:HOH421 2.2 30.4 1.0
CD A:GLU116 3.0 29.3 1.0
C A:ALA96 3.2 25.4 1.0
OE1 A:GLU116 3.4 30.9 1.0
MG A:MG302 3.5 57.3 1.0
OE2 A:GLU166 4.0 64.3 1.0
CA A:GLY97 4.1 25.5 1.0
N A:GLY97 4.1 24.5 1.0
OE2 A:GLU112 4.1 35.0 1.0
O A:HOH450 4.2 21.8 0.8
CA A:ALA96 4.2 22.6 1.0
N A:ALA96 4.2 22.2 1.0
NH2 A:ARG84 4.3 27.0 1.0
CG A:GLU116 4.3 31.4 1.0
O A:HOH468 4.3 28.9 1.0
O A:HOH418 4.4 21.4 1.0
NE2 A:GLN82 4.4 29.5 1.0
O A:HOH460 4.4 32.8 1.0
OE1 A:GLN82 4.5 26.2 1.0
CB A:ALA96 4.6 19.7 1.0
O A:HOH474 4.6 56.0 1.0
CD A:GLN82 4.8 33.9 1.0
CD A:GLU112 4.8 32.2 1.0

Magnesium binding site 2 out of 8 in 5qto

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Magnesium binding site 2 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 -- Crystal Structure of NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:57.3
occ:1.00
 O A:HOH410 1.8 48.0 1.0
OE2 A:GLU112 2.2 35.0 1.0
O A:HOH427 2.2 24.9 1.0
O A:HOH415 2.3 56.0 1.0
OE2 A:GLU166 2.3 64.3 1.0
OE2 A:GLU116 2.7 30.6 1.0
CD A:GLU112 3.1 32.2 1.0
CD A:GLU166 3.2 68.6 1.0
OE1 A:GLU112 3.3 31.8 1.0
OE1 A:GLU166 3.5 62.3 1.0
MG A:MG301 3.5 30.4 1.0
CD A:GLU116 3.5 29.3 1.0
CG A:GLU116 3.6 31.4 1.0
OE2 A:GLU115 3.9 34.2 1.0
O A:HOH421 4.1 30.4 1.0
O A:ALA96 4.1 25.0 1.0
O A:HOH460 4.3 32.8 1.0
CG A:GLU166 4.5 66.2 1.0
CG A:GLU112 4.5 28.6 1.0
OE1 A:GLU116 4.7 30.9 1.0
CA A:GLY97 4.9 25.5 1.0
CB A:GLU115 4.9 30.1 1.0
CB A:GLU112 4.9 26.6 1.0

Magnesium binding site 3 out of 8 in 5qto

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Magnesium binding site 3 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 -- Crystal Structure of NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:31.9
occ:1.00
 O B:ALA96 2.0 28.1 1.0
O B:HOH418 2.0 34.0 1.0
OE2 B:GLU116 2.0 38.4 1.0
O B:HOH443 2.1 30.4 1.0
O B:HOH415 2.1 29.4 1.0
O B:HOH448 2.2 26.1 1.0
CD B:GLU116 3.1 36.8 1.0
C B:ALA96 3.2 24.9 1.0
OE1 B:GLU116 3.4 34.4 1.0
OE2 B:GLU166 3.9 56.2 1.0
O B:HOH446 4.0 32.4 1.0
CA B:GLY97 4.1 28.9 1.0
N B:GLY97 4.1 28.6 1.0
OE2 B:GLU112 4.2 38.2 1.0
N B:ALA96 4.2 25.9 1.0
CA B:ALA96 4.2 27.9 1.0
NH2 B:ARG84 4.3 34.2 1.0
NE2 B:GLN82 4.3 39.7 1.0
MG B:MG303 4.3 72.4 1.0
O B:HOH462 4.4 43.1 0.8
O B:HOH471 4.4 44.9 1.0
CG B:GLU116 4.4 36.4 1.0
OE1 B:GLN82 4.4 38.1 1.0
CB B:ALA96 4.7 28.1 1.0
CD B:GLU166 4.7 71.0 1.0
O B:HOH464 4.7 33.6 0.8
CD B:GLN82 4.8 45.1 1.0
CD B:GLU112 5.0 38.1 1.0

Magnesium binding site 4 out of 8 in 5qto

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Magnesium binding site 4 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 -- Crystal Structure of NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:72.4
occ:1.00
 O B:HOH409 2.2 73.1 1.0
OE2 B:GLU112 2.2 38.2 1.0
OE2 B:GLU166 2.6 56.2 1.0
O B:HOH449 2.6 51.7 1.0
OE2 B:GLU115 3.1 51.8 1.0
OE2 B:GLU116 3.1 38.4 1.0
OE1 B:GLU166 3.2 70.9 1.0
CD B:GLU112 3.2 38.1 1.0
CD B:GLU166 3.2 71.0 1.0
O B:HOH443 3.3 30.4 1.0
CG B:GLU116 3.5 36.4 1.0
OE1 B:GLU112 3.6 36.4 1.0
CD B:GLU116 3.7 36.8 1.0
CB B:GLU115 3.9 38.7 1.0
CD B:GLU115 4.2 47.8 1.0
MG B:MG302 4.3 31.9 1.0
CG B:GLU112 4.5 38.3 1.0
CA B:GLU112 4.6 34.9 1.0
O B:GLU112 4.7 34.2 1.0
CG B:GLU115 4.7 43.0 1.0
O B:ALA96 4.7 28.1 1.0
CG B:GLU166 4.7 66.6 1.0
CB B:GLU112 4.8 38.7 1.0
CB B:GLU116 4.9 34.3 1.0
OE1 B:GLU116 4.9 34.4 1.0
O B:HOH462 4.9 43.1 0.8
N B:GLU116 5.0 36.3 1.0

Magnesium binding site 5 out of 8 in 5qto

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Magnesium binding site 5 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 -- Crystal Structure of NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:78.4
occ:1.00
 O C:HOH440 1.8 31.7 1.0
O C:HOH406 2.3 45.4 1.0
OE2 C:GLU112 2.4 41.9 1.0
OE2 C:GLU166 2.5 70.6 1.0
O C:HOH443 2.8 57.8 1.0
OE2 C:GLU116 2.8 37.2 1.0
O C:HOH417 3.1 53.4 1.0
CD C:GLU166 3.1 76.1 1.0
MG C:MG303 3.2 32.7 1.0
CD C:GLU112 3.3 46.2 1.0
OE1 C:GLU166 3.3 74.3 1.0
OE1 C:GLU112 3.4 49.1 1.0
CD C:GLU116 3.9 35.6 1.0
O C:HOH415 3.9 37.6 1.0
O C:ALA96 3.9 28.2 1.0
CG C:GLU116 4.2 35.2 1.0
OE2 C:GLU115 4.4 45.7 1.0
CG C:GLU166 4.4 71.3 1.0
CA C:GLY97 4.4 35.0 1.0
O C:HOH447 4.5 31.2 1.0
CG C:GLU112 4.7 39.9 1.0
O C:HOH466 4.7 49.6 1.0
C C:ALA96 4.8 32.6 1.0
OE1 C:GLU116 4.9 39.7 1.0

Magnesium binding site 6 out of 8 in 5qto

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Magnesium binding site 6 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 -- Crystal Structure of NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:32.7
occ:1.00
 OE2 C:GLU116 1.9 37.2 1.0
O C:HOH423 2.0 26.4 1.0
O C:HOH440 2.1 31.7 1.0
O C:HOH447 2.1 31.2 1.0
O C:ALA96 2.1 28.2 1.0
O C:HOH415 2.3 37.6 1.0
CD C:GLU116 3.0 35.6 1.0
MG C:MG302 3.2 78.4 1.0
OE1 C:GLU116 3.3 39.7 1.0
C C:ALA96 3.3 32.6 1.0
OE2 C:GLU166 3.5 70.6 1.0
O C:HOH413 4.2 34.5 1.0
N C:GLY97 4.2 33.8 1.0
N C:ALA96 4.2 30.9 1.0
CA C:GLY97 4.2 35.0 1.0
CA C:ALA96 4.3 29.1 1.0
NE2 C:GLN82 4.3 32.6 1.0
OE2 C:GLU112 4.3 41.9 1.0
CG C:GLU116 4.3 35.2 1.0
NH2 C:ARG84 4.3 33.2 1.0
OE1 C:GLN82 4.4 32.4 1.0
CD C:GLU166 4.7 76.1 1.0
O C:HOH459 4.7 42.7 1.0
CB C:ALA96 4.7 29.5 1.0
CD C:GLN82 4.8 38.0 1.0

Magnesium binding site 7 out of 8 in 5qto

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Magnesium binding site 7 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 -- Crystal Structure of NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:42.6
occ:1.00
 O D:HOH406 2.0 28.9 1.0
OE2 D:GLU116 2.0 37.3 1.0
O D:HOH409 2.2 31.0 1.0
MG D:MG302 2.4 40.0 1.0
O D:HOH428 2.5 36.1 1.0
O D:ALA96 2.6 43.3 1.0
CD D:GLU116 3.1 46.1 1.0
OE1 D:GLU116 3.6 37.4 1.0
C D:ALA96 3.8 44.0 1.0
OE2 D:GLU166 3.8 84.5 1.0
OE2 D:GLU112 3.9 49.6 1.0
NE2 D:GLN82 3.9 43.3 1.0
OE1 D:GLN82 4.2 41.4 1.0
NH2 D:ARG84 4.2 43.0 1.0
CG D:GLU116 4.4 43.9 1.0
CD D:GLN82 4.5 47.4 1.0
N D:ALA96 4.5 45.1 1.0
N D:GLY97 4.7 40.1 1.0
CA D:GLY97 4.7 41.5 1.0
CA D:ALA96 4.7 44.5 1.0
O D:HOH407 4.7 42.0 1.0
CD D:GLU112 4.7 51.7 1.0
O D:HOH408 4.8 34.7 0.8
CD D:GLU166 4.8 84.8 1.0
O D:HOH402 4.8 40.9 1.0
CG D:GLU112 5.0 56.3 1.0

Magnesium binding site 8 out of 8 in 5qto

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Magnesium binding site 8 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 -- Crystal Structure of NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:40.0
occ:1.00
 O D:HOH428 1.9 36.1 1.0
OE2 D:GLU112 2.1 49.6 1.0
MG D:MG301 2.4 42.6 1.0
O D:HOH407 2.4 42.0 1.0
OE2 D:GLU116 2.8 37.3 1.0
O D:ALA96 2.9 43.3 1.0
OE2 D:GLU166 2.9 84.5 1.0
CD D:GLU112 3.0 51.7 1.0
O D:HOH406 3.1 28.9 1.0
CA D:GLY97 3.5 41.5 1.0
O D:HOH402 3.6 40.9 1.0
OE1 D:GLU112 3.7 53.9 1.0
C D:ALA96 3.8 44.0 1.0
CG D:GLU112 3.9 56.3 1.0
CD D:GLU116 4.0 46.1 1.0
N D:GLY97 4.1 40.1 1.0
CD D:GLU166 4.2 84.8 1.0
O D:HOH409 4.3 31.0 1.0
C D:GLY97 4.7 43.3 1.0
OE1 D:GLU116 4.8 37.4 1.0
CG D:GLU116 4.8 43.9 1.0
OE1 D:GLU166 4.9 85.0 1.0
N D:LEU98 4.9 44.1 1.0

Reference:

Y.Dubianok, T.Krojer, H.Kovacs, F.Moriaud, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft. Pandda Analysis Group Deposition To Be Published.
Page generated: Tue Aug 12 18:41:56 2025

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