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Magnesium in PDB 5qk5: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1267773786

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1267773786

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 Z1267773786:
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 Z1267773786, PDB code: 5qk5 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) 78.11 / 1.63
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.440, 59.960, 79.980, 79.36, 81.22, 75.51
R / Rfree (%) 23.1 / 26.6

Other elements in 5qk5:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1267773786 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 Z1267773786 (pdb code 5qk5). 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 Z1267773786, PDB code: 5qk5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qk5

Go back to Magnesium Binding Sites List in 5qk5
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 Z1267773786


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 Z1267773786 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:29.5
occ:1.00
 O A:HOH441 2.0 21.4 1.0
OE2 A:GLU116 2.0 23.4 1.0
O A:HOH462 2.1 21.9 1.0
O A:HOH415 2.1 23.6 1.0
O A:ALA96 2.2 23.9 1.0
O A:HOH426 2.2 26.0 1.0
CD A:GLU116 3.1 26.5 1.0
C A:ALA96 3.3 21.7 1.0
OE1 A:GLU116 3.4 25.6 1.0
MG A:MG302 3.4 64.2 1.0
OE2 A:GLU166 3.8 51.7 1.0
O A:HOH459 4.1 24.6 0.8
OE2 A:GLU112 4.1 32.1 1.0
CA A:GLY97 4.1 23.5 1.0
N A:GLY97 4.2 23.4 1.0
CA A:ALA96 4.2 20.7 1.0
N A:ALA96 4.2 18.4 1.0
NH2 A:ARG84 4.3 25.3 1.0
O A:HOH414 4.3 20.9 1.0
CG A:GLU116 4.4 23.0 1.0
NE2 A:GLN82 4.4 29.9 1.0
OE1 A:GLN82 4.5 25.3 1.0
O A:HOH472 4.5 27.4 1.0
O A:HOH469 4.5 34.5 1.0
CB A:ALA96 4.6 17.8 1.0
CD A:GLN82 4.8 33.3 1.0
O A:HOH476 4.8 43.1 1.0
CD A:GLU112 4.9 27.0 1.0
CD A:GLU166 5.0 65.8 1.0

Magnesium binding site 2 out of 8 in 5qk5

Go back to Magnesium Binding Sites List in 5qk5
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 Z1267773786


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 Z1267773786 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:64.2
occ:1.00
 O A:HOH441 2.0 21.4 1.0
O A:HOH403 2.1 36.2 1.0
OE2 A:GLU112 2.1 32.1 1.0
O A:HOH405 2.4 50.5 1.0
OE2 A:GLU166 2.5 51.7 1.0
OE2 A:GLU116 2.8 23.4 1.0
CD A:GLU112 3.0 27.0 1.0
OE1 A:GLU112 3.2 30.1 1.0
CD A:GLU166 3.2 65.8 1.0
MG A:MG301 3.4 29.5 1.0
OE1 A:GLU166 3.5 54.6 1.0
CD A:GLU116 3.7 26.5 1.0
CG A:GLU116 4.0 23.0 1.0
O A:HOH469 4.0 34.5 1.0
O A:ALA96 4.0 23.9 1.0
O A:HOH426 4.1 26.0 1.0
OE2 A:GLU115 4.1 32.7 1.0
CG A:GLU166 4.4 61.8 1.0
CG A:GLU112 4.4 26.1 1.0
CA A:GLY97 4.7 23.5 1.0
OE1 A:GLU116 4.8 25.6 1.0
CB A:GLU112 4.9 24.5 1.0
C A:ALA96 4.9 21.7 1.0
O A:HOH462 4.9 21.9 1.0

Magnesium binding site 3 out of 8 in 5qk5

Go back to Magnesium Binding Sites List in 5qk5
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 Z1267773786


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 Z1267773786 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:27.3
occ:1.00
 O B:ALA96 1.9 28.0 1.0
O B:HOH442 2.0 29.2 1.0
OE2 B:GLU116 2.0 33.5 1.0
O B:HOH415 2.1 30.8 1.0
O B:HOH440 2.1 25.7 1.0
O B:HOH441 2.2 32.3 1.0
CD B:GLU116 3.0 36.0 1.0
C B:ALA96 3.1 21.2 1.0
OE1 B:GLU116 3.3 29.4 1.0
N B:GLY97 4.0 26.5 1.0
OE2 B:GLU112 4.0 34.1 1.0
CA B:GLY97 4.1 24.1 1.0
CA B:ALA96 4.1 23.9 1.0
O B:HOH445 4.1 28.3 1.0
N B:ALA96 4.1 23.3 1.0
OE2 B:GLU166 4.1 49.2 1.0
NH2 B:ARG84 4.3 28.6 1.0
NE2 B:GLN82 4.4 36.0 1.0
CG B:GLU116 4.4 31.6 1.0
O B:HOH474 4.4 40.1 1.0
OE1 B:GLN82 4.4 34.7 1.0
O B:HOH464 4.5 38.5 0.9
CB B:ALA96 4.6 26.6 1.0
CD B:GLN82 4.8 42.8 1.0
CD B:GLU166 4.8 67.3 1.0
CD B:GLU112 4.9 35.2 1.0
MG B:MG303 4.9 75.4 1.0

Magnesium binding site 4 out of 8 in 5qk5

Go back to Magnesium Binding Sites List in 5qk5
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 Z1267773786


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 Z1267773786 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:75.4
occ:1.00
 O B:HOH419 2.5 62.1 1.0
OE2 B:GLU112 2.7 34.1 1.0
OE2 B:GLU166 2.7 49.2 1.0
OE1 B:GLU166 2.8 64.8 1.0
OE2 B:GLU115 2.9 56.2 1.0
O B:HOH407 3.1 51.7 1.0
CD B:GLU166 3.1 67.3 1.0
CB B:GLU115 3.4 36.8 1.0
CG B:GLU116 3.4 31.6 1.0
OE2 B:GLU116 3.5 33.5 1.0
CD B:GLU112 3.6 35.2 1.0
CD B:GLU115 3.9 50.4 1.0
CD B:GLU116 3.9 36.0 1.0
O B:HOH441 4.0 32.3 1.0
OE1 B:GLU112 4.0 38.8 1.0
CG B:GLU115 4.2 43.0 1.0
N B:GLU116 4.5 33.2 1.0
CG B:GLU166 4.5 63.3 1.0
O B:GLU112 4.6 27.4 1.0
C B:GLU115 4.6 36.2 1.0
CA B:GLU115 4.6 34.6 1.0
CB B:GLU116 4.8 29.3 1.0
CA B:GLU112 4.8 30.7 1.0
N B:GLY163 4.9 74.7 1.0
MG B:MG302 4.9 27.3 1.0
CG B:GLU112 4.9 34.7 1.0
CA B:GLU116 4.9 33.0 1.0
OE1 B:GLU115 5.0 63.8 1.0

Magnesium binding site 5 out of 8 in 5qk5

Go back to Magnesium Binding Sites List in 5qk5
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 Z1267773786


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 Z1267773786 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:70.0
occ:1.00
 O C:HOH430 1.8 34.7 1.0
OE2 C:GLU112 2.2 34.4 1.0
OE2 C:GLU166 2.3 78.6 1.0
O C:HOH405 2.4 50.7 1.0
O C:HOH445 2.4 51.3 1.0
OE2 C:GLU116 2.7 29.5 1.0
MG C:MG303 3.1 33.1 1.0
CD C:GLU112 3.2 41.4 1.0
CD C:GLU166 3.2 80.2 1.0
OE1 C:GLU112 3.4 46.4 1.0
OE1 C:GLU166 3.4 79.4 1.0
O C:HOH426 3.5 51.7 1.0
CD C:GLU116 3.6 32.4 1.0
O C:ALA96 3.7 28.5 1.0
O C:HOH416 3.8 33.0 1.0
CG C:GLU116 3.9 30.1 1.0
OE2 C:GLU115 4.3 45.3 1.0
CA C:GLY97 4.5 31.8 1.0
CG C:GLU112 4.6 38.0 1.0
O C:HOH455 4.6 28.6 1.0
CG C:GLU166 4.6 70.6 1.0
OE1 C:GLU116 4.7 34.7 1.0
C C:ALA96 4.7 31.9 1.0
O C:HOH420 4.9 24.6 1.0

Magnesium binding site 6 out of 8 in 5qk5

Go back to Magnesium Binding Sites List in 5qk5
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 Z1267773786


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 Z1267773786 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:33.1
occ:1.00
 OE2 C:GLU116 1.8 29.5 1.0
O C:HOH420 2.0 24.6 1.0
O C:HOH430 2.1 34.7 1.0
O C:HOH455 2.1 28.6 1.0
O C:ALA96 2.1 28.5 1.0
O C:HOH416 2.2 33.0 1.0
CD C:GLU116 2.9 32.4 1.0
MG C:MG302 3.1 70.0 1.0
C C:ALA96 3.3 31.9 1.0
OE1 C:GLU116 3.3 34.7 1.0
OE2 C:GLU166 3.4 78.6 1.0
OE2 C:GLU112 4.1 34.4 1.0
N C:GLY97 4.2 33.1 1.0
N C:ALA96 4.2 23.9 1.0
O C:HOH421 4.2 36.7 1.0
CA C:GLY97 4.2 31.8 1.0
CA C:ALA96 4.2 24.7 1.0
CG C:GLU116 4.3 30.1 1.0
NE2 C:GLN82 4.4 30.9 1.0
NH2 C:ARG84 4.4 33.8 1.0
OE1 C:GLN82 4.5 32.0 1.0
CD C:GLU166 4.6 80.2 1.0
O C:HOH464 4.7 44.8 1.0
CB C:ALA96 4.8 24.8 1.0
CD C:GLN82 4.9 35.3 1.0
CD C:GLU112 5.0 41.4 1.0
O C:HOH405 5.0 50.7 1.0

Magnesium binding site 7 out of 8 in 5qk5

Go back to Magnesium Binding Sites List in 5qk5
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 Z1267773786


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 Z1267773786 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:39.1
occ:1.00
 OE2 D:GLU116 2.0 37.0 1.0
O D:HOH410 2.0 27.7 1.0
O D:HOH403 2.1 29.5 1.0
MG D:MG302 2.2 39.6 1.0
O D:ALA96 2.5 39.9 1.0
O D:HOH424 2.5 43.1 1.0
CD D:GLU116 3.0 47.2 1.0
OE1 D:GLU116 3.3 43.5 1.0
OE2 D:GLU112 3.6 52.4 1.0
C D:ALA96 3.6 43.6 1.0
OE2 D:GLU166 3.8 90.2 1.0
NE2 D:GLN82 4.0 39.6 1.0
NH2 D:ARG84 4.2 46.8 1.0
OE1 D:GLN82 4.3 47.2 1.0
CG D:GLU116 4.3 44.3 1.0
N D:ALA96 4.3 41.9 1.0
CA D:GLY97 4.5 41.8 1.0
CA D:ALA96 4.5 44.0 1.0
N D:GLY97 4.5 39.4 1.0
CD D:GLU112 4.6 50.0 1.0
CD D:GLN82 4.6 48.6 1.0
O D:HOH413 4.7 47.9 1.0
O D:HOH402 4.7 41.0 1.0
CG D:GLU112 4.8 50.5 1.0
CD D:GLU166 4.8 87.7 1.0
CB D:ALA96 5.0 45.7 1.0

Magnesium binding site 8 out of 8 in 5qk5

Go back to Magnesium Binding Sites List in 5qk5
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 Z1267773786


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 Z1267773786 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:39.6
occ:1.00
 O D:HOH424 1.7 43.1 1.0
OE2 D:GLU112 2.1 52.4 1.0
MG D:MG301 2.2 39.1 1.0
O D:HOH402 2.6 41.0 1.0
O D:ALA96 2.8 39.9 1.0
OE2 D:GLU116 2.9 37.0 1.0
O D:HOH410 2.9 27.7 1.0
OE2 D:GLU166 3.0 90.2 1.0
CD D:GLU112 3.2 50.0 1.0
CA D:GLY97 3.5 41.8 1.0
O D:HOH413 3.7 47.9 1.0
C D:ALA96 3.8 43.6 1.0
OE1 D:GLU112 3.9 49.5 1.0
CD D:GLU116 4.0 47.2 1.0
CG D:GLU112 4.1 50.5 1.0
N D:GLY97 4.1 39.4 1.0
O D:HOH403 4.2 29.5 1.0
CD D:GLU166 4.2 87.7 1.0
OE1 D:GLU116 4.7 43.5 1.0
C D:GLY97 4.7 44.4 1.0
CG D:GLU116 4.8 44.3 1.0
N D:LEU98 4.9 43.0 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 Sep 30 02:29:47 2024

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