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Magnesium in PDB 5qk6: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1343633025

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1343633025

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 Z1343633025:
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 Z1343633025, PDB code: 5qk6 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) 78.45 / 1.51
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.260, 59.800, 80.310, 79.26, 81.50, 75.67
R / Rfree (%) 22.7 / 25.5

Other elements in 5qk6:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1343633025 also contains other interesting chemical elements:

Fluorine (F) 1 atom
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 Z1343633025 (pdb code 5qk6). 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 Z1343633025, PDB code: 5qk6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qk6

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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 Z1343633025


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 Z1343633025 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:23.9
occ:1.00
 OE2 A:GLU116 2.0 22.4 1.0
O A:HOH418 2.1 22.3 1.0
O A:HOH435 2.1 24.0 1.0
O A:HOH450 2.1 21.3 1.0
O A:ALA96 2.1 22.1 1.0
O A:HOH458 2.2 20.5 1.0
CD A:GLU116 3.1 22.1 1.0
C A:ALA96 3.3 21.0 1.0
MG A:MG302 3.3 55.4 1.0
OE1 A:GLU116 3.4 23.4 1.0
OE2 A:GLU166 3.9 48.2 1.0
O A:HOH469 4.0 46.6 1.0
OE2 A:GLU112 4.1 29.0 1.0
CA A:GLY97 4.1 20.4 1.0
N A:GLY97 4.2 20.7 1.0
N A:ALA96 4.2 18.1 1.0
CA A:ALA96 4.2 19.6 1.0
NH2 A:ARG84 4.2 21.8 1.0
O A:HOH452 4.3 30.0 1.0
O A:HOH422 4.3 20.1 1.0
NE2 A:GLN82 4.4 27.5 1.0
OE1 A:GLN82 4.4 26.0 1.0
CG A:GLU116 4.4 22.6 1.0
O A:HOH471 4.4 26.8 1.0
O A:HOH463 4.6 33.3 1.0
CB A:ALA96 4.7 18.1 1.0
CD A:GLN82 4.8 31.0 1.0
CD A:GLU112 4.9 26.9 1.0

Magnesium binding site 2 out of 8 in 5qk6

Go back to Magnesium Binding Sites List in 5qk6
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 Z1343633025


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 Z1343633025 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:55.4
occ:1.00
 O A:HOH405 1.8 36.4 1.0
O A:HOH450 2.1 21.3 1.0
OE2 A:GLU112 2.1 29.0 1.0
O A:HOH428 2.4 46.2 1.0
OE2 A:GLU166 2.5 48.2 1.0
OE2 A:GLU116 2.5 22.4 1.0
CD A:GLU166 3.1 66.7 1.0
CD A:GLU112 3.1 26.9 1.0
OE1 A:GLU166 3.3 60.9 1.0
MG A:MG301 3.3 23.9 1.0
OE1 A:GLU112 3.4 29.8 1.0
CD A:GLU116 3.5 22.1 1.0
CG A:GLU116 3.7 22.6 1.0
O A:HOH469 3.9 46.6 1.0
O A:HOH435 3.9 24.0 1.0
O A:ALA96 4.0 22.1 1.0
OE2 A:GLU115 4.3 34.4 1.0
CG A:GLU166 4.3 59.1 1.0
CG A:GLU112 4.5 26.0 1.0
O A:HOH463 4.6 33.3 1.0
OE1 A:GLU116 4.6 23.4 1.0
CA A:GLY97 4.8 20.4 1.0
CB A:GLU112 4.9 24.4 1.0
C A:ALA96 4.9 21.0 1.0
O A:HOH458 5.0 20.5 1.0

Magnesium binding site 3 out of 8 in 5qk6

Go back to Magnesium Binding Sites List in 5qk6
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 Z1343633025


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 Z1343633025 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:27.0
occ:1.00
 O B:ALA96 2.0 24.6 1.0
OE2 B:GLU116 2.1 31.1 1.0
O B:HOH432 2.1 25.3 1.0
O B:HOH413 2.1 26.8 1.0
O B:HOH445 2.2 27.7 1.0
O B:HOH412 2.2 26.6 1.0
CD B:GLU116 3.1 30.4 1.0
C B:ALA96 3.2 22.3 1.0
OE1 B:GLU116 3.4 26.9 1.0
OE2 B:GLU166 3.8 49.8 1.0
MG B:MG304 3.9 66.5 1.0
N B:GLY97 4.1 25.5 1.0
CA B:GLY97 4.1 23.2 1.0
OE2 B:GLU112 4.2 32.9 1.0
N B:ALA96 4.2 22.4 1.0
CA B:ALA96 4.2 22.9 1.0
NH2 B:ARG84 4.2 26.2 1.0
O B:HOH424 4.2 24.9 1.0
NE2 B:GLN82 4.4 32.4 1.0
O B:HOH472 4.4 39.6 1.0
OE1 B:GLN82 4.4 31.0 1.0
CG B:GLU116 4.4 29.4 1.0
O B:HOH469 4.4 38.7 0.9
O B:HOH464 4.6 33.7 0.9
CB B:ALA96 4.7 25.7 1.0
CD B:GLU166 4.7 65.6 1.0
CD B:GLN82 4.8 39.3 1.0
CD B:GLU112 5.0 32.8 1.0

Magnesium binding site 4 out of 8 in 5qk6

Go back to Magnesium Binding Sites List in 5qk6
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 Z1343633025


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 Z1343633025 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:66.5
occ:1.00
 O B:HOH404 1.7 70.1 1.0
OE2 B:GLU112 2.2 32.9 1.0
OE2 B:GLU166 2.3 49.8 1.0
OE2 B:GLU116 2.7 31.1 1.0
O B:HOH440 2.8 50.6 1.0
O B:HOH445 2.9 27.7 1.0
CD B:GLU166 3.1 65.6 1.0
OE1 B:GLU166 3.2 69.5 1.0
CD B:GLU112 3.3 32.8 1.0
CG B:GLU116 3.4 29.4 1.0
OE2 B:GLU115 3.4 40.9 1.0
CD B:GLU116 3.4 30.4 1.0
OE1 B:GLU112 3.6 34.7 1.0
MG B:MG303 3.9 27.0 1.0
CB B:GLU115 4.4 34.1 1.0
O B:ALA96 4.4 24.6 1.0
O B:HOH412 4.5 26.6 1.0
CG B:GLU166 4.6 59.6 1.0
CD B:GLU115 4.6 42.1 1.0
CG B:GLU112 4.6 30.1 1.0
OE1 B:GLU116 4.6 26.9 1.0
CB B:GLU116 4.8 26.2 1.0
O B:GLU112 4.9 28.1 1.0
CB B:GLU112 5.0 30.0 1.0

Magnesium binding site 5 out of 8 in 5qk6

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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 Z1343633025


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 Z1343633025 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:41.5
occ:1.00
 MG C:MG303 2.2 31.0 1.0
O C:HOH402 2.4 41.2 1.0
OE2 C:GLU116 2.9 31.8 1.0
O C:ALA96 2.9 27.1 1.0
OE2 C:GLU166 3.0 65.3 1.0
O C:HOH427 3.0 30.4 1.0
O C:HOH451 3.0 45.2 1.0
O C:HOH456 3.1 27.6 1.0
OE2 C:GLU112 3.1 36.0 1.0
O C:HOH408 3.2 53.8 1.0
O C:HOH434 3.5 51.0 1.0
CA C:GLY97 3.6 29.3 1.0
CD C:GLU112 3.8 36.0 1.0
OE1 C:GLU112 3.9 42.2 1.0
C C:ALA96 4.0 29.9 1.0
CD C:GLU116 4.1 30.9 1.0
CD C:GLU166 4.1 67.0 1.0
O C:HOH429 4.2 26.0 1.0
N C:GLY97 4.3 27.3 1.0
OE1 C:GLU166 4.7 74.5 1.0
OE1 C:GLU116 4.9 33.4 1.0
O C:HOH457 4.9 43.0 1.0
C C:GLY97 4.9 30.1 1.0
CG C:GLU116 5.0 28.6 1.0
O C:HOH466 5.0 37.2 1.0

Magnesium binding site 6 out of 8 in 5qk6

Go back to Magnesium Binding Sites List in 5qk6
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 Z1343633025


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 Z1343633025 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:31.0
occ:1.00
 OE2 C:GLU116 2.0 31.8 1.0
O C:HOH429 2.1 26.0 1.0
O C:HOH427 2.1 30.4 1.0
O C:HOH456 2.2 27.6 1.0
MG C:MG302 2.2 41.5 1.0
O C:ALA96 2.2 27.1 1.0
CD C:GLU116 3.1 30.9 1.0
OE1 C:GLU116 3.4 33.4 1.0
C C:ALA96 3.4 29.9 1.0
O C:HOH402 3.5 41.2 1.0
OE2 C:GLU112 4.1 36.0 1.0
N C:ALA96 4.1 23.1 1.0
O C:HOH411 4.2 25.1 1.0
CA C:ALA96 4.2 22.7 1.0
CA C:GLY97 4.3 29.3 1.0
N C:GLY97 4.3 27.3 1.0
OE2 C:GLU166 4.3 65.3 1.0
NH2 C:ARG84 4.3 29.1 1.0
NE2 C:GLN82 4.4 33.6 1.0
OE1 C:GLN82 4.4 31.5 1.0
CG C:GLU116 4.4 28.6 1.0
O C:HOH466 4.6 37.2 1.0
O C:HOH451 4.7 45.2 1.0
CB C:ALA96 4.7 24.5 1.0
CD C:GLN82 4.8 37.6 1.0
O C:HOH457 5.0 43.0 1.0
CD C:GLU112 5.0 36.0 1.0

Magnesium binding site 7 out of 8 in 5qk6

Go back to Magnesium Binding Sites List in 5qk6
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 Z1343633025


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 Z1343633025 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:28.0
occ:1.00
 O D:HOH427 2.0 29.9 1.0
O D:HOH428 2.0 27.4 1.0
OE2 D:GLU116 2.0 29.4 1.0
MG D:MG302 2.1 37.4 1.0
O D:HOH404 2.1 25.8 1.0
O D:ALA96 2.1 27.8 1.0
O D:HOH433 3.0 64.3 1.0
CD D:GLU116 3.1 33.5 1.0
C D:ALA96 3.3 28.1 1.0
OE1 D:GLU116 3.4 29.7 1.0
OE2 D:GLU166 3.8 81.6 1.0
OE2 D:GLU112 3.9 50.0 1.0
CA D:GLY97 4.1 32.4 1.0
N D:ALA96 4.2 26.5 1.0
N D:GLY97 4.2 28.5 1.0
CA D:ALA96 4.2 25.4 1.0
NH2 D:ARG84 4.3 28.1 1.0
O D:HOH410 4.4 27.2 1.0
O D:HOH430 4.4 32.7 1.0
CG D:GLU116 4.4 29.2 1.0
OE1 D:GLN82 4.4 31.0 1.0
NE2 D:GLN82 4.5 32.0 1.0
O D:HOH438 4.5 33.0 1.0
CB D:ALA96 4.6 27.0 1.0
O D:HOH402 4.6 51.0 1.0
CD D:GLU112 4.6 47.6 1.0
CG D:GLU112 4.7 50.0 1.0
O D:HOH421 4.8 62.1 1.0
CD D:GLN82 4.9 35.9 1.0
CD D:GLU166 5.0 81.7 1.0

Magnesium binding site 8 out of 8 in 5qk6

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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 Z1343633025


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 Z1343633025 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:37.4
occ:1.00
 O D:HOH433 1.9 64.3 1.0
MG D:MG301 2.1 28.0 1.0
OE2 D:GLU166 2.7 81.6 1.0
O D:HOH427 2.8 29.9 1.0
OE2 D:GLU112 2.8 50.0 1.0
OE2 D:GLU116 2.8 29.4 1.0
O D:HOH421 3.0 62.1 1.0
O D:ALA96 3.0 27.8 1.0
O D:HOH428 3.0 27.4 1.0
O D:HOH402 3.5 51.0 1.0
CA D:GLY97 3.6 32.4 1.0
CD D:GLU112 3.7 47.6 1.0
CD D:GLU166 3.9 81.7 1.0
C D:ALA96 4.0 28.1 1.0
CD D:GLU116 4.0 33.5 1.0
O D:HOH404 4.1 25.8 1.0
O D:HOH430 4.3 32.7 1.0
N D:GLY97 4.3 28.5 1.0
OE1 D:GLU112 4.3 54.1 1.0
CG D:GLU112 4.5 50.0 1.0
OE1 D:GLU166 4.7 84.8 1.0
OE1 D:GLU116 4.8 29.7 1.0
C D:GLY97 4.9 30.3 1.0
O D:HOH438 4.9 33.0 1.0
CG D:GLU116 4.9 29.2 1.0
CG D:GLU166 4.9 69.8 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 Dec 14 21:07:34 2020

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