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Magnesium in PDB 5qk4: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z44590919

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z44590919

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 Z44590919:
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 Z44590919, PDB code: 5qk4 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) 78.20 / 1.62
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.409, 59.931, 80.076, 79.27, 81.33, 75.46
R / Rfree (%) 22.3 / 25.5

Other elements in 5qk4:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z44590919 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 Z44590919 (pdb code 5qk4). 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 Z44590919, PDB code: 5qk4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qk4

Go back to Magnesium Binding Sites List in 5qk4
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 Z44590919


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 Z44590919 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:27.1
occ:1.00
 OE2 A:GLU116 2.1 22.5 1.0
O A:HOH462 2.1 22.9 1.0
O A:HOH421 2.1 21.0 1.0
O A:ALA96 2.1 22.3 1.0
O A:HOH464 2.2 22.0 1.0
O A:HOH428 2.2 25.1 1.0
CD A:GLU116 3.1 25.5 1.0
C A:ALA96 3.3 20.9 1.0
OE1 A:GLU116 3.4 23.3 1.0
MG A:MG302 3.5 58.1 1.0
OE2 A:GLU166 4.0 65.3 1.0
O A:HOH446 4.1 27.8 1.0
OE2 A:GLU112 4.1 32.9 1.0
CA A:GLY97 4.1 21.6 1.0
N A:GLY97 4.1 21.4 1.0
N A:ALA96 4.2 18.9 1.0
CA A:ALA96 4.2 19.4 1.0
NH2 A:ARG84 4.3 23.0 1.0
CG A:GLU116 4.4 23.2 1.0
O A:HOH416 4.4 19.1 1.0
NE2 A:GLN82 4.4 30.1 1.0
O A:HOH479 4.5 27.0 1.0
OE1 A:GLN82 4.5 26.7 1.0
O A:HOH472 4.6 32.1 1.0
CB A:ALA96 4.7 17.4 1.0
CD A:GLN82 4.8 36.4 1.0
CD A:GLU112 4.9 30.2 1.0

Magnesium binding site 2 out of 8 in 5qk4

Go back to Magnesium Binding Sites List in 5qk4
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 Z44590919


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 Z44590919 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:58.1
occ:1.00
 O A:HOH408 1.8 40.9 1.0
OE2 A:GLU112 2.2 32.9 1.0
O A:HOH462 2.2 22.9 1.0
OE2 A:GLU166 2.5 65.3 1.0
OE2 A:GLU116 2.7 22.5 1.0
OE1 A:GLU166 3.1 81.7 1.0
CD A:GLU166 3.1 79.5 1.0
CD A:GLU112 3.2 30.2 1.0
OE1 A:GLU112 3.4 29.9 1.0
MG A:MG301 3.5 27.1 1.0
CD A:GLU116 3.6 25.5 1.0
CG A:GLU116 3.8 23.2 1.0
O A:HOH402 3.8 44.8 1.0
OE2 A:GLU115 4.0 34.3 1.0
O A:HOH428 4.1 25.1 1.0
O A:ALA96 4.2 22.3 1.0
CG A:GLU166 4.5 71.6 1.0
O A:HOH472 4.5 32.1 1.0
CG A:GLU112 4.6 27.7 1.0
OE1 A:GLU116 4.8 23.3 1.0
CA A:GLY97 4.9 21.6 1.0
CB A:GLU112 5.0 25.3 1.0
CB A:GLU115 5.0 26.7 1.0

Magnesium binding site 3 out of 8 in 5qk4

Go back to Magnesium Binding Sites List in 5qk4
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 Z44590919


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 Z44590919 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:28.0
occ:1.00
 O B:ALA96 1.9 24.3 1.0
O B:HOH412 2.0 27.1 1.0
O B:HOH402 2.1 29.1 1.0
OE2 B:GLU116 2.1 33.2 1.0
O B:HOH440 2.1 24.5 1.0
O B:HOH432 2.2 27.6 1.0
CD B:GLU116 3.1 32.3 1.0
C B:ALA96 3.2 21.2 1.0
OE1 B:GLU116 3.4 27.9 1.0
OE2 B:GLU166 3.9 57.7 1.0
OE2 B:GLU112 4.1 35.8 1.0
NE2 B:GLN82 4.1 36.6 1.0
N B:GLY97 4.1 25.4 1.0
CA B:ALA96 4.2 22.5 1.0
CA B:GLY97 4.2 23.7 1.0
O B:HOH429 4.2 24.5 1.0
N B:ALA96 4.2 21.8 1.0
O B:HOH439 4.2 33.7 0.8
NH2 B:ARG84 4.3 28.0 1.0
O B:HOH468 4.4 36.9 1.0
OE1 B:GLN82 4.4 32.5 1.0
CG B:GLU116 4.4 29.8 1.0
O B:HOH460 4.5 34.3 0.8
CD B:GLU166 4.6 74.7 1.0
CB B:ALA96 4.7 25.5 1.0
CD B:GLN82 4.7 42.7 1.0
MG B:MG304 4.7 69.2 1.0
CD B:GLU112 4.9 33.6 1.0
O B:HOH428 4.9 50.8 1.0
OE1 B:GLU166 5.0 76.1 1.0

Magnesium binding site 4 out of 8 in 5qk4

Go back to Magnesium Binding Sites List in 5qk4
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 Z44590919


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 Z44590919 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:69.2
occ:1.00
 OE2 B:GLU166 2.6 57.7 1.0
OE2 B:GLU112 2.7 35.8 1.0
O B:HOH418 2.7 68.7 1.0
O B:HOH428 2.8 50.8 1.0
OE2 B:GLU115 2.8 45.0 1.0
OE1 B:GLU166 3.1 76.1 1.0
CD B:GLU166 3.2 74.7 1.0
OE2 B:GLU116 3.3 33.2 1.0
CG B:GLU116 3.4 29.8 1.0
CB B:GLU115 3.7 31.6 1.0
CD B:GLU112 3.7 33.6 1.0
O B:HOH432 3.7 27.6 1.0
CD B:GLU116 3.8 32.3 1.0
CD B:GLU115 4.0 39.5 1.0
OE1 B:GLU112 4.1 32.7 1.0
CG B:GLU115 4.4 37.9 1.0
N B:GLU116 4.6 33.0 1.0
CG B:GLU166 4.7 64.7 1.0
MG B:MG303 4.7 28.0 1.0
O B:GLU112 4.7 27.8 1.0
C B:GLU115 4.7 31.4 1.0
CB B:GLU116 4.8 27.9 1.0
CA B:GLU115 4.8 29.8 1.0
CA B:GLU112 4.9 27.7 1.0
CG B:GLU112 5.0 31.7 1.0
CA B:GLU116 5.0 28.6 1.0

Magnesium binding site 5 out of 8 in 5qk4

Go back to Magnesium Binding Sites List in 5qk4
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 Z44590919


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 Z44590919 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:43.7
occ:1.00
 MG C:MG303 2.2 31.5 1.0
O C:HOH451 2.8 43.6 1.0
OE2 C:GLU116 2.9 29.4 1.0
O C:ALA96 2.9 26.0 1.0
O C:HOH458 3.1 26.4 1.0
O C:HOH417 3.1 33.1 1.0
OE2 C:GLU112 3.2 33.9 1.0
OE2 C:GLU166 3.2 63.3 0.9
O C:HOH449 3.3 56.0 1.0
O C:HOH467 3.4 58.4 1.0
CA C:GLY97 3.5 30.6 1.0
CD C:GLU112 3.8 34.8 1.0
O C:HOH410 3.9 43.7 1.0
OE1 C:GLU112 3.9 41.7 1.0
C C:ALA96 3.9 27.4 1.0
CD C:GLU166 3.9 74.0 0.9
CD C:GLU116 4.2 30.5 1.0
OE1 C:GLU166 4.2 76.2 0.9
N C:GLY97 4.2 28.3 1.0
O C:HOH424 4.2 27.1 1.0
C C:GLY97 4.8 31.6 1.0
O C:HOH465 4.9 39.3 0.9
OE1 C:GLU116 5.0 34.2 1.0
N C:LEU98 5.0 35.5 1.0

Magnesium binding site 6 out of 8 in 5qk4

Go back to Magnesium Binding Sites List in 5qk4
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 Z44590919


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 Z44590919 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:31.5
occ:1.00
 OE2 C:GLU116 1.9 29.4 1.0
O C:HOH424 2.1 27.1 1.0
O C:HOH458 2.1 26.4 1.0
MG C:MG302 2.2 43.7 1.0
O C:ALA96 2.2 26.0 1.0
O C:HOH417 2.2 33.1 1.0
CD C:GLU116 3.0 30.5 1.0
C C:ALA96 3.3 27.4 1.0
OE1 C:GLU116 3.4 34.2 1.0
OE2 C:GLU166 3.6 63.3 0.9
OE2 C:GLU112 4.1 33.9 1.0
N C:ALA96 4.2 23.1 1.0
N C:GLY97 4.2 28.3 1.0
CA C:GLY97 4.2 30.6 1.0
O C:HOH422 4.2 25.2 0.9
CA C:ALA96 4.3 23.1 1.0
NE2 C:GLN82 4.3 34.9 1.0
NH2 C:ARG84 4.4 29.3 1.0
CG C:GLU116 4.4 30.1 1.0
OE1 C:GLN82 4.4 30.7 1.0
O C:HOH451 4.5 43.6 1.0
O C:HOH465 4.5 39.3 0.9
CD C:GLU166 4.6 74.0 0.9
CB C:ALA96 4.7 22.8 1.0
CD C:GLN82 4.8 36.5 1.0
O C:HOH410 4.9 43.7 1.0
CD C:GLU112 4.9 34.8 1.0

Magnesium binding site 7 out of 8 in 5qk4

Go back to Magnesium Binding Sites List in 5qk4
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 Z44590919


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 Z44590919 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:28.9
occ:1.00
 O D:HOH406 1.8 32.8 1.0
OE2 D:GLU116 1.9 32.0 1.0
O D:HOH413 2.0 29.3 1.0
O D:HOH403 2.1 30.0 1.0
O D:ALA96 2.1 30.9 1.0
MG D:MG302 2.2 40.4 1.0
O D:HOH430 2.8 47.4 1.0
CD D:GLU116 2.9 42.5 1.0
OE1 D:GLU116 3.2 39.8 1.0
C D:ALA96 3.3 32.3 1.0
OE2 D:GLU112 3.7 54.9 1.0
O D:HOH410 3.9 53.7 1.0
N D:ALA96 4.1 35.1 1.0
OE2 D:GLU166 4.1 86.3 1.0
N D:GLY97 4.2 29.8 1.0
CG D:GLU116 4.2 42.4 1.0
CA D:GLY97 4.2 31.8 1.0
CA D:ALA96 4.2 34.0 1.0
NH2 D:ARG84 4.3 35.3 1.0
NE2 D:GLN82 4.4 38.2 1.0
O D:HOH405 4.5 34.4 1.0
OE1 D:GLN82 4.5 39.4 1.0
CD D:GLU112 4.5 50.9 1.0
O D:HOH423 4.6 38.0 1.0
CG D:GLU112 4.6 53.2 1.0
CB D:ALA96 4.7 32.9 1.0
O D:HOH402 4.7 44.8 1.0
CD D:GLU166 4.9 86.9 1.0
CD D:GLN82 4.9 41.0 1.0

Magnesium binding site 8 out of 8 in 5qk4

Go back to Magnesium Binding Sites List in 5qk4
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 Z44590919


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 Z44590919 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:40.4
occ:1.00
 O D:HOH430 1.9 47.4 1.0
MG D:MG301 2.2 28.9 1.0
OE2 D:GLU112 2.4 54.9 1.0
O D:HOH402 2.7 44.8 1.0
O D:HOH406 2.8 32.8 1.0
OE2 D:GLU116 2.8 32.0 1.0
OE2 D:GLU166 2.9 86.3 1.0
O D:HOH413 2.9 29.3 1.0
O D:ALA96 3.0 30.9 1.0
O D:HOH410 3.1 53.7 1.0
CD D:GLU112 3.4 50.9 1.0
CA D:GLY97 3.6 31.8 1.0
C D:ALA96 3.9 32.3 1.0
CD D:GLU166 4.0 86.9 1.0
CD D:GLU116 4.0 42.5 1.0
OE1 D:GLU112 4.1 50.6 1.0
CG D:GLU112 4.2 53.2 1.0
N D:GLY97 4.2 29.8 1.0
O D:HOH403 4.2 30.0 1.0
OE1 D:GLU166 4.5 91.5 1.0
O D:HOH423 4.5 38.0 1.0
OE1 D:GLU116 4.8 39.8 1.0
C D:GLY97 4.8 33.5 1.0
CG D:GLU116 4.9 42.4 1.0
N D:LEU98 4.9 37.7 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 02:27:06 2024

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