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Magnesium in PDB 5qk7: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1918536193

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1918536193

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 Z1918536193:
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 Z1918536193, PDB code: 5qk7 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) 78.68 / 1.66
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.577, 59.461, 80.404, 79.39, 82.31, 76.19
R / Rfree (%) 21.7 / 25.5

Other elements in 5qk7:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1918536193 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 Z1918536193 (pdb code 5qk7). 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 Z1918536193, PDB code: 5qk7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qk7

Go back to Magnesium Binding Sites List in 5qk7
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 Z1918536193


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 Z1918536193 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:35.5
occ:1.00
 O A:ALA96 2.0 27.7 1.0
O A:HOH436 2.1 31.5 1.0
OE2 A:GLU116 2.1 39.7 1.0
O A:HOH449 2.2 29.7 1.0
O A:HOH413 2.2 31.6 1.0
O A:HOH425 2.3 34.8 1.0
MG A:MG302 2.9 79.5 1.0
C A:ALA96 3.2 25.9 1.0
CD A:GLU116 3.2 37.0 1.0
OE1 A:GLU116 3.6 33.4 1.0
N A:GLY97 4.1 29.8 1.0
OE2 A:GLU112 4.1 37.6 1.0
CA A:GLY97 4.1 29.1 1.0
CA A:ALA96 4.2 24.6 1.0
N A:ALA96 4.2 25.5 1.0
NH2 A:ARG84 4.2 26.5 1.0
O A:HOH450 4.3 61.7 1.0
O A:HOH421 4.3 27.2 1.0
OE1 A:GLN82 4.4 34.5 1.0
O A:HOH462 4.4 46.2 1.0
O A:HOH464 4.4 39.8 1.0
NE2 A:GLN82 4.4 32.8 1.0
CG A:GLU116 4.5 35.5 1.0
CB A:ALA96 4.7 22.4 1.0
O A:HOH458 4.7 31.4 0.8
CD A:GLN82 4.8 38.5 1.0
O A:HOH401 4.8 56.8 1.0
CD A:GLU112 4.8 34.2 1.0

Magnesium binding site 2 out of 8 in 5qk7

Go back to Magnesium Binding Sites List in 5qk7
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 Z1918536193


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 Z1918536193 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:79.5
occ:1.00
 O A:HOH436 2.2 31.5 1.0
OE2 A:GLU116 2.2 39.7 1.0
O A:HOH401 2.4 56.8 1.0
MG A:MG301 2.9 35.5 1.0
O A:HOH425 2.9 34.8 1.0
OE1 A:GLU166 3.2 83.4 1.0
CD A:GLU116 3.2 37.0 1.0
OE2 A:GLU166 3.2 86.4 1.0
CD A:GLU166 3.2 87.5 1.0
OE2 A:GLU112 3.3 37.6 1.0
O A:HOH450 3.4 61.7 1.0
CG A:GLU116 3.6 35.5 1.0
O A:HOH415 3.8 52.0 1.0
O A:ALA96 4.1 27.7 1.0
CG A:GLU166 4.2 83.4 1.0
CD A:GLU112 4.2 34.2 1.0
OE1 A:GLU116 4.3 33.4 1.0
OE1 A:GLU112 4.3 42.3 1.0
O A:HOH413 4.4 31.6 1.0
CB A:GLU166 4.7 82.3 1.0
O A:HOH449 4.7 29.7 1.0
O A:HOH462 4.8 46.2 1.0

Magnesium binding site 3 out of 8 in 5qk7

Go back to Magnesium Binding Sites List in 5qk7
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 Z1918536193


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 Z1918536193 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:39.5
occ:1.00
 O B:HOH419 2.1 34.6 1.0
O B:ALA96 2.1 35.1 1.0
OE2 B:GLU116 2.1 43.2 1.0
O B:HOH413 2.1 35.1 1.0
O B:HOH435 2.2 34.7 1.0
O B:HOH459 2.3 34.8 1.0
CD B:GLU116 3.2 40.0 1.0
C B:ALA96 3.2 33.3 1.0
OE1 B:GLU116 3.5 39.0 1.0
OE2 B:GLU166 4.0 85.4 1.0
O B:HOH430 4.1 37.8 1.0
N B:GLY97 4.1 31.4 1.0
NH2 B:ARG84 4.2 31.0 1.0
CA B:GLY97 4.2 33.6 1.0
CA B:ALA96 4.2 31.5 1.0
O B:HOH468 4.2 45.9 1.0
N B:ALA96 4.2 29.4 1.0
NE2 B:GLN82 4.3 36.0 1.0
OE2 B:GLU112 4.4 42.4 1.0
OE1 B:GLN82 4.4 40.9 1.0
CG B:GLU116 4.5 39.6 1.0
O B:HOH471 4.5 49.2 1.0
O B:HOH402 4.6 55.4 1.0
CB B:ALA96 4.6 30.7 1.0
O B:HOH456 4.7 35.3 1.0
CD B:GLN82 4.7 43.0 1.0

Magnesium binding site 4 out of 8 in 5qk7

Go back to Magnesium Binding Sites List in 5qk7
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 Z1918536193


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 Z1918536193 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:83.8
occ:1.00
 O B:HOH423 1.8 59.0 1.0
OE1 B:GLU166 3.0 83.0 1.0
O B:HOH402 3.3 55.4 1.0
O B:HOH435 3.4 34.7 1.0
OE2 B:GLU166 3.6 85.4 1.0
CD B:GLU166 3.6 90.4 1.0
O B:HOH468 3.7 45.9 1.0
C B:K3P304 3.8 59.8 1.0
OE1 B:GLU112 3.8 42.0 1.0
OE2 B:GLU112 4.4 42.4 1.0
OE2 B:GLU115 4.5 56.5 1.0
CD B:GLU112 4.5 41.4 1.0
CG B:GLU166 4.9 81.3 1.0

Magnesium binding site 5 out of 8 in 5qk7

Go back to Magnesium Binding Sites List in 5qk7
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 Z1918536193


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 Z1918536193 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:75.6
occ:1.00
 O C:HOH424 1.7 45.4 1.0
OE2 C:GLU112 2.3 40.6 1.0
O C:HOH452 2.3 58.3 1.0
OE1 C:GLU112 2.9 52.0 1.0
CD C:GLU112 2.9 47.7 1.0
O C:HOH427 3.0 63.9 1.0
OE2 C:GLU166 3.0 91.6 1.0
OE2 C:GLU116 3.2 38.8 1.0
MG C:MG303 3.2 39.5 1.0
O C:ALA96 3.4 34.5 1.0
O C:HOH468 3.6 61.9 1.0
CA C:GLY97 3.8 36.7 1.0
CD C:GLU166 4.0 95.2 1.0
O C:HOH411 4.1 43.5 1.0
OE1 C:GLU166 4.1 90.5 1.0
CD C:GLU116 4.3 36.0 1.0
C C:ALA96 4.3 32.8 1.0
O C:HOH448 4.3 30.6 1.0
CG C:GLU112 4.3 41.4 1.0
N C:GLY97 4.5 33.3 1.0
CG C:GLU116 4.7 34.3 1.0
OE2 C:GLU115 4.7 49.2 1.0
C C:GLY97 5.0 37.3 1.0

Magnesium binding site 6 out of 8 in 5qk7

Go back to Magnesium Binding Sites List in 5qk7
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 Z1918536193


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 Z1918536193 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:39.5
occ:1.00
 O C:HOH448 2.0 30.6 1.0
O C:HOH424 2.0 45.4 1.0
O C:HOH415 2.0 32.0 1.0
OE2 C:GLU116 2.1 38.8 1.0
O C:HOH411 2.2 43.5 1.0
O C:ALA96 2.2 34.5 1.0
MG C:MG302 3.2 75.6 1.0
CD C:GLU116 3.3 36.0 1.0
C C:ALA96 3.4 32.8 1.0
OE1 C:GLU116 3.7 49.5 1.0
OE2 C:GLU166 4.1 91.6 1.0
O C:HOH408 4.2 33.8 0.9
N C:ALA96 4.2 29.5 1.0
NE2 C:GLN82 4.2 35.9 1.0
N C:GLY97 4.2 33.3 1.0
CA C:GLY97 4.2 36.7 1.0
CA C:ALA96 4.2 29.2 1.0
NH2 C:ARG84 4.3 32.6 1.0
OE1 C:GLN82 4.3 42.2 1.0
OE2 C:GLU112 4.3 40.6 1.0
CG C:GLU116 4.6 34.3 1.0
CB C:ALA96 4.6 32.7 1.0
CD C:GLN82 4.7 49.3 1.0
O C:HOH458 5.0 36.8 1.0

Magnesium binding site 7 out of 8 in 5qk7

Go back to Magnesium Binding Sites List in 5qk7
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 Z1918536193


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 Z1918536193 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:41.0
occ:1.00
 O D:HOH426 2.1 29.0 1.0
O D:HOH423 2.2 34.5 1.0
OE2 D:GLU116 2.2 35.0 1.0
O D:ALA96 2.2 30.5 1.0
MG D:MG302 2.4 43.0 1.0
CD D:GLU116 3.3 41.0 1.0
C D:ALA96 3.4 29.9 1.0
OE1 D:GLU116 3.7 44.2 1.0
OE2 D:GLU112 4.1 51.2 1.0
NH2 D:ARG84 4.1 32.8 1.0
NE2 D:GLN82 4.2 36.9 1.0
CA D:GLY97 4.3 33.7 1.0
N D:GLY97 4.3 31.9 1.0
N D:ALA96 4.3 31.1 1.0
OE1 D:GLN82 4.3 32.8 1.0
CA D:ALA96 4.4 30.6 1.0
O D:HOH409 4.4 25.2 0.8
O D:HOH427 4.4 33.9 0.8
CG D:GLU116 4.6 37.5 1.0
O D:HOH430 4.6 44.6 1.0
CB D:ALA96 4.7 31.5 1.0
CD D:GLN82 4.7 40.2 1.0
CD D:GLU112 4.8 49.4 1.0
NH1 D:ARG84 5.0 31.0 1.0
CZ D:ARG84 5.0 32.3 1.0

Magnesium binding site 8 out of 8 in 5qk7

Go back to Magnesium Binding Sites List in 5qk7
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 Z1918536193


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 Z1918536193 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:43.0
occ:1.00
 MG D:MG301 2.4 41.0 1.0
OE2 D:GLU112 2.8 51.2 1.0
OE2 D:GLU116 3.0 35.0 1.0
O D:ALA96 3.1 30.5 1.0
O D:HOH430 3.1 44.6 1.0
O D:HOH426 3.4 29.0 1.0
O D:HOH428 3.4 48.1 1.0
CA D:GLY97 3.6 33.7 1.0
CD D:GLU112 3.6 49.4 1.0
O D:HOH405 3.7 62.3 1.0
C D:ALA96 4.1 29.9 1.0
OE1 D:GLU112 4.2 52.8 1.0
CD D:GLU116 4.2 41.0 1.0
N D:GLY97 4.3 31.9 1.0
OE2 D:GLU166 4.5 0.4 1.0
O D:HOH423 4.5 34.5 1.0
CG D:GLU112 4.6 56.5 1.0
O D:HOH427 4.7 33.9 0.8
C D:GLY97 4.8 33.7 1.0
CD D:GLU166 4.9 90.6 1.0
N D:LEU98 4.9 39.8 1.0
CG D:GLU116 4.9 37.5 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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