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Magnesium in PDB 5qk2: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z54628578

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z54628578

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 Z54628578:
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 Z54628578, PDB code: 5qk2 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) 78.38 / 1.65
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.507, 59.468, 80.087, 79.55, 82.12, 76.18
R / Rfree (%) 22.3 / 26.7

Other elements in 5qk2:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z54628578 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 Z54628578 (pdb code 5qk2). 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 Z54628578, PDB code: 5qk2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qk2

Go back to Magnesium Binding Sites List in 5qk2
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 Z54628578


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 Z54628578 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:31.8
occ:1.00
 O A:ALA96 2.0 23.1 1.0
O A:HOH445 2.1 27.7 1.0
O A:HOH423 2.1 30.9 1.0
O A:HOH456 2.1 23.9 1.0
OE2 A:GLU116 2.2 28.1 1.0
O A:HOH424 2.2 27.4 1.0
MG A:MG302 3.1 67.4 1.0
C A:ALA96 3.2 22.2 1.0
CD A:GLU116 3.2 26.0 1.0
OE1 A:GLU116 3.6 23.8 1.0
N A:GLY97 4.0 26.3 1.0
O A:HOH444 4.1 24.5 0.8
CA A:GLY97 4.1 25.4 1.0
O A:HOH464 4.1 62.9 1.0
NH2 A:ARG84 4.1 26.3 1.0
CA A:ALA96 4.2 22.8 1.0
OE2 A:GLU112 4.2 31.9 1.0
NE2 A:GLN82 4.2 26.8 1.0
O A:HOH467 4.2 32.1 1.0
N A:ALA96 4.2 21.8 1.0
O A:HOH433 4.3 22.1 1.0
OE1 A:GLN82 4.3 26.9 1.0
O A:HOH459 4.5 36.5 1.0
OE2 A:GLU166 4.5 68.2 1.0
CG A:GLU116 4.6 27.0 1.0
CB A:ALA96 4.6 21.2 1.0
CD A:GLN82 4.7 31.1 1.0
CD A:GLU112 4.9 30.4 1.0
CZ A:ARG84 4.9 27.2 1.0
NH1 A:ARG84 4.9 28.4 1.0
O A:HOH404 4.9 48.0 1.0

Magnesium binding site 2 out of 8 in 5qk2

Go back to Magnesium Binding Sites List in 5qk2
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 Z54628578


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 Z54628578 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:67.4
occ:1.00
 O A:HOH404 1.9 48.0 1.0
O A:HOH445 2.0 27.7 1.0
OE2 A:GLU116 2.3 28.1 1.0
OE2 A:GLU166 2.3 68.2 1.0
OE2 A:GLU112 2.4 31.9 1.0
OE1 A:GLU166 2.7 68.7 1.0
CD A:GLU166 2.8 78.9 1.0
MG A:MG301 3.1 31.8 1.0
CD A:GLU116 3.3 26.0 1.0
O A:HOH423 3.3 30.9 1.0
O A:HOH434 3.3 49.6 1.0
CD A:GLU112 3.4 30.4 1.0
O A:HOH464 3.5 62.9 1.0
OE1 A:GLU112 3.5 35.5 1.0
CG A:GLU116 3.6 27.0 1.0
O A:ALA96 3.8 23.1 1.0
CG A:GLU166 4.1 74.5 1.0
O A:HOH459 4.3 36.5 1.0
OE2 A:GLU115 4.3 48.7 1.0
OE1 A:GLU116 4.4 23.8 1.0
O A:HOH424 4.8 27.4 1.0
CG A:GLU112 4.8 29.7 1.0
O A:HOH456 4.8 23.9 1.0
CA A:GLY97 4.8 25.4 1.0
C A:ALA96 4.8 22.2 1.0

Magnesium binding site 3 out of 8 in 5qk2

Go back to Magnesium Binding Sites List in 5qk2
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 Z54628578


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 Z54628578 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:35.6
occ:1.00
 OE2 B:GLU116 1.9 35.3 1.0
O B:ALA96 2.0 25.1 1.0
O B:HOH409 2.1 25.9 1.0
O B:HOH437 2.1 33.4 1.0
O B:HOH436 2.2 29.5 1.0
O B:HOH441 2.2 26.3 1.0
CD B:GLU116 3.0 35.7 1.0
C B:ALA96 3.2 24.9 1.0
OE1 B:GLU116 3.4 37.5 1.0
OE2 B:GLU166 3.7 69.0 1.0
N B:GLY97 4.1 25.1 1.0
CA B:GLY97 4.1 27.0 1.0
N B:ALA96 4.2 23.9 1.0
O B:HOH416 4.2 29.9 1.0
CA B:ALA96 4.2 23.9 1.0
NH2 B:ARG84 4.3 29.2 1.0
NE2 B:GLN82 4.3 33.5 1.0
OE2 B:GLU112 4.3 40.1 1.0
CG B:GLU116 4.3 32.7 1.0
O B:HOH461 4.4 34.8 1.0
OE1 B:GLN82 4.4 35.6 1.0
MG B:MG304 4.4 70.7 1.0
CD B:GLU166 4.5 72.5 1.0
CD B:GLN82 4.7 39.2 1.0
CB B:ALA96 4.8 26.1 1.0
CD B:GLU112 4.9 37.2 1.0

Magnesium binding site 4 out of 8 in 5qk2

Go back to Magnesium Binding Sites List in 5qk2
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 Z54628578


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 Z54628578 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:70.7
occ:1.00
 O B:HOH404 2.4 57.4 1.0
OE2 B:GLU112 2.5 40.1 1.0
OE2 B:GLU166 2.5 69.0 1.0
O B:HOH418 2.7 49.1 1.0
OE2 B:GLU115 3.0 46.6 1.0
CD B:GLU166 3.2 72.5 1.0
OE1 B:GLU166 3.2 70.4 1.0
OE2 B:GLU116 3.3 35.3 1.0
CD B:GLU112 3.5 37.2 1.0
CG B:GLU116 3.6 32.7 1.0
O B:HOH437 3.6 33.4 1.0
OE1 B:GLU112 3.9 37.5 1.0
CD B:GLU116 3.9 35.7 1.0
CB B:GLU115 4.0 40.1 1.0
CD B:GLU115 4.1 48.0 1.0
MG B:MG303 4.4 35.6 1.0
N B:GLY163 4.6 73.1 1.0
CG B:GLU166 4.7 67.8 1.0
CG B:GLU115 4.7 44.3 1.0
CG B:GLU112 4.9 32.2 1.0
O B:ALA96 5.0 25.1 1.0
CB B:GLU116 5.0 32.9 1.0

Magnesium binding site 5 out of 8 in 5qk2

Go back to Magnesium Binding Sites List in 5qk2
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 Z54628578


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 Z54628578 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:49.6
occ:1.00
 MG C:MG303 1.9 35.6 1.0
O C:HOH402 2.5 49.8 1.0
OE2 C:GLU116 2.6 32.6 1.0
O C:ALA96 2.6 26.4 1.0
O C:HOH446 2.8 25.3 1.0
O C:HOH418 2.8 33.7 1.0
OE2 C:GLU166 3.1 79.1 1.0
O C:HOH451 3.2 46.5 1.0
OE2 C:GLU112 3.2 37.1 1.0
CA C:GLY97 3.4 32.0 1.0
O C:HOH426 3.6 40.5 1.0
C C:ALA96 3.6 27.1 1.0
CD C:GLU112 3.8 41.0 1.0
CD C:GLU116 3.8 31.5 1.0
OE1 C:GLU112 3.9 50.0 1.0
N C:GLY97 4.0 28.6 1.0
O C:HOH416 4.0 25.0 1.0
CD C:GLU166 4.1 83.3 1.0
O C:HOH453 4.2 54.6 1.0
OE1 C:GLU116 4.5 37.7 1.0
OE1 C:GLU166 4.7 89.6 1.0
C C:GLY97 4.7 31.8 1.0
CG C:GLU116 4.8 31.7 1.0
CA C:ALA96 5.0 24.8 1.0

Magnesium binding site 6 out of 8 in 5qk2

Go back to Magnesium Binding Sites List in 5qk2
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 Z54628578


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 Z54628578 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:35.6
occ:1.00
 MG C:MG302 1.9 49.6 1.0
O C:HOH446 2.0 25.3 1.0
O C:HOH418 2.0 33.7 1.0
OE2 C:GLU116 2.0 32.6 1.0
O C:HOH416 2.1 25.0 1.0
O C:ALA96 2.2 26.4 1.0
CD C:GLU116 3.0 31.5 1.0
OE1 C:GLU116 3.3 37.7 1.0
C C:ALA96 3.3 27.1 1.0
OE2 C:GLU166 3.5 79.1 1.0
O C:HOH402 3.7 49.8 1.0
N C:ALA96 4.1 27.2 1.0
CA C:GLY97 4.2 32.0 1.0
NH2 C:ARG84 4.2 30.5 1.0
OE2 C:GLU112 4.2 37.1 1.0
N C:GLY97 4.2 28.6 1.0
CA C:ALA96 4.2 24.8 1.0
NE2 C:GLN82 4.3 38.5 1.0
OE1 C:GLN82 4.3 41.0 1.0
CG C:GLU116 4.4 31.7 1.0
CB C:ALA96 4.6 27.1 1.0
O C:HOH451 4.7 46.5 1.0
CD C:GLU166 4.7 83.3 1.0
CD C:GLN82 4.7 44.4 1.0
CD C:GLU112 5.0 41.0 1.0

Magnesium binding site 7 out of 8 in 5qk2

Go back to Magnesium Binding Sites List in 5qk2
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 Z54628578


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 Z54628578 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:30.1
occ:1.00
 O D:HOH421 2.0 25.7 1.0
OE2 D:GLU116 2.0 29.8 1.0
O D:HOH415 2.0 22.7 1.0
O D:HOH409 2.0 29.7 1.0
O D:ALA96 2.1 28.5 1.0
MG D:MG302 2.3 38.0 1.0
CD D:GLU116 3.0 32.9 1.0
C D:ALA96 3.3 28.5 1.0
O D:HOH404 3.4 91.9 1.0
OE1 D:GLU116 3.4 34.0 1.0
OE2 D:GLU112 3.8 45.1 1.0
N D:GLY97 4.1 29.4 1.0
CA D:GLY97 4.2 30.9 1.0
N D:ALA96 4.2 28.1 1.0
NH2 D:ARG84 4.2 26.6 1.0
NE2 D:GLN82 4.3 29.6 1.0
CA D:ALA96 4.3 28.0 1.0
O D:HOH431 4.3 31.2 1.0
CG D:GLU116 4.3 31.4 1.0
O D:HOH407 4.4 30.0 1.0
OE1 D:GLN82 4.4 34.7 1.0
O D:HOH436 4.5 31.9 1.0
OE2 D:GLU166 4.5 84.0 1.0
CD D:GLU112 4.6 47.0 1.0
CG D:GLU112 4.7 51.0 1.0
CB D:ALA96 4.8 27.5 1.0
CD D:GLN82 4.8 36.0 1.0

Magnesium binding site 8 out of 8 in 5qk2

Go back to Magnesium Binding Sites List in 5qk2
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 Z54628578


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 Z54628578 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:38.0
occ:1.00
 O D:HOH404 1.8 91.9 1.0
MG D:MG301 2.3 30.1 1.0
OE2 D:GLU112 2.5 45.1 1.0
OE2 D:GLU116 2.8 29.8 1.0
O D:HOH420 3.0 43.6 1.0
O D:HOH421 3.0 25.7 1.0
O D:ALA96 3.1 28.5 1.0
O D:HOH415 3.2 22.7 1.0
CD D:GLU112 3.4 47.0 1.0
CA D:GLY97 3.5 30.9 1.0
OE2 D:GLU166 3.8 84.0 1.0
O D:HOH405 3.9 56.1 1.0
OE1 D:GLU112 4.0 57.9 1.0
CD D:GLU116 4.0 32.9 1.0
C D:ALA96 4.0 28.5 1.0
N D:GLY97 4.2 29.4 1.0
CG D:GLU112 4.2 51.0 1.0
O D:HOH409 4.3 29.7 1.0
O D:HOH431 4.4 31.2 1.0
CD D:GLU166 4.4 86.8 1.0
C D:GLY97 4.7 30.6 1.0
CG D:GLU116 4.8 31.4 1.0
OE1 D:GLU116 4.8 34.0 1.0
N D:LEU98 4.8 35.7 1.0
OE1 D:GLU166 4.9 95.4 1.0
O D:HOH436 5.0 31.9 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 02:27:04 2024

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