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Magnesium in PDB 5qjb: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869

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 Z1787627869:
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 Z1787627869, PDB code: 5qjb 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) 77.93 / 1.66
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.598, 60.134, 79.856, 79.31, 80.90, 75.37
R / Rfree (%) 25 / 29.2

Other elements in 5qjb:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869 also contains other interesting chemical elements:

Chlorine (Cl) 4 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 Z1787627869 (pdb code 5qjb). 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 Z1787627869, PDB code: 5qjb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjb

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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 Z1787627869


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 Z1787627869 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:32.6
occ:1.00
 O A:ALA96 2.0 25.1 1.0
O A:HOH439 2.0 23.9 1.0
OE2 A:GLU116 2.0 26.6 1.0
O A:HOH426 2.1 23.9 1.0
O A:HOH455 2.2 22.8 1.0
O A:HOH406 2.3 28.9 1.0
CD A:GLU116 3.0 30.0 1.0
C A:ALA96 3.2 23.6 1.0
OE1 A:GLU116 3.4 30.8 1.0
MG A:MG302 3.5 77.8 1.0
OE2 A:GLU166 4.0 53.0 0.5
OE2 A:GLU112 4.0 37.5 1.0
N A:GLY97 4.1 24.9 1.0
CA A:GLY97 4.1 26.3 1.0
NH2 A:ARG84 4.2 29.1 1.0
N A:ALA96 4.2 20.9 1.0
CA A:ALA96 4.2 24.2 1.0
O A:HOH460 4.2 31.3 0.8
NE2 A:GLN82 4.2 34.3 1.0
O A:HOH422 4.3 24.6 1.0
CG A:GLU116 4.4 30.2 1.0
O A:HOH475 4.5 34.0 1.0
OE1 A:GLN82 4.5 31.4 1.0
O A:HOH468 4.6 37.4 1.0
CB A:ALA96 4.6 22.8 1.0
O A:HOH474 4.6 52.5 1.0
CD A:GLN82 4.7 36.2 1.0
CD A:GLU112 4.8 32.3 1.0

Magnesium binding site 2 out of 8 in 5qjb

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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 Z1787627869


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 Z1787627869 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:77.8
occ:1.00
 O A:HOH439 1.9 23.9 1.0
O A:HOH410 2.0 47.2 1.0
OE2 A:GLU112 2.1 37.5 1.0
O A:HOH420 2.4 57.3 1.0
OE2 A:GLU166 2.6 53.0 0.5
OE2 A:GLU116 2.9 26.6 1.0
CD A:GLU112 3.0 32.3 1.0
OE1 A:GLU112 3.0 30.4 1.0
CD A:GLU166 3.4 56.3 0.5
MG A:MG301 3.5 32.6 1.0
OE1 A:GLU166 3.8 55.9 0.5
CD A:GLU116 3.9 30.0 1.0
OE2 A:GLU115 4.1 33.6 1.0
O A:ALA96 4.1 25.1 1.0
O A:HOH406 4.1 28.9 1.0
CG A:GLU116 4.1 30.2 1.0
O A:HOH468 4.1 37.4 1.0
CG A:GLU112 4.4 29.8 1.0
CA A:GLY97 4.6 26.3 1.0
CG A:GLU166 4.6 56.4 0.5
O A:HOH403 4.9 52.0 1.0
OE1 A:GLU116 4.9 30.8 1.0
C A:ALA96 5.0 23.6 1.0
CB A:GLU112 5.0 28.6 1.0
O A:HOH455 5.0 22.8 1.0

Magnesium binding site 3 out of 8 in 5qjb

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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 Z1787627869


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 Z1787627869 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:33.7
occ:1.00
 O B:HOH444 1.8 33.9 1.0
O B:HOH438 1.9 34.4 1.0
OE2 B:GLU116 2.0 36.4 1.0
O B:ALA96 2.1 31.8 1.0
O B:HOH434 2.2 29.4 1.0
O B:HOH450 2.6 37.9 1.0
CD B:GLU116 3.0 37.9 1.0
C B:ALA96 3.3 29.5 1.0
OE1 B:GLU116 3.3 32.6 1.0
OE2 B:GLU166 3.9 49.5 1.0
O B:HOH432 4.0 31.3 1.0
OE1 B:GLN82 4.1 38.6 1.0
N B:ALA96 4.2 28.4 1.0
NE2 B:GLN82 4.2 35.9 1.0
N B:GLY97 4.2 30.4 1.0
OE2 B:GLU112 4.2 38.5 1.0
CA B:GLY97 4.3 32.0 1.0
CA B:ALA96 4.3 29.6 1.0
NH2 B:ARG84 4.3 30.6 1.0
CG B:GLU116 4.3 36.4 1.0
MG B:MG303 4.4 78.0 1.0
O B:HOH469 4.5 46.5 1.0
CD B:GLN82 4.6 44.2 1.0
CD B:GLU166 4.7 67.3 1.0
O B:HOH467 4.8 27.9 0.8
CB B:ALA96 4.8 31.1 1.0
O B:HOH440 4.8 54.6 1.0

Magnesium binding site 4 out of 8 in 5qjb

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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 Z1787627869


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 Z1787627869 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:78.0
occ:1.00
 O B:HOH440 2.1 54.6 1.0
OE2 B:GLU112 2.2 38.5 1.0
O B:HOH436 2.6 64.0 1.0
OE2 B:GLU166 2.9 49.5 1.0
OE2 B:GLU115 3.1 51.5 1.0
OE2 B:GLU116 3.1 36.4 1.0
CD B:GLU112 3.2 41.3 1.0
OE1 B:GLU166 3.2 61.2 1.0
CD B:GLU166 3.4 67.3 1.0
O B:HOH450 3.4 37.9 1.0
CG B:GLU116 3.6 36.4 1.0
OE1 B:GLU112 3.6 41.1 1.0
CD B:GLU116 3.8 37.9 1.0
CB B:GLU115 4.0 43.6 1.0
CD B:GLU115 4.2 49.7 1.0
MG B:MG302 4.4 33.7 1.0
CG B:GLU112 4.5 38.8 1.0
CA B:GLU112 4.6 37.1 1.0
O B:GLU112 4.6 33.4 1.0
CB B:GLU112 4.7 40.9 1.0
CG B:GLU115 4.7 46.4 1.0
O B:ALA96 4.8 31.8 1.0
CB B:GLU116 4.9 34.7 1.0
N B:GLU116 4.9 37.8 1.0
O B:HOH444 4.9 33.9 1.0
OE1 B:GLU116 5.0 32.6 1.0
CG B:GLU166 5.0 67.3 1.0

Magnesium binding site 5 out of 8 in 5qjb

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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 Z1787627869


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 Z1787627869 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:80.6
occ:1.00
 O C:HOH460 1.9 60.7 1.0
O C:HOH439 2.3 40.2 1.0
O C:HOH405 2.7 35.4 1.0
OE1 C:GLU112 3.0 47.6 1.0
OE1 C:GLU166 3.2 82.0 1.0
OE2 C:GLU112 3.2 41.5 1.0
OE2 C:GLU166 3.2 78.7 1.0
CD C:GLU166 3.4 85.5 1.0
CD C:GLU112 3.5 43.4 1.0
O C:HOH470 3.9 64.1 1.0
O C:K07304 3.9 69.8 0.9
OE2 C:GLU115 4.2 46.3 1.0
OE2 C:GLU116 4.2 32.6 1.0
MG C:MG303 4.4 32.8 1.0
CG C:GLU166 4.5 78.9 1.0
O C:HOH451 4.7 47.1 1.0
C4 C:K07304 4.8 70.1 0.9
CA C:GLY97 4.8 31.3 1.0
O C:HOH408 4.8 39.3 1.0
O C:ALA96 4.9 32.7 1.0

Magnesium binding site 6 out of 8 in 5qjb

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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 Z1787627869


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 Z1787627869 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:32.8
occ:1.00
 O C:HOH445 2.0 29.1 1.0
OE2 C:GLU116 2.0 32.6 1.0
O C:HOH408 2.0 39.3 1.0
O C:HOH430 2.1 26.5 1.0
O C:HOH439 2.2 40.2 1.0
O C:ALA96 2.2 32.7 1.0
CD C:GLU116 3.1 34.0 1.0
OE2 C:GLU166 3.2 78.7 1.0
C C:ALA96 3.3 32.8 1.0
OE1 C:GLU116 3.5 35.4 1.0
CA C:GLY97 4.1 31.3 1.0
NH2 C:ARG84 4.1 30.6 1.0
OE2 C:GLU112 4.2 41.5 1.0
N C:GLY97 4.2 33.7 1.0
O C:HOH414 4.3 37.3 0.9
CA C:ALA96 4.3 29.9 1.0
MG C:MG302 4.4 80.6 1.0
N C:ALA96 4.4 29.1 1.0
NE2 C:GLN82 4.4 31.6 1.0
CD C:GLU166 4.4 85.5 1.0
CG C:GLU116 4.5 33.7 1.0
O C:HOH461 4.5 41.3 0.9
OE1 C:GLN82 4.5 33.5 1.0
O C:HOH459 4.7 37.6 1.0
CB C:ALA96 4.8 27.6 1.0
CD C:GLN82 4.9 36.5 1.0
CD C:GLU112 4.9 43.4 1.0
CZ C:ARG84 5.0 32.7 1.0
NH1 C:ARG84 5.0 32.1 1.0

Magnesium binding site 7 out of 8 in 5qjb

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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 Z1787627869


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 Z1787627869 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:40.6
occ:1.00
 OE2 D:GLU116 2.2 58.2 1.0
MG D:MG302 2.3 48.9 1.0
O D:HOH415 2.4 32.5 1.0
O D:HOH402 2.4 34.2 1.0
O D:HOH426 3.1 41.5 1.0
OE2 D:GLU166 3.2 86.6 1.0
CD D:GLU116 3.3 61.7 1.0
O D:ALA96 3.6 58.8 1.0
OE2 D:GLU112 3.8 58.7 1.0
NE2 D:GLN82 3.8 59.5 1.0
OE1 D:GLU116 3.8 57.5 1.0
OE1 D:GLN82 4.1 55.5 1.0
CD D:GLU166 4.2 92.0 1.0
CD D:GLN82 4.4 59.1 1.0
NH2 D:ARG84 4.4 54.0 0.5
C D:ALA96 4.4 59.6 1.0
CG D:GLU116 4.5 59.8 1.0
O D:HOH412 4.5 72.6 1.0
CG D:GLU166 4.7 87.1 1.0
CG1 D:VAL168 4.8 77.4 1.0
N D:ALA96 4.9 47.2 1.0
CD D:GLU112 4.9 62.2 1.0

Magnesium binding site 8 out of 8 in 5qjb

Go back to Magnesium Binding Sites List in 5qjb
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 Z1787627869


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 Z1787627869 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:48.9
occ:1.00
 O D:HOH426 2.2 41.5 1.0
OE2 D:GLU112 2.3 58.7 1.0
MG D:MG301 2.3 40.6 1.0
OE2 D:GLU166 2.5 86.6 1.0
O D:HOH415 2.6 32.5 1.0
O D:HOH401 3.1 37.4 1.0
OE2 D:GLU116 3.2 58.2 1.0
O D:ALA96 3.4 58.8 1.0
CD D:GLU112 3.5 62.2 1.0
CA D:GLY97 3.6 59.3 1.0
CD D:GLU166 3.8 92.0 1.0
O D:HOH412 4.0 72.6 1.0
C D:ALA96 4.1 59.6 1.0
O D:HOH402 4.2 34.2 1.0
OE1 D:GLU112 4.3 60.2 1.0
N D:GLY97 4.3 57.7 1.0
CD D:GLU116 4.4 61.7 1.0
OE1 D:GLU166 4.5 91.3 1.0
CG D:GLU112 4.5 60.0 1.0
CG D:GLU166 4.8 87.1 1.0
C D:GLY97 4.9 58.7 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 02:13:16 2024

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