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Magnesium in PDB 5qjz: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1696822287

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1696822287

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 Z1696822287:
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 Z1696822287, PDB code: 5qjz 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) 78.15 / 1.52
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.426, 59.817, 79.902, 79.61, 81.70, 75.99
R / Rfree (%) 22.6 / 26.3

Other elements in 5qjz:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1696822287 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 Z1696822287 (pdb code 5qjz). 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 Z1696822287, PDB code: 5qjz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjz

Go back to Magnesium Binding Sites List in 5qjz
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 Z1696822287


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 Z1696822287 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:33.8
occ:1.00
 O A:ALA96 2.0 28.9 1.0
O A:HOH433 2.1 28.5 1.0
OE2 A:GLU116 2.1 31.2 1.0
O A:HOH418 2.1 28.9 1.0
O A:HOH423 2.1 33.1 1.0
O A:HOH454 2.2 28.6 1.0
CD A:GLU116 3.1 31.1 1.0
MG A:MG302 3.2 35.6 1.0
C A:ALA96 3.2 28.4 1.0
OE1 A:GLU116 3.3 28.1 1.0
OE2 A:GLU166 3.7 42.5 1.0
OE2 A:GLU112 4.0 31.1 1.0
O A:HOH463 4.1 45.1 1.0
N A:GLY97 4.1 29.1 1.0
N A:ALA96 4.1 24.3 1.0
CA A:GLY97 4.2 28.3 1.0
CA A:ALA96 4.2 26.9 1.0
NE2 A:GLN82 4.3 33.4 1.0
NH2 A:ARG84 4.3 29.6 1.0
O A:HOH417 4.3 24.0 1.0
CG A:GLU116 4.4 29.8 1.0
OE1 A:GLN82 4.5 31.0 1.0
O A:HOH464 4.5 39.4 1.0
O A:HOH448 4.6 40.7 1.0
CB A:ALA96 4.8 26.2 1.0
CD A:GLN82 4.8 38.7 1.0
CD A:GLU112 4.9 32.8 1.0
CD A:GLU166 4.9 56.9 1.0
O A:HOH468 4.9 57.3 1.0
O A:HOH412 5.0 34.1 1.0

Magnesium binding site 2 out of 8 in 5qjz

Go back to Magnesium Binding Sites List in 5qjz
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 Z1696822287


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 Z1696822287 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:35.6
occ:1.00
 O A:HOH412 1.9 34.1 1.0
O A:HOH448 2.0 40.7 1.0
OE2 A:GLU112 2.1 31.1 1.0
O A:HOH433 2.1 28.5 1.0
OE2 A:GLU166 2.2 42.5 1.0
OE2 A:GLU116 2.2 31.2 1.0
CD A:GLU112 3.1 32.8 1.0
CD A:GLU166 3.1 56.9 1.0
CD A:GLU116 3.2 31.1 1.0
MG A:MG301 3.2 33.8 1.0
OE1 A:GLU166 3.4 49.5 1.0
OE1 A:GLU112 3.4 33.8 1.0
CG A:GLU116 3.5 29.8 1.0
O A:HOH423 3.8 33.1 1.0
O A:HOH463 3.8 45.1 1.0
O A:ALA96 3.9 28.9 1.0
OE2 A:GLU115 4.1 37.0 1.0
OE1 A:GLU116 4.3 28.1 1.0
CG A:GLU166 4.4 51.9 1.0
CG A:GLU112 4.4 28.6 1.0
CB A:GLU112 4.8 27.9 1.0
C A:ALA96 4.8 28.4 1.0
CA A:GLY97 4.8 28.3 1.0
O A:HOH418 4.9 28.9 1.0

Magnesium binding site 3 out of 8 in 5qjz

Go back to Magnesium Binding Sites List in 5qjz
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 Z1696822287


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 Z1696822287 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:34.8
occ:1.00
 O B:ALA96 2.0 31.3 1.0
O B:HOH431 2.0 31.5 1.0
OE2 B:GLU116 2.0 40.5 1.0
O B:HOH428 2.1 36.0 1.0
O B:HOH404 2.1 35.0 1.0
O B:HOH436 2.1 37.2 1.0
CD B:GLU116 3.1 39.5 1.0
C B:ALA96 3.2 30.8 1.0
MG B:MG303 3.2 46.5 1.0
OE1 B:GLU116 3.4 37.2 1.0
OE2 B:GLU166 3.6 44.0 1.0
OE2 B:GLU112 4.0 36.7 1.0
N B:GLY97 4.1 34.4 1.0
N B:ALA96 4.1 29.8 1.0
CA B:GLY97 4.1 37.7 1.0
CA B:ALA96 4.2 30.6 1.0
O B:HOH429 4.2 31.9 1.0
O B:HOH461 4.2 49.2 1.0
NE2 B:GLN82 4.3 39.2 1.0
NH2 B:ARG84 4.3 35.8 1.0
OE1 B:GLN82 4.4 40.8 1.0
CG B:GLU116 4.4 37.1 1.0
CB B:ALA96 4.6 32.8 1.0
CD B:GLN82 4.8 47.3 1.0
CD B:GLU166 4.8 67.5 1.0
O B:HOH463 4.9 46.7 1.0
O B:HOH420 4.9 45.8 1.0
CD B:GLU112 5.0 42.9 1.0

Magnesium binding site 4 out of 8 in 5qjz

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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 Z1696822287


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 Z1696822287 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:46.5
occ:1.00
 OE2 B:GLU112 1.9 36.7 1.0
O B:HOH410 2.0 47.7 1.0
O B:HOH436 2.1 37.2 1.0
OE2 B:GLU116 2.2 40.5 1.0
OE2 B:GLU166 2.3 44.0 1.0
O B:HOH420 2.4 45.8 1.0
CD B:GLU112 3.0 42.9 1.0
CD B:GLU116 3.1 39.5 1.0
CD B:GLU166 3.2 67.5 1.0
MG B:MG302 3.2 34.8 1.0
CG B:GLU116 3.4 37.1 1.0
OE1 B:GLU166 3.4 72.2 1.0
OE1 B:GLU112 3.4 40.0 1.0
O B:HOH461 3.6 49.2 1.0
O B:ALA96 3.7 31.3 1.0
O B:HOH428 3.8 36.0 1.0
OE2 B:GLU115 4.1 50.2 1.0
OE1 B:GLU116 4.2 37.2 1.0
CG B:GLU112 4.4 39.7 1.0
CG B:GLU166 4.5 65.1 1.0
CA B:GLY97 4.7 37.7 1.0
C B:ALA96 4.7 30.8 1.0
O B:HOH404 4.8 35.0 1.0
O B:HOH431 4.8 31.5 1.0
CB B:GLU112 4.8 36.8 1.0
CB B:GLU116 4.9 36.5 1.0

Magnesium binding site 5 out of 8 in 5qjz

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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 Z1696822287


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 Z1696822287 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:50.5
occ:1.00
 O C:HOH455 1.8 50.5 1.0
O C:HOH402 2.1 35.3 1.0
MG C:MG303 2.1 37.9 1.0
OE2 C:GLU166 2.6 48.1 1.0
OE2 C:GLU116 2.7 33.9 1.0
O C:HOH444 2.9 49.3 1.0
OE2 C:GLU112 2.9 36.9 1.0
O C:HOH412 3.0 40.5 1.0
O C:ALA96 3.0 33.4 1.0
O C:HOH439 3.1 31.5 1.0
CA C:GLY97 3.7 39.4 1.0
CD C:GLU112 3.7 44.5 1.0
CD C:GLU166 3.8 54.4 1.0
OE1 C:GLU112 3.9 47.4 1.0
CD C:GLU116 3.9 37.9 1.0
C C:ALA96 4.0 37.8 1.0
O C:HOH438 4.1 32.2 1.0
N C:GLY97 4.4 36.0 1.0
O C:HOH461 4.4 57.6 1.0
OE1 C:GLU166 4.5 57.6 1.0
CG C:GLU166 4.7 54.6 1.0
OE1 C:GLU116 4.7 37.4 1.0
CG C:GLU116 4.7 33.3 1.0
C C:GLY97 5.0 41.0 1.0
CG C:GLU112 5.0 38.7 1.0

Magnesium binding site 6 out of 8 in 5qjz

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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 Z1696822287


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 Z1696822287 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:37.9
occ:1.00
 O C:HOH439 1.9 31.5 1.0
OE2 C:GLU116 2.0 33.9 1.0
O C:HOH438 2.1 32.2 1.0
MG C:MG302 2.1 50.5 1.0
O C:HOH412 2.1 40.5 1.0
O C:ALA96 2.1 33.4 1.0
O C:HOH455 2.8 50.5 1.0
CD C:GLU116 3.0 37.9 1.0
O C:HOH402 3.3 35.3 1.0
C C:ALA96 3.3 37.8 1.0
OE1 C:GLU116 3.3 37.4 1.0
OE2 C:GLU166 3.4 48.1 1.0
OE2 C:GLU112 4.0 36.9 1.0
CA C:GLY97 4.1 39.4 1.0
N C:GLY97 4.2 36.0 1.0
N C:ALA96 4.2 31.0 1.0
CA C:ALA96 4.3 31.1 1.0
CG C:GLU116 4.3 33.3 1.0
NE2 C:GLN82 4.4 39.6 1.0
OE1 C:GLN82 4.5 38.2 1.0
NH2 C:ARG84 4.6 41.7 1.0
CD C:GLU166 4.6 54.4 1.0
CB C:ALA96 4.7 30.2 1.0
O C:HOH444 4.8 49.3 1.0
CD C:GLU112 4.9 44.5 1.0
CD C:GLN82 4.9 45.9 1.0

Magnesium binding site 7 out of 8 in 5qjz

Go back to Magnesium Binding Sites List in 5qjz
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 Z1696822287


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 Z1696822287 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:37.6
occ:1.00
 O D:HOH415 1.9 32.3 1.0
OE2 D:GLU116 1.9 37.5 1.0
MG D:MG302 2.1 43.6 1.0
O D:HOH404 2.1 34.0 1.0
O D:ALA96 2.3 36.6 1.0
CD D:GLU116 3.0 48.3 1.0
O D:HOH423 3.2 45.2 1.0
OE1 D:GLU116 3.3 36.3 1.0
OE2 D:GLU166 3.4 64.1 1.0
C D:ALA96 3.5 38.5 1.0
OE2 D:GLU112 3.5 56.5 1.0
N D:ALA96 4.2 35.9 1.0
CA D:GLY97 4.2 37.5 1.0
CG D:GLU116 4.3 43.0 1.0
N D:GLY97 4.3 39.2 1.0
NE2 D:GLN82 4.3 40.6 1.0
CA D:ALA96 4.4 36.3 1.0
NH2 D:ARG84 4.4 44.3 1.0
OE1 D:GLN82 4.4 42.6 1.0
CD D:GLU112 4.4 56.2 1.0
CD D:GLU166 4.5 74.8 1.0
O D:HOH416 4.6 47.5 1.0
CG D:GLU112 4.6 59.9 1.0
O D:HOH402 4.8 48.2 1.0
CD D:GLN82 4.8 51.2 1.0
CB D:ALA96 4.8 39.1 1.0
CG D:GLU166 5.0 70.3 1.0

Magnesium binding site 8 out of 8 in 5qjz

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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 Z1696822287


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 Z1696822287 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:43.6
occ:1.00
 MG D:MG301 2.1 37.6 1.0
O D:HOH423 2.3 45.2 1.0
OE2 D:GLU166 2.4 64.1 1.0
OE2 D:GLU112 2.6 56.5 1.0
O D:HOH416 2.7 47.5 1.0
OE2 D:GLU116 2.8 37.5 1.0
O D:HOH415 2.8 32.3 1.0
O D:ALA96 3.2 36.6 1.0
CD D:GLU112 3.5 56.2 1.0
CD D:GLU166 3.6 74.8 1.0
CA D:GLY97 3.7 37.5 1.0
O D:HOH402 4.0 48.2 1.0
CD D:GLU116 4.0 48.3 1.0
OE1 D:GLU112 4.1 55.5 1.0
C D:ALA96 4.2 38.5 1.0
O D:HOH404 4.2 34.0 1.0
CG D:GLU166 4.3 70.3 1.0
CG D:GLU112 4.4 59.9 1.0
N D:GLY97 4.5 39.2 1.0
OE1 D:GLU166 4.5 68.2 1.0
OE1 D:GLU116 4.8 36.3 1.0
CG D:GLU116 4.9 43.0 1.0
C D:GLY97 4.9 44.4 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 02:25:00 2024

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