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Magnesium in PDB 5qjw: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z198194396

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z198194396

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 Z198194396:
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 Z198194396, PDB code: 5qjw 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) 78.13 / 1.57
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.535, 59.991, 80.050, 79.16, 81.16, 75.31
R / Rfree (%) 23.2 / 26.7

Other elements in 5qjw:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z198194396 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 Z198194396 (pdb code 5qjw). 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 Z198194396, PDB code: 5qjw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjw

Go back to Magnesium Binding Sites List in 5qjw
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 Z198194396


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 Z198194396 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:28.5
occ:1.00
 O A:HOH441 2.0 22.6 1.0
O A:ALA96 2.1 24.2 1.0
O A:HOH412 2.1 21.9 1.0
O A:HOH463 2.1 21.1 1.0
OE2 A:GLU116 2.1 23.4 1.0
O A:HOH435 2.2 25.3 1.0
CD A:GLU116 3.1 26.5 1.0
C A:ALA96 3.2 22.2 1.0
OE1 A:GLU116 3.4 24.1 1.0
MG A:MG302 3.4 59.5 1.0
OE2 A:GLU166 3.9 46.2 1.0
O A:HOH442 4.1 28.0 1.0
N A:GLY97 4.1 22.2 1.0
CA A:GLY97 4.1 22.4 1.0
OE2 A:GLU112 4.2 31.3 1.0
NH2 A:ARG84 4.2 24.1 1.0
N A:ALA96 4.2 17.9 1.0
CA A:ALA96 4.2 19.7 1.0
O A:HOH422 4.3 20.3 1.0
NE2 A:GLN82 4.4 28.5 1.0
O A:HOH471 4.4 26.5 1.0
O A:HOH470 4.4 32.4 1.0
CG A:GLU116 4.5 25.4 1.0
OE1 A:GLN82 4.5 26.4 1.0
CB A:ALA96 4.6 18.4 1.0
CD A:GLN82 4.8 31.1 1.0
CD A:GLU112 4.9 27.2 1.0

Magnesium binding site 2 out of 8 in 5qjw

Go back to Magnesium Binding Sites List in 5qjw
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 Z198194396


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 Z198194396 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:59.5
occ:1.00
 O A:HOH404 2.0 38.7 1.0
O A:HOH441 2.0 22.6 1.0
OE2 A:GLU112 2.1 31.3 1.0
O A:HOH413 2.4 42.6 1.0
OE2 A:GLU166 2.5 46.2 1.0
OE2 A:GLU116 2.7 23.4 1.0
CD A:GLU112 3.0 27.2 1.0
CD A:GLU166 3.1 63.1 1.0
OE1 A:GLU166 3.3 53.2 1.0
OE1 A:GLU112 3.3 28.4 1.0
MG A:MG301 3.4 28.5 1.0
CD A:GLU116 3.6 26.5 1.0
CG A:GLU116 3.9 25.4 1.0
O A:ALA96 4.0 24.2 1.0
O A:HOH435 4.0 25.3 1.0
OE2 A:GLU115 4.1 33.1 1.0
O A:HOH470 4.1 32.4 1.0
CG A:GLU166 4.3 58.3 1.0
CG A:GLU112 4.4 27.1 1.0
CA A:GLY97 4.7 22.4 1.0
OE1 A:GLU116 4.7 24.1 1.0
CB A:GLU112 4.8 24.8 1.0
C A:ALA96 4.9 22.2 1.0

Magnesium binding site 3 out of 8 in 5qjw

Go back to Magnesium Binding Sites List in 5qjw
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 Z198194396


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 Z198194396 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:28.4
occ:1.00
 O B:HOH425 1.9 28.1 1.0
O B:ALA96 2.0 27.5 1.0
OE2 B:GLU116 2.0 32.5 1.0
O B:HOH421 2.1 28.3 1.0
O B:HOH428 2.1 26.6 1.0
O B:HOH437 2.2 27.7 1.0
CD B:GLU116 3.1 33.6 1.0
C B:ALA96 3.2 21.2 1.0
OE1 B:GLU116 3.4 28.1 1.0
OE2 B:GLU166 3.8 49.4 1.0
OE2 B:GLU112 4.1 35.4 1.0
N B:GLY97 4.1 24.9 1.0
N B:ALA96 4.2 23.1 1.0
O B:HOH432 4.2 26.3 1.0
CA B:GLY97 4.2 24.2 1.0
CA B:ALA96 4.2 24.4 1.0
NE2 B:GLN82 4.2 35.7 1.0
NH2 B:ARG84 4.3 27.3 1.0
OE1 B:GLN82 4.4 33.2 1.0
CG B:GLU116 4.4 31.6 1.0
MG B:MG303 4.4 77.0 1.0
O B:HOH454 4.5 41.2 1.0
O B:HOH468 4.6 41.6 1.0
CD B:GLU166 4.6 67.8 1.0
CD B:GLN82 4.7 38.8 1.0
CB B:ALA96 4.7 26.9 1.0
O B:HOH456 4.7 48.5 1.0
CD B:GLU112 5.0 35.0 1.0

Magnesium binding site 4 out of 8 in 5qjw

Go back to Magnesium Binding Sites List in 5qjw
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 Z198194396


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 Z198194396 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:77.0
occ:1.00
 O B:HOH416 1.9 63.2 1.0
OE2 B:GLU112 2.3 35.4 1.0
O B:HOH456 2.4 48.5 1.0
OE2 B:GLU166 2.6 49.4 1.0
OE2 B:GLU115 3.1 45.8 1.0
OE2 B:GLU116 3.2 32.5 1.0
OE1 B:GLU166 3.3 67.6 1.0
CD B:GLU112 3.3 35.0 1.0
CD B:GLU166 3.3 67.8 1.0
CG B:GLU116 3.4 31.6 1.0
O B:HOH437 3.4 27.7 1.0
OE1 B:GLU112 3.7 35.3 1.0
CD B:GLU116 3.7 33.6 1.0
CB B:GLU115 3.8 32.6 1.0
CD B:GLU115 4.2 43.7 1.0
MG B:MG302 4.4 28.4 1.0
CG B:GLU112 4.6 34.1 1.0
O B:GLU112 4.6 30.1 1.0
CG B:GLU115 4.6 39.8 1.0
N B:GLU116 4.7 34.5 1.0
CA B:GLU112 4.7 31.3 1.0
CB B:GLU116 4.8 28.4 1.0
CG B:GLU166 4.8 57.4 1.0
O B:ALA96 4.8 27.5 1.0
CB B:GLU112 4.9 35.4 1.0
OE1 B:GLU116 4.9 28.1 1.0
O B:HOH425 5.0 28.1 1.0
C B:GLU115 5.0 33.7 1.0

Magnesium binding site 5 out of 8 in 5qjw

Go back to Magnesium Binding Sites List in 5qjw
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 Z198194396


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 Z198194396 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:49.2
occ:1.00
 MG C:MG303 2.3 32.9 1.0
OE2 C:GLU166 2.5 72.1 1.0
O C:HOH404 2.7 42.0 1.0
OE2 C:GLU116 2.7 33.4 1.0
OE2 C:GLU112 2.8 35.0 1.0
O C:ALA96 3.1 26.2 1.0
O C:HOH430 3.1 49.5 1.0
O C:HOH431 3.2 32.9 1.0
O C:HOH440 3.2 47.7 1.0
O C:HOH461 3.3 60.4 1.0
O C:HOH450 3.3 27.8 1.0
CD C:GLU112 3.6 39.1 1.0
CD C:GLU166 3.6 70.7 1.0
OE1 C:GLU112 3.6 48.0 1.0
CA C:GLY97 3.8 30.2 1.0
CD C:GLU116 3.9 35.2 1.0
OE1 C:GLU166 4.1 67.2 1.0
C C:ALA96 4.1 28.8 1.0
N C:GLY97 4.4 28.7 1.0
O C:HOH435 4.4 26.1 1.0
CG C:GLU116 4.7 32.9 1.0
CG C:GLU166 4.8 61.2 1.0
OE1 C:GLU116 4.8 34.4 1.0
CG C:GLU112 4.9 35.1 1.0

Magnesium binding site 6 out of 8 in 5qjw

Go back to Magnesium Binding Sites List in 5qjw
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 Z198194396


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 Z198194396 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:32.9
occ:1.00
 OE2 C:GLU116 1.9 33.4 1.0
O C:HOH435 2.1 26.1 1.0
O C:HOH450 2.1 27.8 1.0
O C:HOH431 2.1 32.9 1.0
O C:ALA96 2.2 26.2 1.0
MG C:MG302 2.3 49.2 1.0
CD C:GLU116 3.0 35.2 1.0
C C:ALA96 3.3 28.8 1.0
OE1 C:GLU116 3.3 34.4 1.0
OE2 C:GLU166 3.9 72.1 1.0
O C:HOH404 4.0 42.0 1.0
OE2 C:GLU112 4.1 35.0 1.0
O C:HOH410 4.2 26.6 0.9
N C:ALA96 4.2 22.9 1.0
CA C:GLY97 4.2 30.2 1.0
CA C:ALA96 4.3 23.7 1.0
N C:GLY97 4.3 28.7 1.0
NH2 C:ARG84 4.4 32.1 1.0
CG C:GLU116 4.4 32.9 1.0
NE2 C:GLN82 4.4 33.5 1.0
OE1 C:GLN82 4.4 29.8 1.0
CD C:GLU166 4.7 70.7 1.0
O C:HOH440 4.7 47.7 1.0
O C:HOH464 4.7 39.0 0.9
CB C:ALA96 4.8 22.3 1.0
CD C:GLN82 4.9 35.7 1.0
CD C:GLU112 4.9 39.1 1.0

Magnesium binding site 7 out of 8 in 5qjw

Go back to Magnesium Binding Sites List in 5qjw
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 Z198194396


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 Z198194396 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:34.8
occ:1.00
 O D:HOH410 1.9 26.9 1.0
OE2 D:GLU116 2.0 35.5 1.0
O D:HOH401 2.0 25.4 1.0
MG D:MG302 2.2 39.0 1.0
O D:ALA96 2.4 34.3 1.0
O D:HOH422 2.5 45.0 1.0
CD D:GLU116 3.1 42.0 1.0
OE1 D:GLU116 3.4 37.6 1.0
C D:ALA96 3.4 40.7 1.0
OE2 D:GLU112 3.7 51.5 1.0
OE2 D:GLU166 4.0 73.5 1.0
O D:HOH402 4.2 57.4 1.0
NE2 D:GLN82 4.2 37.9 1.0
N D:ALA96 4.2 38.7 1.0
NH2 D:ARG84 4.2 40.7 1.0
CA D:GLY97 4.2 40.1 1.0
N D:GLY97 4.3 39.2 1.0
CA D:ALA96 4.3 39.9 1.0
OE1 D:GLN82 4.4 42.6 1.0
CG D:GLU116 4.4 41.6 1.0
CD D:GLU112 4.6 50.4 1.0
CB D:ALA96 4.7 38.9 1.0
CD D:GLN82 4.7 46.2 1.0
O D:HOH406 4.7 43.5 1.0
CG D:GLU112 4.9 50.6 1.0

Magnesium binding site 8 out of 8 in 5qjw

Go back to Magnesium Binding Sites List in 5qjw
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 Z198194396


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 Z198194396 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:39.0
occ:1.00
 O D:HOH422 1.7 45.0 1.0
MG D:MG301 2.2 34.8 1.0
OE2 D:GLU112 2.3 51.5 1.0
O D:HOH406 2.7 43.5 1.0
OE2 D:GLU116 2.8 35.5 1.0
OE2 D:GLU166 3.0 73.5 1.0
O D:ALA96 3.0 34.3 1.0
O D:HOH410 3.0 26.9 1.0
O D:HOH402 3.0 57.4 1.0
CD D:GLU112 3.3 50.4 1.0
CA D:GLY97 3.5 40.1 1.0
OE1 D:GLU112 4.0 47.2 1.0
C D:ALA96 4.0 40.7 1.0
CD D:GLU116 4.0 42.0 1.0
CG D:GLU112 4.2 50.6 1.0
O D:HOH401 4.2 25.4 1.0
CD D:GLU166 4.2 78.5 1.0
N D:GLY97 4.2 39.2 1.0
C D:GLY97 4.8 40.8 1.0
OE1 D:GLU116 4.8 37.6 1.0
CG D:GLU116 4.8 41.6 1.0
OE1 D:GLU166 4.8 67.8 1.0
N D:LEU98 4.9 40.0 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 02:23:13 2024

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