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Magnesium in PDB 5qjy: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z94597856

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z94597856

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 Z94597856:
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 Z94597856, PDB code: 5qjy 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) 78.29 / 1.77
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.513, 59.925, 80.141, 79.30, 81.43, 75.55
R / Rfree (%) 21.4 / 25.9

Other elements in 5qjy:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z94597856 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 Z94597856 (pdb code 5qjy). 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 Z94597856, PDB code: 5qjy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjy

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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 Z94597856


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 Z94597856 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:35.4
occ:1.00
 OE2 A:GLU116 2.0 27.9 1.0
O A:HOH412 2.0 29.0 1.0
O A:HOH423 2.0 29.2 1.0
O A:ALA96 2.1 24.8 1.0
O A:HOH437 2.1 22.9 1.0
O A:HOH438 2.1 26.3 1.0
CD A:GLU116 3.0 28.5 1.0
C A:ALA96 3.3 26.5 1.0
OE1 A:GLU116 3.3 30.5 1.0
MG A:MG302 3.4 63.4 1.0
OE2 A:GLU166 3.8 71.0 1.0
N A:GLY97 4.1 25.7 0.6
N A:ALA96 4.2 24.4 1.0
OE2 A:GLU112 4.2 38.7 1.0
CA A:GLY97 4.2 26.6 0.6
CA A:ALA96 4.2 25.3 1.0
NE2 A:GLN82 4.3 28.7 1.0
O A:HOH418 4.3 24.3 1.0
O A:HOH444 4.3 18.4 0.6
CG A:GLU116 4.3 30.0 1.0
NH2 A:ARG84 4.3 29.3 1.0
OE1 A:GLN82 4.4 27.0 1.0
O A:HOH451 4.4 37.8 1.0
O A:HOH456 4.6 32.4 1.0
O A:HOH459 4.7 62.2 1.0
CD A:GLN82 4.7 33.2 1.0
CB A:ALA96 4.7 24.2 1.0
CD A:GLU112 4.9 34.4 1.0
O A:HOH409 4.9 42.5 1.0
CD A:GLU166 5.0 79.7 1.0

Magnesium binding site 2 out of 8 in 5qjy

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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 Z94597856


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 Z94597856 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:63.4
occ:1.00
 O A:HOH409 1.9 42.5 1.0
O A:HOH437 2.1 22.9 1.0
OE2 A:GLU112 2.1 38.7 1.0
OE2 A:GLU166 2.6 71.0 1.0
O A:HOH401 2.6 44.5 1.0
OE2 A:GLU116 2.7 27.9 1.0
CD A:GLU112 3.0 34.4 1.0
OE1 A:GLU112 3.1 34.1 1.0
CD A:GLU166 3.2 79.7 1.0
MG A:MG301 3.4 35.4 1.0
OE1 A:GLU166 3.4 79.5 1.0
CD A:GLU116 3.7 28.5 1.0
CG A:GLU116 3.9 30.0 1.0
O A:HOH423 4.0 29.2 1.0
OE2 A:GLU115 4.0 39.5 1.0
O A:HOH451 4.0 37.8 1.0
O A:ALA96 4.0 24.8 1.0
CG A:GLU112 4.4 31.8 1.0
CG A:GLU166 4.5 72.0 1.0
CA A:GLY97 4.6 26.6 0.6
OE1 A:GLU116 4.8 30.5 1.0
CB A:GLU112 4.9 28.4 1.0
O A:HOH438 4.9 26.3 1.0
C A:ALA96 4.9 26.5 1.0

Magnesium binding site 3 out of 8 in 5qjy

Go back to Magnesium Binding Sites List in 5qjy
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 Z94597856


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 Z94597856 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:34.9
occ:1.00
 O B:ALA96 2.0 33.6 1.0
OE2 B:GLU116 2.0 42.4 1.0
O B:HOH406 2.1 33.5 1.0
O B:HOH407 2.1 32.7 1.0
O B:HOH436 2.2 25.5 1.0
O B:HOH443 2.3 35.5 1.0
CD B:GLU116 3.0 39.7 1.0
C B:ALA96 3.2 29.8 1.0
OE1 B:GLU116 3.3 37.5 1.0
OE2 B:GLU112 3.9 46.5 1.0
OE2 B:GLU166 4.0 54.5 1.0
N B:GLY97 4.1 28.8 1.0
CA B:GLY97 4.1 32.6 1.0
N B:ALA96 4.1 28.7 1.0
CA B:ALA96 4.2 28.7 1.0
NE2 B:GLN82 4.2 46.2 1.0
O B:HOH415 4.2 34.0 1.0
NH2 B:ARG84 4.3 36.1 1.0
MG B:MG303 4.3 86.8 1.0
CG B:GLU116 4.4 37.6 1.0
OE1 B:GLN82 4.5 41.0 1.0
O B:HOH463 4.5 43.5 1.0
CB B:ALA96 4.6 29.7 1.0
CD B:GLN82 4.7 48.0 1.0
CD B:GLU166 4.8 68.6 1.0
CD B:GLU112 4.8 43.6 1.0

Magnesium binding site 4 out of 8 in 5qjy

Go back to Magnesium Binding Sites List in 5qjy
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 Z94597856


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 Z94597856 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:86.8
occ:1.00
 OE2 B:GLU112 2.2 46.5 1.0
O B:HOH420 2.3 66.8 1.0
O B:HOH424 2.7 49.2 1.0
OE2 B:GLU166 2.8 54.5 1.0
OE1 B:GLU166 3.0 71.5 1.0
OE2 B:GLU116 3.1 42.4 1.0
CD B:GLU112 3.1 43.6 1.0
OE2 B:GLU115 3.2 56.7 1.0
CD B:GLU166 3.3 68.6 1.0
OE1 B:GLU112 3.4 41.8 1.0
CG B:GLU116 3.4 37.6 1.0
O B:HOH443 3.4 35.5 1.0
CD B:GLU116 3.7 39.7 1.0
CB B:GLU115 4.1 45.2 1.0
MG B:MG302 4.3 34.9 1.0
CD B:GLU115 4.3 53.5 1.0
CG B:GLU112 4.4 41.8 1.0
O B:GLU112 4.7 35.2 1.0
CA B:GLU112 4.8 37.4 1.0
O B:ALA96 4.8 33.6 1.0
CB B:GLU112 4.8 40.4 1.0
CG B:GLU166 4.8 67.5 1.0
N B:GLU116 4.9 40.6 1.0
CB B:GLU116 4.9 35.3 1.0
CG B:GLU115 4.9 48.8 1.0
OE1 B:GLU116 4.9 37.5 1.0
O B:HOH406 4.9 33.5 1.0

Magnesium binding site 5 out of 8 in 5qjy

Go back to Magnesium Binding Sites List in 5qjy
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 Z94597856


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 Z94597856 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:64.6
occ:1.00
 O C:HOH447 1.4 60.3 1.0
O C:HOH402 2.2 49.0 1.0
MG C:MG303 2.6 36.5 1.0
OE2 C:GLU112 2.7 34.9 1.0
OE2 C:GLU166 2.7 68.2 1.0
OE2 C:GLU116 2.7 36.3 1.0
O C:ALA96 3.0 35.9 1.0
O C:HOH411 3.3 55.1 1.0
CD C:GLU112 3.3 40.7 1.0
O C:HOH421 3.4 34.2 1.0
OE1 C:GLU112 3.4 49.7 1.0
CA C:GLY97 3.6 33.7 1.0
O C:HOH438 3.6 37.5 1.0
CD C:GLU166 3.7 75.2 1.0
O C:HOH442 3.8 62.6 1.0
CD C:GLU116 3.9 36.9 1.0
C C:ALA96 4.0 32.4 1.0
OE1 C:GLU166 4.2 80.8 1.0
N C:GLY97 4.2 33.8 1.0
O C:HOH417 4.5 31.6 1.0
CG C:GLU116 4.5 35.0 1.0
CG C:GLU112 4.6 37.1 1.0
OE1 C:GLU116 4.8 39.8 1.0
CG C:GLU166 4.9 68.5 1.0
C C:GLY97 4.9 37.2 1.0

Magnesium binding site 6 out of 8 in 5qjy

Go back to Magnesium Binding Sites List in 5qjy
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 Z94597856


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 Z94597856 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:36.5
occ:1.00
 OE2 C:GLU116 1.9 36.3 1.0
O C:HOH417 2.0 31.6 1.0
O C:HOH438 2.0 37.5 1.0
O C:HOH421 2.1 34.2 1.0
O C:ALA96 2.1 35.9 1.0
O C:HOH447 2.3 60.3 1.0
MG C:MG302 2.6 64.6 1.0
CD C:GLU116 3.0 36.9 1.0
C C:ALA96 3.3 32.4 1.0
OE1 C:GLU116 3.4 39.8 1.0
OE2 C:GLU166 3.6 68.2 1.0
N C:ALA96 4.2 29.6 1.0
NE2 C:GLN82 4.2 40.2 1.0
O C:HOH402 4.2 49.0 1.0
N C:GLY97 4.2 33.8 1.0
CA C:ALA96 4.2 28.8 1.0
CA C:GLY97 4.3 33.7 1.0
OE1 C:GLN82 4.3 39.4 1.0
NH2 C:ARG84 4.3 34.3 1.0
OE2 C:GLU112 4.4 34.9 1.0
CG C:GLU116 4.4 35.0 1.0
CD C:GLN82 4.7 45.9 1.0
CB C:ALA96 4.7 27.1 1.0
CD C:GLU166 4.8 75.2 1.0

Magnesium binding site 7 out of 8 in 5qjy

Go back to Magnesium Binding Sites List in 5qjy
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 Z94597856


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 Z94597856 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:40.3
occ:1.00
 OE2 D:GLU116 2.0 41.1 1.0
O D:HOH403 2.1 33.0 1.0
O D:HOH416 2.2 42.6 1.0
O D:HOH425 2.4 47.8 1.0
MG D:MG302 2.5 45.2 1.0
O D:ALA96 3.0 60.8 0.7
CD D:GLU116 3.2 51.4 1.0
NE2 D:GLN82 3.5 47.0 1.0
OE1 D:GLU116 3.6 46.9 1.0
OE2 D:GLU166 3.8 84.2 1.0
OE1 D:GLN82 4.0 50.4 1.0
NH2 D:ARG84 4.0 40.3 1.0
C D:ALA96 4.0 61.2 0.7
CD D:GLN82 4.2 52.0 1.0
OE2 D:GLU112 4.4 72.8 1.0
CG D:GLU116 4.4 51.3 1.0
O D:HOH408 4.5 51.3 1.0
CD D:GLU166 4.6 88.2 1.0
CA D:GLY97 4.6 66.1 0.7
N D:GLY97 4.8 65.3 0.7
O D:HOH404 4.8 29.7 0.7
CG D:GLU166 4.8 78.4 1.0
N D:ALA96 4.8 53.1 0.7
CZ D:ARG84 4.9 45.4 1.0
NH1 D:ARG84 4.9 39.9 1.0
CG1 D:VAL168 5.0 63.1 1.0

Magnesium binding site 8 out of 8 in 5qjy

Go back to Magnesium Binding Sites List in 5qjy
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 Z94597856


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 Z94597856 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:45.2
occ:1.00
 O D:HOH425 1.8 47.8 1.0
OE2 D:GLU112 2.1 72.8 1.0
MG D:MG301 2.5 40.3 1.0
OE2 D:GLU116 2.7 41.1 1.0
OE2 D:GLU166 2.8 84.2 1.0
O D:HOH413 2.9 49.6 1.0
O D:ALA96 3.0 60.8 0.7
O D:HOH403 3.1 33.0 1.0
O D:HOH408 3.1 51.3 1.0
CD D:GLU112 3.2 65.2 1.0
CA D:GLY97 3.6 66.1 0.7
CG D:GLU112 3.7 62.2 1.0
CD D:GLU116 3.9 51.4 1.0
C D:ALA96 4.0 61.2 0.7
CD D:GLU166 4.0 88.2 1.0
OE1 D:GLU112 4.1 71.4 1.0
O D:HOH416 4.2 42.6 1.0
N D:GLY97 4.2 65.3 0.7
N D:LEU98 4.6 72.0 0.7
OE1 D:GLU116 4.6 46.9 1.0
CG D:GLU116 4.6 51.3 1.0
C D:GLY97 4.7 66.8 0.7
OE1 D:GLU166 4.8 84.4 1.0
CG D:GLU166 4.9 78.4 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 02:23:38 2024

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