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Magnesium in PDB 5qjn: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1439422127

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1439422127

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 Z1439422127:
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 Z1439422127, PDB code: 5qjn 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) 78.02 / 1.77
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.450, 59.880, 79.890, 79.29, 81.26, 75.44
R / Rfree (%) 22.9 / 27.3

Other elements in 5qjn:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1439422127 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 Z1439422127 (pdb code 5qjn). 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 Z1439422127, PDB code: 5qjn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjn

Go back to Magnesium Binding Sites List in 5qjn
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 Z1439422127


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 Z1439422127 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:31.8
occ:1.00
 OE2 A:GLU116 2.0 25.1 1.0
O A:HOH439 2.0 24.3 1.0
O A:ALA96 2.0 25.2 1.0
O A:HOH414 2.1 27.1 1.0
O A:HOH449 2.1 24.3 1.0
O A:HOH417 2.2 27.1 1.0
CD A:GLU116 3.0 27.8 1.0
C A:ALA96 3.2 23.2 1.0
MG A:MG302 3.3 60.2 1.0
OE1 A:GLU116 3.3 30.9 1.0
OE2 A:GLU166 3.9 56.7 1.0
O A:HOH444 4.1 21.6 0.7
OE2 A:GLU112 4.1 32.4 1.0
N A:GLY97 4.1 24.7 1.0
CA A:GLY97 4.1 26.2 1.0
N A:ALA96 4.1 20.6 1.0
CA A:ALA96 4.2 22.2 1.0
NE2 A:GLN82 4.3 29.2 1.0
NH2 A:ARG84 4.3 26.6 1.0
O A:HOH419 4.3 23.6 1.0
CG A:GLU116 4.4 26.7 1.0
O A:HOH466 4.5 28.4 1.0
OE1 A:GLN82 4.5 27.5 1.0
O A:HOH459 4.7 35.4 1.0
CB A:ALA96 4.7 19.4 1.0
O B:HOH466 4.7 50.2 1.0
CD A:GLN82 4.8 31.2 1.0
CD A:GLU112 4.8 27.2 1.0

Magnesium binding site 2 out of 8 in 5qjn

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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 Z1439422127


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 Z1439422127 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:60.2
occ:1.00
 OE2 A:GLU112 2.0 32.4 1.0
O A:HOH403 2.1 43.9 1.0
O A:HOH439 2.1 24.3 1.0
OE2 A:GLU166 2.4 56.7 1.0
O A:HOH404 2.4 46.9 1.0
OE2 A:GLU116 2.6 25.1 1.0
CD A:GLU112 2.9 27.2 1.0
OE1 A:GLU112 3.1 30.0 1.0
CD A:GLU166 3.2 67.9 1.0
MG A:MG301 3.3 31.8 1.0
OE1 A:GLU166 3.5 61.6 1.0
CD A:GLU116 3.5 27.8 1.0
CG A:GLU116 3.8 26.7 1.0
O A:ALA96 3.9 25.2 1.0
O A:HOH417 4.0 27.1 1.0
OE2 A:GLU115 4.1 36.5 1.0
CG A:GLU112 4.3 27.7 1.0
CG A:GLU166 4.5 57.1 1.0
O A:HOH459 4.5 35.4 1.0
CA A:GLY97 4.6 26.2 1.0
OE1 A:GLU116 4.6 30.9 1.0
CB A:GLU112 4.7 25.5 1.0
C A:ALA96 4.8 23.2 1.0
O A:HOH401 4.9 39.4 1.0
O A:HOH449 4.9 24.3 1.0

Magnesium binding site 3 out of 8 in 5qjn

Go back to Magnesium Binding Sites List in 5qjn
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 Z1439422127


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 Z1439422127 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:34.5
occ:1.00
 O B:ALA96 2.0 28.4 1.0
O B:HOH431 2.1 35.5 1.0
OE2 B:GLU116 2.1 43.5 1.0
O B:HOH441 2.1 34.0 1.0
O B:HOH440 2.2 29.0 1.0
O B:HOH410 2.3 30.7 1.0
CD B:GLU116 3.1 41.6 1.0
C B:ALA96 3.2 25.6 1.0
OE1 B:GLU116 3.4 37.6 1.0
OE2 B:GLU166 3.8 51.2 1.0
N B:ALA96 4.1 29.4 1.0
CA B:GLY97 4.1 29.2 1.0
OE2 B:GLU112 4.1 43.4 1.0
N B:GLY97 4.1 26.3 1.0
CA B:ALA96 4.2 27.8 1.0
O B:HOH433 4.2 34.9 1.0
MG B:MG303 4.2 73.8 1.0
CG B:GLU116 4.4 39.1 1.0
NH2 B:ARG84 4.5 31.3 1.0
NE2 B:GLN82 4.5 45.0 1.0
OE1 B:GLN82 4.5 45.1 1.0
CD B:GLU166 4.6 68.8 1.0
CB B:ALA96 4.6 31.1 1.0
O B:HOH468 4.6 46.3 1.0
CD B:GLN82 4.9 44.2 1.0
CD B:GLU112 4.9 40.6 1.0

Magnesium binding site 4 out of 8 in 5qjn

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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 Z1439422127


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 Z1439422127 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:73.8
occ:1.00
 OE2 B:GLU112 2.0 43.4 1.0
O B:HOH408 2.5 62.1 1.0
O B:HOH453 2.6 46.4 1.0
OE2 B:GLU166 2.7 51.2 1.0
OE2 B:GLU115 3.0 58.6 1.0
OE2 B:GLU116 3.0 43.5 1.0
CD B:GLU112 3.1 40.6 1.0
OE1 B:GLU166 3.3 68.4 1.0
CG B:GLU116 3.4 39.1 1.0
O B:HOH441 3.4 34.0 1.0
CD B:GLU166 3.4 68.8 1.0
CD B:GLU116 3.6 41.6 1.0
OE1 B:GLU112 3.6 36.4 1.0
CB B:GLU115 3.9 41.9 1.0
CD B:GLU115 4.1 54.7 1.0
MG B:MG302 4.2 34.5 1.0
CG B:GLU112 4.4 40.1 1.0
CA B:GLU112 4.6 35.8 1.0
CB B:GLU112 4.6 40.4 1.0
CG B:GLU115 4.7 47.5 1.0
O B:ALA96 4.7 28.4 1.0
O B:GLU112 4.7 34.2 1.0
OE1 B:GLU116 4.8 37.6 1.0
CB B:GLU116 4.8 37.1 1.0
N B:GLU116 4.9 43.2 1.0
CG B:GLU166 4.9 64.0 1.0

Magnesium binding site 5 out of 8 in 5qjn

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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 Z1439422127


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 Z1439422127 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:68.2
occ:1.00
 O C:HOH411 1.9 40.8 1.0
O C:HOH413 2.3 45.2 1.0
OE2 C:GLU112 2.3 38.0 1.0
O C:HOH419 2.5 54.7 1.0
OE2 C:GLU166 2.5 73.0 1.0
CD C:GLU112 3.0 40.8 1.0
O C:HOH408 3.0 61.3 1.0
OE1 C:GLU112 3.0 51.1 1.0
OE2 C:GLU116 3.1 37.2 1.0
MG C:MG303 3.4 35.3 1.0
CD C:GLU166 3.4 74.8 1.0
OE1 C:GLU166 3.6 77.8 1.0
O C:ALA96 3.7 28.4 1.0
O C:HOH424 4.0 35.9 1.0
CD C:GLU116 4.1 34.4 1.0
CA C:GLY97 4.2 33.0 1.0
OE2 C:GLU115 4.2 42.9 1.0
CG C:GLU116 4.4 33.2 1.0
CG C:GLU112 4.5 38.0 1.0
O C:HOH445 4.5 28.9 1.0
C C:ALA96 4.6 31.4 1.0
O C:HOH469 4.6 50.8 1.0
CG C:GLU166 4.6 64.8 1.0
N C:GLY97 4.8 30.0 1.0

Magnesium binding site 6 out of 8 in 5qjn

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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 Z1439422127


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 Z1439422127 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:35.3
occ:1.00
 OE2 C:GLU116 1.9 37.2 1.0
O C:HOH411 1.9 40.8 1.0
O C:HOH445 1.9 28.9 1.0
O C:HOH412 2.0 32.4 1.0
O C:HOH424 2.1 35.9 1.0
O C:ALA96 2.1 28.4 1.0
CD C:GLU116 3.0 34.4 1.0
C C:ALA96 3.3 31.4 1.0
OE1 C:GLU116 3.3 41.7 1.0
MG C:MG302 3.4 68.2 1.0
OE2 C:GLU166 3.6 73.0 1.0
O C:HOH431 4.1 34.5 1.0
N C:ALA96 4.2 29.4 1.0
N C:GLY97 4.2 30.0 1.0
CA C:ALA96 4.2 28.9 1.0
OE2 C:GLU112 4.2 38.0 1.0
CA C:GLY97 4.3 33.0 1.0
NH2 C:ARG84 4.3 34.4 1.0
OE1 C:GLN82 4.3 31.2 1.0
NE2 C:GLN82 4.3 37.3 1.0
CG C:GLU116 4.3 33.2 1.0
O C:HOH460 4.6 46.0 1.0
CB C:ALA96 4.7 29.1 1.0
CD C:GLN82 4.7 40.5 1.0
O C:HOH413 4.8 45.2 1.0
CD C:GLU166 4.9 74.8 1.0

Magnesium binding site 7 out of 8 in 5qjn

Go back to Magnesium Binding Sites List in 5qjn
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 Z1439422127


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 Z1439422127 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:42.6
occ:1.00
 OE2 D:GLU116 2.2 45.5 1.0
O D:HOH417 2.3 31.6 1.0
O D:HOH412 2.3 31.4 1.0
O D:HOH427 2.4 39.9 1.0
MG D:MG302 2.5 39.4 1.0
OE2 D:GLU166 3.1 77.3 1.0
CD D:GLU116 3.3 51.2 1.0
NE2 D:GLN82 3.4 38.0 1.0
O D:ALA96 3.4 37.1 1.0
OE1 D:GLU116 3.8 46.4 1.0
OE2 D:GLU112 4.0 58.6 1.0
NH2 D:ARG84 4.0 42.2 1.0
OE1 D:GLN82 4.1 45.4 1.0
CD D:GLN82 4.2 44.2 1.0
CD D:GLU166 4.2 81.6 1.0
C D:ALA96 4.5 47.3 1.0
CG D:GLU166 4.5 72.9 1.0
CG D:GLU116 4.6 48.0 1.0
NH1 D:ARG84 4.6 39.1 1.0
O D:HOH409 4.7 46.5 1.0
CZ D:ARG84 4.7 43.1 1.0
CG1 D:VAL168 5.0 72.6 1.0

Magnesium binding site 8 out of 8 in 5qjn

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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 Z1439422127


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 Z1439422127 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:39.4
occ:1.00
 O D:HOH427 2.0 39.9 1.0
OE2 D:GLU112 2.1 58.6 1.0
MG D:MG301 2.5 42.6 1.0
O D:HOH404 2.6 42.2 1.0
OE2 D:GLU166 2.7 77.3 1.0
O D:HOH417 2.8 31.6 1.0
OE2 D:GLU116 2.9 45.5 1.0
O D:ALA96 3.0 37.1 1.0
CD D:GLU112 3.3 55.2 1.0
CA D:GLY97 3.5 43.5 1.0
O D:HOH409 3.6 46.5 1.0
CD D:GLU166 3.9 81.6 1.0
C D:ALA96 4.0 47.3 1.0
OE1 D:GLU112 4.0 58.3 1.0
CD D:GLU116 4.1 51.2 1.0
CG D:GLU112 4.2 58.0 1.0
N D:GLY97 4.2 41.8 1.0
O D:HOH412 4.2 31.4 1.0
OE1 D:GLU166 4.7 79.6 1.0
C D:GLY97 4.8 44.6 1.0
OE1 D:GLU116 4.8 46.4 1.0
CG D:GLU166 4.8 72.9 1.0
N D:LEU98 4.9 45.0 1.0
CG D:GLU116 4.9 48.0 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 02:19:09 2024

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