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Magnesium in PDB 5qja: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1497321453

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1497321453

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 Z1497321453:
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 Z1497321453, PDB code: 5qja 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) 78.35 / 1.64
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.437, 59.840, 80.189, 79.33, 81.51, 75.50
R / Rfree (%) 22.5 / 25.7

Other elements in 5qja:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1497321453 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 Z1497321453 (pdb code 5qja). 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 Z1497321453, PDB code: 5qja:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qja

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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 Z1497321453


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 Z1497321453 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:26.3
occ:1.00
 O A:HOH429 2.0 22.8 1.0
OE2 A:GLU116 2.0 25.8 1.0
O A:ALA96 2.1 21.1 1.0
O A:HOH435 2.2 20.6 1.0
O A:HOH438 2.2 25.5 1.0
O A:HOH462 2.2 19.1 1.0
CD A:GLU116 3.1 27.1 1.0
C A:ALA96 3.3 21.3 1.0
OE1 A:GLU116 3.5 23.7 1.0
MG A:MG302 3.6 41.9 1.0
OE2 A:GLU166 3.8 56.9 1.0
N A:ALA96 4.2 17.5 1.0
O A:HOH450 4.2 21.3 0.8
O A:HOH431 4.2 17.9 1.0
CA A:ALA96 4.2 19.7 1.0
NH2 A:ARG84 4.2 22.5 1.0
N A:GLY97 4.2 21.3 1.0
CA A:GLY97 4.2 21.0 1.0
OE2 A:GLU112 4.3 27.1 1.0
OE1 A:GLN82 4.3 27.8 1.0
NE2 A:GLN82 4.4 27.8 1.0
CG A:GLU116 4.5 22.8 1.0
O A:HOH470 4.5 23.1 1.0
CB A:ALA96 4.6 17.1 1.0
CD A:GLN82 4.7 30.5 1.0
O A:HOH474 4.8 50.5 1.0

Magnesium binding site 2 out of 8 in 5qja

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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 Z1497321453


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 Z1497321453 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:41.9
occ:1.00
 O A:HOH404 1.8 29.4 1.0
OE2 A:GLU112 2.2 27.1 1.0
OE2 A:GLU166 2.2 56.9 1.0
O A:HOH435 2.2 20.6 1.0
OE2 A:GLU116 2.6 25.8 1.0
O A:HOH403 2.8 37.8 1.0
CD A:GLU166 2.9 60.2 1.0
OE1 A:GLU166 3.0 48.7 1.0
CD A:GLU112 3.1 29.8 1.0
OE1 A:GLU112 3.4 31.2 1.0
CD A:GLU116 3.4 27.1 1.0
MG A:MG301 3.6 26.3 1.0
CG A:GLU116 3.6 22.8 1.0
OE2 A:GLU115 4.0 32.2 1.0
O A:ALA96 4.1 21.1 1.0
O A:HOH438 4.1 25.5 1.0
CG A:GLU166 4.2 51.8 1.0
CG A:GLU112 4.5 25.8 1.0
OE1 A:GLU116 4.6 23.7 1.0
O A:HOH466 4.7 28.8 1.0
CB A:GLU112 4.9 23.6 1.0
CB A:GLU115 4.9 26.6 1.0
CA A:GLY97 5.0 21.0 1.0

Magnesium binding site 3 out of 8 in 5qja

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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 Z1497321453


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 Z1497321453 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:30.6
occ:1.00
 O B:ALA96 1.9 24.9 1.0
O B:HOH406 2.0 27.7 1.0
OE2 B:GLU116 2.0 34.8 1.0
O B:HOH412 2.1 28.2 1.0
O B:HOH419 2.1 27.5 1.0
O B:HOH436 2.2 29.9 1.0
CD B:GLU116 3.0 33.1 1.0
C B:ALA96 3.2 22.3 1.0
OE1 B:GLU116 3.3 28.3 1.0
OE2 B:GLU166 3.7 51.3 1.0
MG B:MG303 3.7 52.6 1.0
N B:GLY97 4.1 25.7 1.0
N B:ALA96 4.1 24.6 1.0
CA B:ALA96 4.1 23.6 1.0
OE2 B:GLU112 4.2 33.7 1.0
O B:HOH407 4.2 26.8 1.0
CA B:GLY97 4.2 22.7 1.0
NH2 B:ARG84 4.3 25.9 1.0
NE2 B:GLN82 4.3 39.5 1.0
O B:HOH421 4.3 31.0 0.8
CG B:GLU116 4.3 31.1 1.0
OE1 B:GLN82 4.4 32.0 1.0
CB B:ALA96 4.5 28.2 1.0
CD B:GLU166 4.7 62.2 1.0
CD B:GLN82 4.7 39.0 1.0
O B:HOH465 4.9 33.5 0.8
O B:HOH469 5.0 38.4 1.0
O A:HOH422 5.0 33.5 0.8
O B:HOH450 5.0 45.2 1.0

Magnesium binding site 4 out of 8 in 5qja

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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 Z1497321453


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 Z1497321453 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:52.6
occ:1.00
 OE2 B:GLU112 2.0 33.7 1.0
OE2 B:GLU166 2.3 51.3 1.0
O B:HOH401 2.3 57.0 1.0
O B:HOH450 2.4 45.2 1.0
O B:HOH436 2.6 29.9 1.0
OE2 B:GLU116 2.6 34.8 1.0
CD B:GLU112 3.0 33.6 1.0
CD B:GLU166 3.3 62.2 1.0
CD B:GLU116 3.3 33.1 1.0
CG B:GLU116 3.4 31.1 1.0
OE1 B:GLU112 3.4 33.0 1.0
OE1 B:GLU166 3.5 64.7 1.0
OE2 B:GLU115 3.7 44.0 1.0
MG B:MG302 3.7 30.6 1.0
O B:ALA96 4.1 24.9 1.0
CG B:GLU112 4.4 30.4 1.0
O B:HOH412 4.4 28.2 1.0
OE1 B:GLU116 4.5 28.3 1.0
CB B:GLU115 4.6 40.4 1.0
CG B:GLU166 4.6 57.1 1.0
CB B:GLU112 4.7 30.0 1.0
O B:HOH465 4.7 33.5 0.8
O B:HOH467 4.8 47.1 0.8
CD B:GLU115 4.8 42.4 1.0
CB B:GLU116 4.8 28.9 1.0
CA B:GLU112 4.8 28.4 1.0
O B:GLU112 4.9 28.4 1.0
C B:ALA96 4.9 22.3 1.0

Magnesium binding site 5 out of 8 in 5qja

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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 Z1497321453


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 Z1497321453 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:41.5
occ:1.00
 MG C:MG303 2.2 33.1 1.0
O C:HOH447 2.8 56.6 1.0
OE2 C:GLU116 2.9 29.6 1.0
O C:ALA96 2.9 25.4 1.0
OE2 C:GLU166 2.9 59.6 1.0
O C:HOH433 3.1 33.5 1.0
O C:HOH451 3.1 26.9 1.0
OE2 C:GLU112 3.2 39.9 1.0
O C:HOH435 3.3 38.2 0.9
OE1 C:GLU112 3.6 45.2 1.0
O C:HOH404 3.6 45.5 1.0
CA C:GLY97 3.6 29.6 1.0
CD C:GLU112 3.7 35.6 1.0
C C:ALA96 3.9 28.6 1.0
CD C:GLU166 4.0 62.2 1.0
CD C:GLU116 4.1 30.1 1.0
N C:GLY97 4.3 28.3 1.0
O D:HOH417 4.4 43.5 0.9
O C:HOH444 4.4 26.4 1.0
OE1 C:GLU166 4.7 63.7 1.0
O C:HOH472 4.7 49.8 1.0
CG C:GLU166 4.8 56.6 1.0
O C:HOH464 4.9 31.6 0.9
OE1 C:GLU116 4.9 33.9 1.0
C C:GLY97 4.9 30.0 1.0
CG C:GLU116 5.0 27.7 1.0
CG C:GLU112 5.0 32.8 1.0

Magnesium binding site 6 out of 8 in 5qja

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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 Z1497321453


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 Z1497321453 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:33.1
occ:1.00
 OE2 C:GLU116 1.9 29.6 1.0
O C:ALA96 2.1 25.4 1.0
O C:HOH444 2.1 26.4 1.0
O C:HOH433 2.1 33.5 1.0
MG C:MG302 2.2 41.5 1.0
O C:HOH451 2.3 26.9 1.0
CD C:GLU116 3.0 30.1 1.0
C C:ALA96 3.3 28.6 1.0
OE1 C:GLU116 3.3 33.9 1.0
OE2 C:GLU166 3.6 59.6 1.0
OE2 C:GLU112 4.1 39.9 1.0
N C:ALA96 4.1 25.8 1.0
CA C:ALA96 4.2 23.8 1.0
N C:GLY97 4.3 28.3 1.0
O C:HOH410 4.3 22.8 0.9
CA C:GLY97 4.3 29.6 1.0
NE2 C:GLN82 4.3 32.3 1.0
CG C:GLU116 4.3 27.7 1.0
OE1 C:GLN82 4.4 31.2 1.0
NH2 C:ARG84 4.5 29.2 1.0
O C:HOH464 4.6 31.6 0.9
O C:HOH404 4.6 45.5 1.0
CB C:ALA96 4.7 23.8 1.0
O C:HOH447 4.8 56.6 1.0
CD C:GLN82 4.8 39.0 1.0
CD C:GLU112 4.9 35.6 1.0
CD C:GLU166 4.9 62.2 1.0

Magnesium binding site 7 out of 8 in 5qja

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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 Z1497321453


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 Z1497321453 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:31.9
occ:1.00
 O D:HOH425 2.0 30.2 1.0
O D:HOH410 2.1 27.1 1.0
OE2 D:GLU116 2.1 30.6 1.0
MG D:MG302 2.1 38.1 1.0
O D:ALA96 2.3 34.3 1.0
CD D:GLU116 3.1 37.9 1.0
C D:ALA96 3.4 33.7 1.0
OE1 D:GLU116 3.5 34.4 1.0
O D:HOH401 3.9 44.3 1.0
OE2 D:GLU112 4.1 53.7 1.0
N D:ALA96 4.2 31.0 1.0
NH2 D:ARG84 4.2 35.3 1.0
NE2 D:GLN82 4.2 33.2 1.0
OE2 D:GLU166 4.2 69.8 1.0
OE1 D:GLN82 4.3 35.2 1.0
CA D:ALA96 4.3 32.4 1.0
N D:GLY97 4.4 33.5 1.0
CA D:GLY97 4.4 35.2 1.0
CG D:GLU116 4.4 37.5 1.0
O D:HOH404 4.5 31.9 0.8
CD D:GLN82 4.7 39.7 1.0
CB D:ALA96 4.8 32.9 1.0
CD D:GLU112 4.8 51.0 1.0
O D:HOH445 4.9 32.0 0.8
CG D:GLU112 4.9 56.4 1.0

Magnesium binding site 8 out of 8 in 5qja

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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 Z1497321453


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 Z1497321453 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:38.1
occ:1.00
 MG D:MG301 2.1 31.9 1.0
O D:HOH425 2.9 30.2 1.0
OE2 D:GLU116 2.9 30.6 1.0
O D:ALA96 2.9 34.3 1.0
OE2 D:GLU166 3.0 69.8 1.0
O D:HOH401 3.0 44.3 1.0
OE2 D:GLU112 3.1 53.7 1.0
O D:HOH428 3.3 33.1 0.8
CA D:GLY97 3.6 35.2 1.0
CD D:GLU112 3.8 51.0 1.0
C D:ALA96 3.9 33.7 1.0
CD D:GLU116 4.1 37.9 1.0
O D:HOH410 4.1 27.1 1.0
CD D:GLU166 4.2 67.6 1.0
N D:GLY97 4.3 33.5 1.0
OE1 D:GLU112 4.3 58.0 1.0
O D:HOH434 4.3 38.8 0.8
CG D:GLU112 4.5 56.4 1.0
OE1 D:GLU166 4.9 57.1 1.0
OE1 D:GLU116 4.9 34.4 1.0
C D:GLY97 4.9 38.2 1.0
O D:HOH445 4.9 32.0 0.8

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 02:11:44 2024

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