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Magnesium in PDB 5qjs: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z979145504

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z979145504

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 Z979145504:
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 Z979145504, PDB code: 5qjs 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) 78.11 / 1.58
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.461, 59.941, 79.923, 79.53, 81.32, 75.46
R / Rfree (%) 23.5 / 27.2

Other elements in 5qjs:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z979145504 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 Z979145504 (pdb code 5qjs). 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 Z979145504, PDB code: 5qjs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjs

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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 Z979145504


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 Z979145504 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:30.3
occ:1.00
 O A:HOH451 2.0 23.3 1.0
O A:ALA96 2.0 25.3 1.0
O A:HOH452 2.1 25.6 1.0
OE2 A:GLU116 2.1 24.2 1.0
O A:HOH417 2.2 25.3 1.0
O A:HOH422 2.2 27.2 1.0
CD A:GLU116 3.1 28.6 1.0
C A:ALA96 3.2 23.8 1.0
MG A:MG302 3.3 62.3 1.0
OE1 A:GLU116 3.4 28.0 1.0
OE2 A:GLU166 4.0 60.9 1.0
OE2 A:GLU112 4.0 36.8 1.0
CA A:GLY97 4.1 25.7 1.0
N A:GLY97 4.1 25.5 1.0
O A:HOH455 4.1 28.2 1.0
N A:ALA96 4.2 20.0 1.0
CA A:ALA96 4.2 22.6 1.0
NH2 A:ARG84 4.3 27.8 1.0
O A:HOH428 4.3 24.1 1.0
NE2 A:GLN82 4.4 30.9 1.0
O A:HOH471 4.4 27.2 1.0
CG A:GLU116 4.4 28.1 1.0
O A:HOH465 4.5 41.8 1.0
OE1 A:GLN82 4.5 29.2 1.0
CB A:ALA96 4.7 19.5 1.0
O A:HOH478 4.7 53.0 1.0
CD A:GLU112 4.8 31.0 1.0
CD A:GLN82 4.8 35.6 1.0
O A:HOH409 4.9 45.3 1.0

Magnesium binding site 2 out of 8 in 5qjs

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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 Z979145504


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 Z979145504 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:62.3
occ:1.00
 O A:HOH409 1.9 45.3 1.0
O A:HOH451 2.0 23.3 1.0
OE2 A:GLU112 2.1 36.8 1.0
OE2 A:GLU166 2.5 60.9 1.0
O A:HOH416 2.6 48.5 1.0
OE2 A:GLU116 2.7 24.2 1.0
CD A:GLU112 3.0 31.0 1.0
OE1 A:GLU112 3.2 32.4 1.0
CD A:GLU166 3.3 71.0 1.0
MG A:MG301 3.3 30.3 1.0
OE1 A:GLU166 3.5 63.2 1.0
CD A:GLU116 3.6 28.6 1.0
CG A:GLU116 3.9 28.1 1.0
O A:ALA96 4.0 25.3 1.0
O A:HOH422 4.0 27.2 1.0
O A:HOH465 4.1 41.8 1.0
OE2 A:GLU115 4.1 39.4 1.0
CG A:GLU112 4.4 31.8 1.0
CG A:GLU166 4.5 67.2 1.0
OE1 A:GLU116 4.7 28.0 1.0
CA A:GLY97 4.7 25.7 1.0
O A:HOH401 4.8 50.9 1.0
O A:HOH452 4.9 25.6 1.0
CB A:GLU112 4.9 27.9 1.0
C A:ALA96 4.9 23.8 1.0
O A:HOH478 5.0 53.0 1.0

Magnesium binding site 3 out of 8 in 5qjs

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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 Z979145504


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 Z979145504 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:32.9
occ:1.00
 O B:HOH414 2.0 32.7 1.0
O B:ALA96 2.0 28.5 1.0
O B:HOH415 2.1 32.0 1.0
O B:HOH443 2.1 28.8 1.0
OE2 B:GLU116 2.1 38.4 1.0
O B:HOH450 2.2 33.5 1.0
CD B:GLU116 3.1 38.2 1.0
C B:ALA96 3.2 23.9 1.0
OE1 B:GLU116 3.5 33.0 1.0
OE2 B:GLU166 3.8 50.6 1.0
MG B:MG303 4.0 82.9 1.0
OE2 B:GLU112 4.0 40.9 1.0
N B:GLY97 4.1 27.0 1.0
CA B:GLY97 4.1 29.8 1.0
O B:HOH432 4.1 30.5 1.0
N B:ALA96 4.2 24.1 1.0
NE2 B:GLN82 4.2 41.3 1.0
CA B:ALA96 4.2 24.9 1.0
NH2 B:ARG84 4.3 32.2 1.0
OE1 B:GLN82 4.3 37.2 1.0
O B:HOH447 4.4 47.7 0.8
O B:HOH469 4.5 42.4 1.0
CG B:GLU116 4.5 35.9 1.0
CD B:GLN82 4.7 45.1 1.0
CB B:ALA96 4.7 28.2 1.0
CD B:GLU166 4.8 69.8 1.0

Magnesium binding site 4 out of 8 in 5qjs

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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 Z979145504


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 Z979145504 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:82.9
occ:1.00
 OE2 B:GLU112 2.1 40.9 1.0
O B:HOH420 2.2 52.4 1.0
OE2 B:GLU166 2.6 50.6 1.0
O B:HOH452 2.6 50.1 1.0
OE2 B:GLU116 2.7 38.4 1.0
O B:HOH450 3.0 33.5 1.0
CD B:GLU112 3.1 42.6 1.0
CG B:GLU116 3.3 35.9 1.0
CD B:GLU116 3.4 38.2 1.0
CD B:GLU166 3.4 69.8 1.0
OE2 B:GLU115 3.5 56.5 1.0
OE1 B:GLU166 3.5 70.1 1.0
OE1 B:GLU112 3.6 38.5 1.0
MG B:MG302 4.0 32.9 1.0
CB B:GLU115 4.3 40.4 1.0
O B:ALA96 4.4 28.5 1.0
CG B:GLU112 4.4 38.6 1.0
O B:HOH414 4.5 32.7 1.0
CD B:GLU115 4.6 49.4 1.0
OE1 B:GLU116 4.6 33.0 1.0
CB B:GLU112 4.7 36.9 1.0
CA B:GLU112 4.7 33.0 1.0
CB B:GLU116 4.7 32.2 1.0
O B:GLU112 4.8 33.5 1.0
CG B:GLU166 4.9 65.6 1.0
N B:GLU116 4.9 38.4 1.0

Magnesium binding site 5 out of 8 in 5qjs

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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 Z979145504


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 Z979145504 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:65.7
occ:1.00
 O C:HOH436 1.8 35.8 1.0
O C:HOH403 2.2 43.5 1.0
OE2 C:GLU166 2.3 64.7 1.0
OE2 C:GLU112 2.3 38.9 1.0
O C:HOH425 2.8 56.2 1.0
OE2 C:GLU116 2.8 35.7 1.0
MG C:MG303 3.1 36.6 1.0
CD C:GLU112 3.2 43.0 1.0
CD C:GLU166 3.3 71.7 1.0
O C:HOH407 3.3 60.2 1.0
OE1 C:GLU112 3.4 50.0 1.0
O C:ALA96 3.6 29.9 1.0
OE1 C:GLU166 3.6 72.5 1.0
O C:HOH419 3.8 36.1 1.0
CD C:GLU116 3.8 33.2 1.0
CG C:GLU116 4.2 30.6 1.0
CA C:GLY97 4.3 33.8 1.0
O C:HOH443 4.4 31.3 1.0
OE2 C:GLU115 4.5 43.5 1.0
CG C:GLU166 4.5 65.6 1.0
C C:ALA96 4.6 34.4 1.0
CG C:GLU112 4.6 39.3 1.0
OE1 C:GLU116 4.9 35.7 1.0
N C:GLY97 4.9 33.9 1.0
O C:HOH464 4.9 52.3 1.0
O C:HOH411 4.9 29.6 1.0

Magnesium binding site 6 out of 8 in 5qjs

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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 Z979145504


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 Z979145504 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:36.6
occ:1.00
 OE2 C:GLU116 1.8 35.7 1.0
O C:HOH411 2.0 29.6 1.0
O C:HOH436 2.0 35.8 1.0
O C:HOH443 2.1 31.3 1.0
O C:HOH419 2.1 36.1 1.0
O C:ALA96 2.2 29.9 1.0
CD C:GLU116 3.0 33.2 1.0
MG C:MG302 3.1 65.7 1.0
C C:ALA96 3.3 34.4 1.0
OE1 C:GLU116 3.3 35.7 1.0
OE2 C:GLU166 3.4 64.7 1.0
OE2 C:GLU112 4.2 38.9 1.0
CA C:GLY97 4.2 33.8 1.0
N C:GLY97 4.2 33.9 1.0
N C:ALA96 4.2 27.7 1.0
CA C:ALA96 4.3 26.7 1.0
CG C:GLU116 4.3 30.6 1.0
NE2 C:GLN82 4.4 35.9 1.0
NH2 C:ARG84 4.4 34.3 1.0
OE1 C:GLN82 4.4 36.9 1.0
CD C:GLU166 4.7 71.7 1.0
O C:HOH403 4.7 43.5 1.0
CB C:ALA96 4.8 27.0 1.0
CD C:GLN82 4.9 41.3 1.0

Magnesium binding site 7 out of 8 in 5qjs

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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 Z979145504


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 Z979145504 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:38.4
occ:1.00
 OE2 D:GLU116 1.9 40.2 1.0
O D:HOH405 2.0 29.1 1.0
O D:HOH413 2.1 30.6 1.0
MG D:MG302 2.2 42.4 1.0
O D:HOH426 2.5 40.9 1.0
O D:ALA96 2.5 37.8 1.0
CD D:GLU116 3.0 52.0 1.0
OE1 D:GLU116 3.4 47.3 1.0
C D:ALA96 3.6 46.8 1.0
OE2 D:GLU112 3.7 55.1 1.0
OE2 D:GLU166 3.7 84.7 1.0
NE2 D:GLN82 4.0 46.5 1.0
CG D:GLU116 4.3 47.0 1.0
OE1 D:GLN82 4.3 50.9 1.0
NH2 D:ARG84 4.3 44.1 1.0
N D:ALA96 4.3 47.0 1.0
CA D:GLY97 4.5 46.3 1.0
CA D:ALA96 4.5 47.5 1.0
N D:GLY97 4.5 42.5 1.0
O D:HOH407 4.6 52.7 1.0
CD D:GLN82 4.6 51.8 1.0
CD D:GLU112 4.7 57.8 1.0
CD D:GLU166 4.8 85.3 1.0
O D:HOH402 4.8 48.5 1.0
CG D:GLU112 4.9 60.6 1.0
CB D:ALA96 4.9 45.4 1.0

Magnesium binding site 8 out of 8 in 5qjs

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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 Z979145504


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 Z979145504 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:42.4
occ:1.00
 O D:HOH426 1.7 40.9 1.0
OE2 D:GLU112 2.0 55.1 1.0
MG D:MG301 2.2 38.4 1.0
O D:HOH402 2.7 48.5 1.0
OE2 D:GLU116 2.9 40.2 1.0
O D:ALA96 2.9 37.8 1.0
O D:HOH405 2.9 29.1 1.0
OE2 D:GLU166 3.0 84.7 1.0
CD D:GLU112 3.2 57.8 1.0
O D:HOH407 3.4 52.7 1.0
CA D:GLY97 3.5 46.3 1.0
C D:ALA96 3.9 46.8 1.0
CD D:GLU116 4.0 52.0 1.0
OE1 D:GLU112 4.0 57.1 1.0
CG D:GLU112 4.1 60.6 1.0
N D:GLY97 4.2 42.5 1.0
CD D:GLU166 4.2 85.3 1.0
O D:HOH413 4.2 30.6 1.0
OE1 D:GLU116 4.7 47.3 1.0
C D:GLY97 4.7 47.5 1.0
CG D:GLU116 4.9 47.0 1.0
N D:LEU98 4.9 52.7 1.0
OE1 D:GLU166 5.0 81.0 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 02:22:35 2024

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