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Magnesium in PDB 5qjo: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z57292369

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z57292369

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 Z57292369:
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 Z57292369, PDB code: 5qjo 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) 78.20 / 1.98
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.061, 59.567, 79.930, 79.55, 81.90, 75.89
R / Rfree (%) 21 / 24.9

Other elements in 5qjo:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z57292369 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 Z57292369 (pdb code 5qjo). 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 Z57292369, PDB code: 5qjo:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjo

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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 Z57292369


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 Z57292369 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:26.4
occ:1.00
 O A:HOH421 2.0 19.0 1.0
O A:HOH423 2.1 21.8 1.0
OE2 A:GLU116 2.1 23.2 1.0
O A:HOH458 2.1 19.2 1.0
O A:HOH462 2.1 23.4 1.0
O A:ALA96 2.2 19.2 1.0
CD A:GLU116 3.1 21.9 1.0
MG A:MG302 3.3 68.1 1.0
C A:ALA96 3.4 18.2 1.0
OE1 A:GLU116 3.4 23.1 1.0
O A:HOH432 4.0 20.6 0.9
NH2 A:ARG84 4.2 21.6 1.0
NE2 A:GLN82 4.2 21.0 1.0
N A:ALA96 4.3 17.3 1.0
O A:HOH422 4.3 18.4 1.0
N A:GLY97 4.3 19.7 1.0
CA A:ALA96 4.3 16.6 1.0
OE2 A:GLU112 4.3 28.8 1.0
CA A:GLY97 4.3 19.2 1.0
O A:HOH474 4.3 36.3 1.0
OE1 A:GLN82 4.3 19.4 1.0
OE2 A:GLU166 4.4 91.8 1.0
O A:HOH470 4.4 25.1 1.0
CG A:GLU116 4.4 23.8 1.0
O A:HOH465 4.4 28.8 1.0
CB A:ALA96 4.7 14.8 1.0
CD A:GLN82 4.7 25.3 1.0
CD A:GLU112 5.0 27.6 1.0
CZ A:ARG84 5.0 21.4 1.0
NH1 A:ARG84 5.0 20.6 1.0

Magnesium binding site 2 out of 8 in 5qjo

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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 Z57292369


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 Z57292369 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:68.1
occ:1.00
 O A:HOH407 2.2 38.0 1.0
O A:HOH462 2.2 23.4 1.0
O A:HOH417 2.3 39.7 1.0
OE2 A:GLU166 2.3 91.8 1.0
OE2 A:GLU112 2.4 28.8 1.0
OE2 A:GLU116 2.5 23.2 1.0
CD A:GLU112 3.2 27.6 1.0
OE1 A:GLU112 3.2 30.9 1.0
CD A:GLU166 3.3 89.3 1.0
MG A:MG301 3.3 26.4 1.0
CD A:GLU116 3.5 21.9 1.0
OE1 A:GLU166 3.5 76.9 1.0
CG A:GLU116 3.8 23.8 1.0
O A:HOH423 3.8 21.8 1.0
O A:ALA96 4.0 19.2 1.0
OE2 A:GLU115 4.2 32.3 1.0
O A:HOH465 4.3 28.8 1.0
CG A:GLU112 4.6 24.7 1.0
OE1 A:GLU116 4.6 23.1 1.0
CG A:GLU166 4.6 81.0 1.0
O A:HOH474 4.7 36.3 1.0
CA A:GLY97 4.8 19.2 1.0
O A:HOH458 4.9 19.2 1.0
C A:ALA96 4.9 18.2 1.0
O A:HOH421 4.9 19.0 1.0

Magnesium binding site 3 out of 8 in 5qjo

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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 Z57292369


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 Z57292369 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:27.6
occ:1.00
 O B:ALA96 2.0 21.6 1.0
OE2 B:GLU116 2.0 29.8 1.0
O B:HOH420 2.0 24.3 1.0
O B:HOH455 2.1 23.2 1.0
O B:HOH404 2.1 23.6 1.0
O B:HOH445 2.1 26.7 1.0
CD B:GLU116 3.0 28.3 1.0
C B:ALA96 3.2 22.5 1.0
OE1 B:GLU116 3.3 30.2 1.0
OE2 B:GLU166 4.0 65.5 1.0
N B:GLY97 4.1 22.2 1.0
CA B:GLY97 4.1 23.0 1.0
N B:ALA96 4.2 20.0 1.0
CA B:ALA96 4.2 21.2 1.0
OE2 B:GLU112 4.2 38.2 1.0
O B:HOH417 4.2 29.4 1.0
NE2 B:GLN82 4.3 32.8 1.0
OE1 B:GLN82 4.3 29.9 1.0
NH2 B:ARG84 4.3 24.1 1.0
CG B:GLU116 4.3 26.7 1.0
CD B:GLU166 4.4 79.2 1.0
O B:HOH466 4.6 29.4 0.9
O B:HOH475 4.6 33.1 1.0
CB B:ALA96 4.6 21.9 1.0
CD B:GLN82 4.7 37.0 1.0
MG B:MG303 4.7 70.7 1.0
OE1 B:GLU166 4.8 74.7 1.0
CD B:GLU112 5.0 32.7 1.0

Magnesium binding site 4 out of 8 in 5qjo

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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 Z57292369


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 Z57292369 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:70.7
occ:1.00
 OE2 B:GLU166 2.4 65.5 1.0
OE2 B:GLU112 2.5 38.2 1.0
O B:HOH437 2.5 56.6 1.0
O B:HOH432 2.7 43.1 1.0
OE2 B:GLU115 2.9 49.5 1.0
CD B:GLU166 3.2 79.2 1.0
OE1 B:GLU166 3.3 74.7 1.0
CD B:GLU112 3.4 32.7 1.0
OE2 B:GLU116 3.5 29.8 1.0
CG B:GLU116 3.5 26.7 1.0
OE1 B:GLU112 3.6 35.9 1.0
CB B:GLU115 3.8 34.9 1.0
O B:HOH445 3.8 26.7 1.0
CD B:GLU116 4.0 28.3 1.0
CD B:GLU115 4.0 41.3 1.0
CG B:GLU115 4.5 41.0 1.0
CG B:GLU166 4.7 76.0 1.0
MG B:MG302 4.7 27.6 1.0
CG B:GLU112 4.8 29.6 1.0
N B:GLU116 4.8 30.2 1.0
N B:GLY163 4.8 83.4 1.0
O B:GLU112 4.8 31.5 1.0
C B:GLU115 4.9 30.6 1.0
CB B:GLU116 4.9 28.0 1.0
CA B:GLU112 4.9 28.2 1.0
CA B:GLU115 5.0 29.3 1.0
NH1 B:ARG111 5.0 35.9 1.0

Magnesium binding site 5 out of 8 in 5qjo

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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 Z57292369


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 Z57292369 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:43.0
occ:1.00
 MG C:MG303 2.1 29.0 1.0
OE2 C:GLU116 2.7 28.1 1.0
OE2 C:GLU166 2.8 67.4 1.0
O C:HOH447 3.0 50.9 1.0
O C:ALA96 3.0 27.6 1.0
O C:HOH453 3.0 36.7 1.0
O C:HOH415 3.1 37.3 1.0
O C:HOH454 3.1 18.6 1.0
OE2 C:GLU112 3.1 34.4 1.0
O C:HOH407 3.5 46.7 1.0
OE1 C:GLU112 3.6 40.5 1.0
CA C:GLY97 3.7 31.1 1.0
CD C:GLU112 3.7 35.7 1.0
CD C:GLU166 3.8 73.2 1.0
C C:ALA96 4.0 25.0 1.0
CD C:GLU116 4.0 30.4 1.0
O C:HOH463 4.2 52.9 1.0
O C:HOH422 4.3 22.7 1.0
N C:GLY97 4.3 25.2 1.0
OE1 C:GLU166 4.4 73.4 1.0
CG C:GLU166 4.8 66.0 1.0
OE1 C:GLU116 4.8 39.8 1.0
CG C:GLU116 4.8 28.1 1.0
O C:HOH410 4.9 55.3 1.0
C C:GLY97 5.0 31.5 1.0

Magnesium binding site 6 out of 8 in 5qjo

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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 Z57292369


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 Z57292369 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:29.0
occ:1.00
 OE2 C:GLU116 1.9 28.1 1.0
O C:HOH454 2.1 18.6 1.0
MG C:MG302 2.1 43.0 1.0
O C:HOH415 2.1 37.3 1.0
O C:ALA96 2.2 27.6 1.0
O C:HOH422 2.2 22.7 1.0
CD C:GLU116 3.0 30.4 1.0
C C:ALA96 3.3 25.0 1.0
OE1 C:GLU116 3.4 39.8 1.0
OE2 C:GLU166 3.5 67.4 1.0
OE2 C:GLU112 4.1 34.4 1.0
N C:GLY97 4.2 25.2 1.0
CA C:GLY97 4.2 31.1 1.0
N C:ALA96 4.2 21.4 1.0
CA C:ALA96 4.2 22.0 1.0
CG C:GLU116 4.4 28.1 1.0
NE2 C:GLN82 4.4 31.2 1.0
O C:HOH453 4.5 36.7 1.0
OE1 C:GLN82 4.5 30.4 1.0
NH2 C:ARG84 4.5 28.3 1.0
CB C:ALA96 4.7 21.7 1.0
CD C:GLU166 4.8 73.2 1.0
O C:HOH407 4.8 46.7 1.0
CD C:GLU112 4.8 35.7 1.0
CD C:GLN82 4.9 32.6 1.0
O C:HOH447 5.0 50.9 1.0

Magnesium binding site 7 out of 8 in 5qjo

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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 Z57292369


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 Z57292369 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:36.9
occ:1.00
 OE2 D:GLU116 2.0 28.5 1.0
O D:HOH411 2.1 29.3 1.0
O D:HOH410 2.2 24.6 1.0
MG D:MG302 2.2 36.5 1.0
O D:ALA96 2.3 27.5 1.0
CD D:GLU116 3.1 30.9 1.0
OE1 D:GLU116 3.5 31.8 1.0
C D:ALA96 3.6 30.0 1.0
OE2 D:GLU112 3.7 52.8 1.0
NE2 D:GLN82 4.0 31.4 1.0
NH2 D:ARG84 4.2 28.0 1.0
OE2 D:GLU166 4.3 99.8 1.0
CG D:GLU116 4.3 31.9 1.0
OE1 D:GLN82 4.3 32.9 1.0
O D:HOH417 4.4 30.4 0.9
N D:GLY97 4.4 33.0 1.0
CA D:GLY97 4.4 34.6 1.0
N D:ALA96 4.4 29.5 1.0
O D:HOH413 4.5 30.5 0.9
CA D:ALA96 4.5 32.9 1.0
CD D:GLU112 4.6 49.2 1.0
CD D:GLN82 4.6 35.4 1.0
O D:HOH427 4.7 32.7 1.0
CG D:GLU112 4.7 50.8 1.0
O D:HOH414 4.9 45.6 1.0
NH1 D:ARG84 5.0 28.2 1.0

Magnesium binding site 8 out of 8 in 5qjo

Go back to Magnesium Binding Sites List in 5qjo
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 Z57292369


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 Z57292369 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:36.5
occ:1.00
 OE2 D:GLU112 2.1 52.8 1.0
MG D:MG301 2.2 36.9 1.0
O D:ALA96 2.9 27.5 1.0
O D:HOH427 3.0 32.7 1.0
OE2 D:GLU116 3.0 28.5 1.0
O D:HOH410 3.0 24.6 1.0
OE2 D:GLU166 3.2 99.8 1.0
CD D:GLU112 3.3 49.2 1.0
CA D:GLY97 3.5 34.6 1.0
C D:ALA96 3.9 30.0 1.0
O D:HOH414 3.9 45.6 1.0
OE1 D:GLU112 4.1 50.2 1.0
CG D:GLU112 4.1 50.8 1.0
N D:GLY97 4.1 33.0 1.0
CD D:GLU116 4.2 30.9 1.0
O D:HOH411 4.3 29.3 1.0
CD D:GLU166 4.4 96.9 1.0
O D:HOH417 4.4 30.4 0.9
C D:GLY97 4.7 37.5 1.0
O D:HOH436 4.8 46.4 0.9
O D:HOH430 4.8 44.2 0.9
N D:LEU98 4.8 39.1 1.0
OE1 D:GLU116 4.9 31.8 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 02:19:14 2024

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