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Magnesium in PDB 5qjt: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z969560582

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z969560582

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 Z969560582:
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 Z969560582, PDB code: 5qjt 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) 78.36 / 1.62
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.447, 59.865, 80.233, 79.16, 81.53, 75.51
R / Rfree (%) 22 / 25.1

Other elements in 5qjt:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z969560582 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 Z969560582 (pdb code 5qjt). 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 Z969560582, PDB code: 5qjt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjt

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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 Z969560582


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 Z969560582 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:26.1
occ:1.00
 O A:HOH437 2.0 24.1 1.0
OE2 A:GLU116 2.1 23.3 1.0
O A:ALA96 2.1 23.2 1.0
O A:HOH464 2.1 21.0 1.0
O A:HOH447 2.1 22.9 1.0
O A:HOH449 2.2 27.0 1.0
CD A:GLU116 3.1 24.3 1.0
C A:ALA96 3.2 22.4 1.0
MG A:MG302 3.3 63.5 1.0
OE1 A:GLU116 3.4 25.0 1.0
OE2 A:GLU166 4.1 62.3 1.0
CA A:GLY97 4.1 21.9 1.0
N A:GLY97 4.1 21.7 1.0
O A:HOH471 4.2 49.1 1.0
OE2 A:GLU112 4.2 29.9 1.0
N A:ALA96 4.2 17.7 1.0
O A:HOH450 4.2 26.5 0.8
CA A:ALA96 4.2 20.1 1.0
O A:HOH423 4.2 21.4 1.0
NH2 A:ARG84 4.2 24.1 1.0
O A:HOH475 4.4 28.3 1.0
CG A:GLU116 4.4 23.6 1.0
NE2 A:GLN82 4.4 29.8 1.0
OE1 A:GLN82 4.5 25.1 1.0
CB A:ALA96 4.6 18.2 1.0
O A:HOH469 4.6 32.3 1.0
CD A:GLN82 4.8 31.4 1.0
CD A:GLU112 5.0 30.7 1.0

Magnesium binding site 2 out of 8 in 5qjt

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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 Z969560582


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 Z969560582 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:63.5
occ:1.00
 O A:HOH447 1.9 22.9 1.0
O A:HOH406 2.0 38.4 1.0
OE2 A:GLU112 2.1 29.9 1.0
OE2 A:GLU166 2.4 62.3 1.0
OE2 A:GLU116 2.6 23.3 1.0
CD A:GLU112 3.0 30.7 1.0
O A:HOH414 3.1 49.6 1.0
CD A:GLU166 3.2 71.5 1.0
OE1 A:GLU112 3.3 29.7 1.0
MG A:MG301 3.3 26.1 1.0
OE1 A:GLU166 3.4 65.2 1.0
CD A:GLU116 3.5 24.3 1.0
O A:HOH471 3.8 49.1 1.0
CG A:GLU116 3.8 23.6 1.0
O A:ALA96 3.8 23.2 1.0
O A:HOH449 3.9 27.0 1.0
OE2 A:GLU115 4.2 37.3 1.0
O A:HOH469 4.3 32.3 1.0
CG A:GLU166 4.4 61.5 1.0
CG A:GLU112 4.4 28.4 1.0
OE1 A:GLU116 4.6 25.0 1.0
CA A:GLY97 4.6 21.9 1.0
C A:ALA96 4.8 22.4 1.0
O A:HOH464 4.8 21.0 1.0
CB A:GLU112 4.8 26.4 1.0
O A:HOH401 4.9 49.3 1.0

Magnesium binding site 3 out of 8 in 5qjt

Go back to Magnesium Binding Sites List in 5qjt
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 Z969560582


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 Z969560582 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:31.1
occ:1.00
 O B:ALA96 2.0 27.0 1.0
OE2 B:GLU116 2.1 34.1 1.0
O B:HOH430 2.1 28.3 1.0
O B:HOH409 2.1 31.1 1.0
O B:HOH444 2.1 26.0 1.0
O B:HOH445 2.2 30.2 1.0
CD B:GLU116 3.1 35.2 1.0
C B:ALA96 3.2 23.8 1.0
OE1 B:GLU116 3.4 30.6 1.0
OE2 B:GLU166 3.9 60.2 1.0
OE2 B:GLU112 4.1 37.8 1.0
N B:GLY97 4.1 26.9 1.0
CA B:GLY97 4.1 26.2 1.0
N B:ALA96 4.2 24.4 1.0
MG B:MG304 4.2 77.0 1.0
CA B:ALA96 4.2 25.5 1.0
O B:HOH425 4.2 28.6 1.0
O B:HOH432 4.3 39.2 1.0
NH2 B:ARG84 4.3 28.1 1.0
OE1 B:GLN82 4.4 34.4 1.0
CG B:GLU116 4.4 35.2 1.0
NE2 B:GLN82 4.4 33.3 1.0
O B:HOH463 4.4 43.2 1.0
O B:HOH471 4.6 39.8 1.0
CB B:ALA96 4.7 28.4 1.0
CD B:GLN82 4.8 40.3 1.0
CD B:GLU166 4.8 72.6 1.0
CD B:GLU112 4.9 36.6 1.0

Magnesium binding site 4 out of 8 in 5qjt

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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 Z969560582


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 Z969560582 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:77.0
occ:1.00
 O B:HOH402 2.1 68.0 1.0
OE2 B:GLU112 2.2 37.8 1.0
OE2 B:GLU166 2.4 60.2 1.0
O B:HOH420 2.6 53.3 1.0
OE2 B:GLU116 3.0 34.1 1.0
O B:HOH445 3.1 30.2 1.0
CD B:GLU112 3.2 36.6 1.0
OE2 B:GLU115 3.2 45.6 1.0
CD B:GLU166 3.2 72.6 1.0
OE1 B:GLU166 3.4 74.4 1.0
CG B:GLU116 3.5 35.2 1.0
OE1 B:GLU112 3.5 36.5 1.0
CD B:GLU116 3.7 35.2 1.0
CB B:GLU115 4.2 36.0 1.0
MG B:MG303 4.2 31.1 1.0
CD B:GLU115 4.4 44.1 1.0
CG B:GLU112 4.5 34.2 1.0
O B:ALA96 4.6 27.0 1.0
CG B:GLU166 4.7 64.7 1.0
O B:HOH430 4.8 28.3 1.0
O B:GLU112 4.8 32.5 1.0
CA B:GLU112 4.8 30.3 1.0
CB B:GLU112 4.8 33.6 1.0
OE1 B:GLU116 4.8 30.6 1.0
CB B:GLU116 4.9 32.9 1.0
CG B:GLU115 5.0 42.9 1.0

Magnesium binding site 5 out of 8 in 5qjt

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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 Z969560582


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 Z969560582 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:43.7
occ:1.00
 O C:HOH402 2.1 49.7 1.0
MG C:MG303 2.1 33.7 1.0
OE2 C:GLU116 2.8 31.7 1.0
O C:ALA96 2.9 26.8 1.0
O C:HOH441 2.9 28.0 1.0
O C:HOH417 3.0 33.9 1.0
O C:HOH437 3.1 42.5 1.0
OE2 C:GLU112 3.2 34.7 1.0
O C:HOH457 3.4 61.2 1.0
OE2 C:GLU166 3.4 64.4 1.0
CA C:GLY97 3.6 28.9 1.0
O C:HOH443 3.7 56.5 1.0
OE1 C:GLU112 3.8 45.9 1.0
CD C:GLU112 3.8 37.0 1.0
C C:ALA96 3.9 28.6 1.0
CD C:GLU166 3.9 72.1 1.0
CD C:GLU116 4.1 33.0 1.0
O C:HOH434 4.2 29.1 1.0
N C:GLY97 4.2 29.5 1.0
OE1 C:GLU166 4.2 80.6 1.0
C C:GLY97 4.9 30.3 1.0
OE1 C:GLU116 4.9 35.5 1.0
CG C:GLU166 4.9 62.8 1.0
CG C:GLU116 4.9 28.6 1.0

Magnesium binding site 6 out of 8 in 5qjt

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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 Z969560582


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 Z969560582 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:33.7
occ:1.00
 OE2 C:GLU116 2.0 31.7 1.0
O C:HOH434 2.0 29.1 1.0
O C:HOH441 2.0 28.0 1.0
O C:ALA96 2.1 26.8 1.0
O C:HOH417 2.1 33.9 1.0
MG C:MG302 2.1 43.7 1.0
CD C:GLU116 3.0 33.0 1.0
C C:ALA96 3.3 28.6 1.0
O C:HOH402 3.3 49.7 1.0
OE1 C:GLU116 3.4 35.5 1.0
OE2 C:GLU166 3.8 64.4 1.0
OE2 C:GLU112 4.1 34.7 1.0
N C:ALA96 4.1 24.9 1.0
CA C:ALA96 4.2 24.1 1.0
CA C:GLY97 4.2 28.9 1.0
N C:GLY97 4.2 29.5 1.0
NH2 C:ARG84 4.3 33.1 1.0
NE2 C:GLN82 4.3 32.1 1.0
CG C:GLU116 4.4 28.6 1.0
OE1 C:GLN82 4.4 33.0 1.0
CB C:ALA96 4.6 23.7 1.0
O C:HOH437 4.7 42.5 1.0
CD C:GLU166 4.8 72.1 1.0
CD C:GLN82 4.8 35.8 1.0
CD C:GLU112 5.0 37.0 1.0

Magnesium binding site 7 out of 8 in 5qjt

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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 Z969560582


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 Z969560582 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:34.1
occ:1.00
 OE2 D:GLU116 2.0 32.6 1.0
O D:HOH420 2.0 29.8 1.0
O D:HOH407 2.0 29.8 1.0
MG D:MG302 2.2 38.9 1.0
O D:ALA96 2.2 32.8 1.0
O D:HOH433 2.7 44.2 1.0
CD D:GLU116 3.0 39.5 1.0
C D:ALA96 3.4 34.6 1.0
OE1 D:GLU116 3.4 35.4 1.0
OE2 D:GLU112 3.7 51.3 1.0
OE2 D:GLU166 4.0 83.7 1.0
N D:ALA96 4.2 33.7 1.0
CA D:GLY97 4.2 35.0 1.0
N D:GLY97 4.2 34.5 1.0
NH2 D:ARG84 4.3 34.0 1.0
CA D:ALA96 4.3 33.9 1.0
NE2 D:GLN82 4.3 35.5 1.0
CG D:GLU116 4.4 38.8 1.0
O D:HOH404 4.4 31.0 0.9
OE1 D:GLN82 4.5 37.6 1.0
CD D:GLU112 4.5 50.4 1.0
O D:HOH427 4.6 36.8 0.9
CG D:GLU112 4.7 52.7 1.0
CB D:ALA96 4.7 33.2 1.0
O D:HOH413 4.7 53.3 1.0
O D:HOH403 4.8 56.0 1.0
CD D:GLN82 4.8 42.5 1.0

Magnesium binding site 8 out of 8 in 5qjt

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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 Z969560582


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 Z969560582 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:38.9
occ:1.00
 O D:HOH433 1.8 44.2 1.0
MG D:MG301 2.2 34.1 1.0
OE2 D:GLU112 2.3 51.3 1.0
O D:HOH413 2.6 53.3 1.0
OE2 D:GLU116 2.8 32.6 1.0
O D:ALA96 3.0 32.8 1.0
OE2 D:GLU166 3.1 83.7 1.0
O D:HOH420 3.2 29.8 1.0
CD D:GLU112 3.3 50.4 1.0
CA D:GLY97 3.5 35.0 1.0
O D:HOH403 3.6 56.0 1.0
OE1 D:GLU112 4.0 57.1 1.0
C D:ALA96 4.0 34.6 1.0
CD D:GLU116 4.0 39.5 1.0
CG D:GLU112 4.2 52.7 1.0
O D:HOH407 4.2 29.8 1.0
CD D:GLU166 4.2 84.3 1.0
N D:GLY97 4.3 34.5 1.0
C D:GLY97 4.8 35.2 1.0
CG D:GLU116 4.8 38.8 1.0
OE1 D:GLU116 4.8 35.4 1.0
N D:LEU98 4.9 36.3 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 02:23:09 2024

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