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Magnesium in PDB 5qjm: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z328695024

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z328695024

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 Z328695024:
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 Z328695024, PDB code: 5qjm 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) 78.34 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.637, 59.950, 80.267, 79.09, 81.28, 75.44
R / Rfree (%) 22.3 / 27.1

Other elements in 5qjm:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z328695024 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 Z328695024 (pdb code 5qjm). 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 Z328695024, PDB code: 5qjm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjm

Go back to Magnesium Binding Sites List in 5qjm
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 Z328695024


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 Z328695024 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:34.3
occ:1.00
 OE2 A:GLU116 2.1 29.5 1.0
O A:ALA96 2.1 24.4 1.0
O A:HOH446 2.1 23.7 1.0
O A:HOH451 2.1 25.9 1.0
O A:HOH427 2.2 27.2 1.0
O A:HOH405 2.3 29.7 1.0
CD A:GLU116 3.1 27.3 1.0
MG A:MG302 3.1 53.7 1.0
C A:ALA96 3.3 23.6 1.0
OE1 A:GLU116 3.4 30.3 1.0
OE2 A:GLU166 3.6 62.3 1.0
CA A:GLY97 4.1 23.4 1.0
N A:GLY97 4.1 22.3 1.0
NH2 A:ARG84 4.2 29.0 1.0
N A:ALA96 4.2 19.5 1.0
CA A:ALA96 4.2 20.6 1.0
OE2 A:GLU112 4.2 34.3 1.0
O A:HOH426 4.2 24.7 0.8
O A:HOH414 4.3 23.1 1.0
NE2 A:GLN82 4.4 27.5 1.0
CG A:GLU116 4.4 31.0 1.0
O A:HOH462 4.4 25.7 1.0
OE1 A:GLN82 4.5 28.3 1.0
O A:HOH456 4.5 33.6 1.0
CB A:ALA96 4.7 18.9 1.0
O A:HOH466 4.8 41.9 1.0
O A:HOH448 4.8 41.1 1.0
CD A:GLN82 4.8 31.8 1.0
CD A:GLU166 4.9 67.0 1.0
O A:HOH403 4.9 35.4 1.0
CD A:GLU112 5.0 34.1 1.0

Magnesium binding site 2 out of 8 in 5qjm

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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 Z328695024


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 Z328695024 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:53.7
occ:1.00
 O A:HOH446 1.9 23.7 1.0
O A:HOH403 1.9 35.4 1.0
O A:HOH448 2.1 41.1 1.0
OE2 A:GLU112 2.2 34.3 1.0
OE2 A:GLU166 2.3 62.3 1.0
OE2 A:GLU116 2.4 29.5 1.0
CD A:GLU112 3.1 34.1 1.0
CD A:GLU166 3.1 67.0 1.0
MG A:MG301 3.1 34.3 1.0
OE1 A:GLU166 3.3 67.9 1.0
CD A:GLU116 3.3 27.3 1.0
OE1 A:GLU112 3.4 33.4 1.0
CG A:GLU116 3.7 31.0 1.0
O A:ALA96 3.7 24.4 1.0
O A:HOH405 3.9 29.7 1.0
O A:HOH456 4.3 33.6 1.0
OE1 A:GLU116 4.4 30.3 1.0
OE2 A:GLU115 4.4 38.4 1.0
CG A:GLU112 4.4 32.4 1.0
CG A:GLU166 4.5 60.3 1.0
CA A:GLY97 4.6 23.4 1.0
O A:HOH451 4.7 25.9 1.0
C A:ALA96 4.7 23.6 1.0
CB A:GLU112 4.7 28.6 1.0
O A:HOH427 4.9 27.2 1.0

Magnesium binding site 3 out of 8 in 5qjm

Go back to Magnesium Binding Sites List in 5qjm
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 Z328695024


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 Z328695024 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:35.5
occ:1.00
 O B:ALA96 2.0 29.4 1.0
O B:HOH432 2.1 31.3 1.0
O B:HOH415 2.1 29.6 1.0
OE2 B:GLU116 2.1 38.7 1.0
O B:HOH448 2.2 32.0 1.0
O B:HOH412 2.2 32.6 1.0
CD B:GLU116 3.1 36.8 1.0
C B:ALA96 3.2 26.2 1.0
OE1 B:GLU116 3.4 37.5 1.0
MG B:MG304 3.5 54.9 1.0
OE2 B:GLU166 4.0 59.0 1.0
N B:GLY97 4.1 27.0 1.0
CA B:GLY97 4.1 27.7 1.0
N B:ALA96 4.1 26.3 1.0
CA B:ALA96 4.2 26.0 1.0
O B:HOH416 4.3 37.4 1.0
NH2 B:ARG84 4.3 29.0 1.0
NE2 B:GLN82 4.3 35.0 1.0
OE2 B:GLU112 4.4 43.3 1.0
OE1 B:GLN82 4.4 37.5 1.0
CG B:GLU116 4.5 37.7 1.0
O B:HOH453 4.5 33.7 0.9
O B:HOH466 4.5 39.6 1.0
CB B:ALA96 4.7 29.2 1.0
CD B:GLN82 4.8 36.4 1.0
CD B:GLU166 4.9 62.0 1.0

Magnesium binding site 4 out of 8 in 5qjm

Go back to Magnesium Binding Sites List in 5qjm
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 Z328695024


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 Z328695024 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:54.9
occ:1.00
 OE2 B:GLU112 1.9 43.3 1.0
O B:HOH401 2.4 62.4 1.0
OE2 B:GLU116 2.5 38.7 1.0
O B:HOH440 2.6 53.2 1.0
O B:HOH432 2.7 31.3 1.0
OE2 B:GLU166 2.8 59.0 1.0
CD B:GLU112 3.0 40.9 1.0
CD B:GLU116 3.3 36.8 1.0
OE1 B:GLU112 3.4 41.4 1.0
CG B:GLU116 3.4 37.7 1.0
MG B:MG303 3.5 35.5 1.0
OE1 B:GLU166 3.5 73.1 1.0
CD B:GLU166 3.5 62.0 1.0
OE2 B:GLU115 3.7 51.2 1.0
O B:ALA96 3.7 29.4 1.0
CG B:GLU112 4.3 39.0 1.0
OE1 B:GLU116 4.4 37.5 1.0
O B:HOH415 4.4 29.6 1.0
C B:ALA96 4.6 26.2 1.0
CB B:GLU112 4.6 39.6 1.0
CA B:GLY97 4.6 27.7 1.0
CA B:GLU112 4.7 35.5 1.0
CB B:GLU115 4.8 38.3 1.0
O B:GLU112 4.8 32.0 1.0
CD B:GLU115 4.9 51.7 1.0
CB B:GLU116 4.9 36.8 1.0
N B:GLY97 4.9 27.0 1.0
CG B:GLU166 4.9 61.5 1.0

Magnesium binding site 5 out of 8 in 5qjm

Go back to Magnesium Binding Sites List in 5qjm
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 Z328695024


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 Z328695024 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:60.0
occ:1.00
 O C:HOH426 1.8 35.8 1.0
O C:HOH415 2.0 48.3 1.0
OE2 C:GLU112 2.1 35.5 1.0
OE2 C:GLU166 2.3 62.9 1.0
OE2 C:GLU116 2.3 36.2 1.0
O C:HOH417 2.9 65.0 1.0
MG C:MG303 2.9 35.5 1.0
O C:HOH447 2.9 51.7 1.0
CD C:GLU112 3.2 40.4 1.0
CD C:GLU166 3.3 63.8 1.0
O C:ALA96 3.3 25.8 1.0
CD C:GLU116 3.4 36.2 1.0
OE1 C:GLU112 3.5 48.8 1.0
OE1 C:GLU166 3.6 58.9 1.0
O C:HOH416 3.7 34.5 1.0
CG C:GLU116 3.8 33.6 1.0
CA C:GLY97 4.2 31.4 1.0
C C:ALA96 4.3 27.2 1.0
O C:HOH446 4.4 28.3 1.0
OE1 C:GLU116 4.4 40.6 1.0
CG C:GLU112 4.5 36.5 1.0
CG C:GLU166 4.6 59.0 1.0
OE2 C:GLU115 4.6 43.4 1.0
N C:GLY97 4.7 29.0 1.0
O C:HOH422 4.7 31.4 1.0
O C:HOH465 4.8 49.7 1.0
CB C:GLU112 4.9 35.3 1.0

Magnesium binding site 6 out of 8 in 5qjm

Go back to Magnesium Binding Sites List in 5qjm
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 Z328695024


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 Z328695024 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:35.5
occ:1.00
 OE2 C:GLU116 2.0 36.2 1.0
O C:HOH446 2.1 28.3 1.0
O C:HOH422 2.1 31.4 1.0
O C:HOH416 2.1 34.5 1.0
O C:HOH426 2.1 35.8 1.0
O C:ALA96 2.2 25.8 1.0
MG C:MG302 2.9 60.0 1.0
CD C:GLU116 3.0 36.2 1.0
OE1 C:GLU116 3.3 40.6 1.0
OE2 C:GLU166 3.3 62.9 1.0
C C:ALA96 3.3 27.2 1.0
N C:ALA96 4.2 24.8 1.0
OE2 C:GLU112 4.2 35.5 1.0
N C:GLY97 4.2 29.0 1.0
CA C:ALA96 4.2 23.8 1.0
CA C:GLY97 4.3 31.4 1.0
NE2 C:GLN82 4.3 37.3 1.0
CG C:GLU116 4.4 33.6 1.0
OE1 C:GLN82 4.4 32.1 1.0
CD C:GLU166 4.5 63.8 1.0
NH2 C:ARG84 4.5 32.4 1.0
O C:HOH415 4.5 48.3 1.0
CB C:ALA96 4.7 24.9 1.0
CD C:GLN82 4.8 41.8 1.0

Magnesium binding site 7 out of 8 in 5qjm

Go back to Magnesium Binding Sites List in 5qjm
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 Z328695024


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 Z328695024 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:39.6
occ:1.00
 OE2 D:GLU116 1.9 41.0 1.0
O D:HOH404 2.1 30.8 1.0
MG D:MG302 2.2 41.7 1.0
O D:HOH407 2.2 32.2 1.0
O D:ALA96 2.5 47.7 1.0
O D:HOH422 2.7 40.7 1.0
CD D:GLU116 3.0 48.8 1.0
OE1 D:GLU116 3.4 46.4 1.0
C D:ALA96 3.6 45.1 1.0
OE2 D:GLU166 3.7 71.3 1.0
OE2 D:GLU112 3.9 55.4 1.0
NE2 D:GLN82 4.1 38.2 1.0
NH2 D:ARG84 4.3 38.8 1.0
CG D:GLU116 4.3 46.5 1.0
OE1 D:GLN82 4.4 41.1 1.0
N D:ALA96 4.4 39.9 1.0
CA D:GLY97 4.5 45.6 1.0
N D:GLY97 4.5 44.0 1.0
O D:HOH403 4.5 54.3 1.0
CA D:ALA96 4.6 44.4 1.0
CD D:GLU166 4.6 75.1 1.0
CD D:GLU112 4.6 60.0 1.0
CD D:GLN82 4.7 45.4 1.0
O D:HOH417 4.7 44.5 1.0
CG D:GLU112 4.8 58.3 1.0
NH1 D:ARG84 4.9 37.1 1.0

Magnesium binding site 8 out of 8 in 5qjm

Go back to Magnesium Binding Sites List in 5qjm
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 Z328695024


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 Z328695024 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:41.7
occ:1.00
 O D:HOH422 1.9 40.7 1.0
MG D:MG301 2.2 39.6 1.0
OE2 D:GLU112 2.4 55.4 1.0
OE2 D:GLU166 2.5 71.3 1.0
O D:HOH417 2.6 44.5 1.0
OE2 D:GLU116 2.8 41.0 1.0
O D:ALA96 2.9 47.7 1.0
O D:HOH404 3.0 30.8 1.0
CD D:GLU112 3.3 60.0 1.0
O D:HOH403 3.5 54.3 1.0
CA D:GLY97 3.6 45.6 1.0
CD D:GLU166 3.7 75.1 1.0
C D:ALA96 3.9 45.1 1.0
CD D:GLU116 4.0 48.8 1.0
OE1 D:GLU112 4.0 62.9 1.0
CG D:GLU112 4.1 58.3 1.0
N D:GLY97 4.2 44.0 1.0
O D:HOH407 4.4 32.2 1.0
OE1 D:GLU166 4.5 77.1 1.0
OE1 D:GLU116 4.7 46.4 1.0
CG D:GLU166 4.7 69.5 1.0
CG D:GLU116 4.8 46.5 1.0
C D:GLY97 4.8 42.1 1.0
N D:LEU98 5.0 42.1 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 Dec 14 21:07:10 2020

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