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Magnesium in PDB 5qjf: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z52425517

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z52425517

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 Z52425517:
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 Z52425517, PDB code: 5qjf 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) 78.31 / 1.63
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.388, 59.416, 79.923, 79.85, 82.34, 76.55
R / Rfree (%) 21.4 / 24.9

Other elements in 5qjf:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z52425517 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 Z52425517 (pdb code 5qjf). 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 Z52425517, PDB code: 5qjf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjf

Go back to Magnesium Binding Sites List in 5qjf
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 Z52425517


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 Z52425517 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:41.1
occ:1.00
 O A:ALA96 2.0 29.6 1.0
OE2 A:GLU116 2.0 37.5 1.0
O A:HOH411 2.1 30.7 1.0
O A:HOH443 2.2 33.5 1.0
O A:HOH449 2.3 33.7 1.0
O A:HOH435 2.3 38.9 1.0
CD A:GLU116 3.1 33.2 1.0
C A:ALA96 3.2 28.3 1.0
MG A:MG302 3.3 67.0 1.0
OE1 A:GLU116 3.4 31.9 1.0
OE2 A:GLU112 3.8 39.9 1.0
N A:GLY97 4.1 27.7 1.0
CA A:GLY97 4.1 28.5 1.0
CA A:ALA96 4.2 27.1 1.0
N A:ALA96 4.2 27.4 1.0
OE1 A:GLN82 4.4 35.3 1.0
NH2 A:ARG84 4.4 30.4 1.0
CG A:GLU116 4.4 35.4 1.0
NE2 A:GLN82 4.4 33.9 1.0
O A:HOH409 4.4 28.3 1.0
O A:HOH462 4.5 33.8 1.0
O A:HOH468 4.5 51.5 1.0
O A:HOH456 4.5 46.9 1.0
CD A:GLU112 4.6 36.6 1.0
CB A:ALA96 4.7 24.9 1.0
CD A:GLN82 4.8 39.7 1.0

Magnesium binding site 2 out of 8 in 5qjf

Go back to Magnesium Binding Sites List in 5qjf
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 Z52425517


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 Z52425517 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:67.0
occ:1.00
 O A:HOH402 2.0 46.4 1.0
O A:HOH443 2.3 33.5 1.0
OE2 A:GLU116 2.4 37.5 1.0
OE2 A:GLU112 2.5 39.9 1.0
O A:HOH428 2.8 61.6 1.0
OE2 A:GLU166 3.0 85.9 0.7
OE1 A:GLU166 3.1 85.5 0.7
CD A:GLU166 3.2 88.1 0.7
MG A:MG301 3.3 41.1 1.0
CD A:GLU116 3.3 33.2 1.0
CG A:GLU116 3.5 35.4 1.0
CD A:GLU112 3.5 36.6 1.0
O A:HOH435 3.5 38.9 1.0
OE1 A:GLU112 3.7 48.8 1.0
O A:ALA96 4.2 29.6 1.0
OE2 A:GLU115 4.2 44.9 1.0
OE1 A:GLU116 4.4 31.9 1.0
CG A:GLU166 4.5 85.9 0.7
O A:HOH456 4.8 46.9 1.0
O A:HOH468 4.9 51.5 1.0
CG A:GLU112 4.9 35.1 1.0
O A:HOH411 4.9 30.7 1.0
CB A:GLU116 5.0 30.9 1.0

Magnesium binding site 3 out of 8 in 5qjf

Go back to Magnesium Binding Sites List in 5qjf
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 Z52425517


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 Z52425517 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:43.7
occ:1.00
 OE2 B:GLU116 2.0 46.9 1.0
O B:ALA96 2.1 37.5 1.0
O B:HOH420 2.1 35.5 1.0
O B:HOH456 2.2 37.1 1.0
O B:HOH430 2.2 39.9 1.0
O B:HOH418 2.3 42.8 1.0
CD B:GLU116 3.1 47.3 1.0
C B:ALA96 3.3 32.7 1.0
OE1 B:GLU116 3.4 49.7 1.0
OE2 B:GLU166 3.6 73.2 1.0
N B:GLY97 4.1 33.5 1.0
CA B:GLY97 4.1 34.3 1.0
N B:ALA96 4.2 32.0 1.0
O B:HOH421 4.2 36.0 1.0
OE2 B:GLU112 4.2 42.2 1.0
CA B:ALA96 4.2 33.2 1.0
O B:HOH404 4.3 53.1 1.0
NH2 B:ARG84 4.3 36.7 1.0
CG B:GLU116 4.4 44.8 1.0
NE2 B:GLN82 4.4 43.6 1.0
O B:HOH469 4.5 38.6 1.0
OE1 B:GLN82 4.5 39.0 1.0
CB B:ALA96 4.6 32.0 1.0
CD B:GLU166 4.7 94.8 1.0
MG B:MG303 4.8 76.9 1.0
CD B:GLN82 4.8 48.6 1.0
CD B:GLU112 5.0 43.7 1.0

Magnesium binding site 4 out of 8 in 5qjf

Go back to Magnesium Binding Sites List in 5qjf
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 Z52425517


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 Z52425517 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:76.9
occ:1.00
 O B:HOH459 1.7 71.9 1.0
O B:HOH404 2.7 53.1 1.0
O B:HOH430 2.8 39.9 1.0
OE1 B:GLU112 3.1 46.7 1.0
OE1 B:GLU166 3.1 93.0 1.0
OE2 B:GLU112 3.4 42.2 1.0
CD B:GLU112 3.6 43.7 1.0
OE2 B:GLU166 3.7 73.2 1.0
CD B:GLU166 3.7 94.8 1.0
OE2 B:GLU115 4.1 54.5 1.0
OE2 B:GLU116 4.5 46.9 1.0
NH1 B:ARG111 4.8 38.5 1.0
MG B:MG302 4.8 43.7 1.0

Magnesium binding site 5 out of 8 in 5qjf

Go back to Magnesium Binding Sites List in 5qjf
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 Z52425517


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 Z52425517 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:52.9
occ:1.00
 MG C:MG303 2.1 40.7 1.0
OE2 C:GLU116 2.6 36.6 1.0
O C:HOH406 2.7 51.4 1.0
OE2 C:GLU112 2.8 44.4 1.0
O C:ALA96 2.8 33.0 1.0
O C:HOH409 2.8 61.7 1.0
O C:HOH447 3.1 42.5 1.0
O C:HOH450 3.3 36.9 1.0
OE2 C:GLU166 3.3 91.7 1.0
CD C:GLU112 3.4 48.5 1.0
O C:HOH457 3.5 58.3 1.0
OE1 C:GLU112 3.5 53.6 1.0
CA C:GLY97 3.6 39.4 1.0
C C:ALA96 3.8 35.3 1.0
CD C:GLU116 3.9 36.3 1.0
O C:HOH443 4.1 33.0 1.0
N C:GLY97 4.2 36.3 1.0
O C:HOH463 4.2 55.4 1.0
CD C:GLU166 4.4 94.9 1.0
CG C:GLU116 4.7 33.8 1.0
CG C:GLU112 4.7 39.4 1.0
OE1 C:GLU116 4.7 43.5 1.0
OE1 C:GLU166 4.8 99.9 1.0
C C:GLY97 4.9 37.6 1.0

Magnesium binding site 6 out of 8 in 5qjf

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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 Z52425517


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 Z52425517 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:40.7
occ:1.00
 O C:HOH443 2.0 33.0 1.0
O C:ALA96 2.1 33.0 1.0
O C:HOH450 2.1 36.9 1.0
MG C:MG302 2.1 52.9 1.0
OE2 C:GLU116 2.1 36.6 1.0
O C:HOH447 2.3 42.5 1.0
O C:HOH457 3.2 58.3 1.0
CD C:GLU116 3.2 36.3 1.0
C C:ALA96 3.2 35.3 1.0
OE1 C:GLU116 3.6 43.5 1.0
O C:HOH406 4.0 51.4 1.0
OE2 C:GLU112 4.0 44.4 1.0
N C:GLY97 4.1 36.3 1.0
CA C:GLY97 4.1 39.4 1.0
N C:ALA96 4.2 31.5 1.0
CA C:ALA96 4.2 29.0 1.0
O C:HOH411 4.2 33.5 1.0
O C:HOH461 4.4 38.3 1.0
NH2 C:ARG84 4.5 35.3 1.0
CG C:GLU116 4.5 33.8 1.0
OE1 C:GLN82 4.5 41.2 1.0
NE2 C:GLN82 4.6 39.5 1.0
CB C:ALA96 4.6 31.8 1.0
OE2 C:GLU166 4.6 91.7 1.0
O C:HOH451 4.7 50.3 1.0
CD C:GLU112 4.8 48.5 1.0
O C:HOH409 4.8 61.7 1.0

Magnesium binding site 7 out of 8 in 5qjf

Go back to Magnesium Binding Sites List in 5qjf
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 Z52425517


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 Z52425517 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:36.3
occ:1.00
 O D:HOH417 2.0 32.9 1.0
OE2 D:GLU116 2.0 38.0 1.0
O D:HOH423 2.1 38.5 1.0
O D:HOH414 2.1 40.2 1.0
O D:ALA96 2.1 34.2 1.0
MG D:MG302 2.2 46.5 1.0
CD D:GLU116 3.1 41.8 1.0
C D:ALA96 3.3 31.8 1.0
OE1 D:GLU116 3.5 41.4 1.0
OE2 D:GLU112 3.7 56.0 1.0
OE2 D:GLU166 4.0 98.2 1.0
CA D:GLY97 4.1 35.9 1.0
N D:GLY97 4.2 34.1 1.0
N D:ALA96 4.2 33.6 1.0
CA D:ALA96 4.3 31.2 1.0
NH2 D:ARG84 4.3 34.4 1.0
O D:HOH408 4.4 33.9 1.0
NE2 D:GLN82 4.4 41.6 1.0
O D:HOH429 4.4 36.0 1.0
CG D:GLU116 4.5 41.0 1.0
OE1 D:GLN82 4.5 40.2 1.0
CD D:GLU112 4.5 53.5 1.0
CB D:ALA96 4.6 31.7 1.0
CG D:GLU112 4.8 60.2 1.0
CD D:GLN82 4.9 47.5 1.0

Magnesium binding site 8 out of 8 in 5qjf

Go back to Magnesium Binding Sites List in 5qjf
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 Z52425517


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 Z52425517 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:46.5
occ:1.00
 MG D:MG301 2.2 36.3 1.0
OE2 D:GLU112 2.5 56.0 1.0
OE2 D:GLU116 2.8 38.0 1.0
O D:HOH423 2.9 38.5 1.0
OE2 D:GLU166 3.0 98.2 1.0
O D:ALA96 3.0 34.2 1.0
O D:HOH404 3.1 52.5 1.0
O D:HOH417 3.1 32.9 1.0
CD D:GLU112 3.4 53.5 1.0
CA D:GLY97 3.6 35.9 1.0
O D:HOH402 3.9 51.2 1.0
OE1 D:GLU112 3.9 53.1 1.0
C D:ALA96 4.0 31.8 1.0
CD D:GLU116 4.0 41.8 1.0
CD D:GLU166 4.2 94.8 1.0
O D:HOH414 4.3 40.2 1.0
N D:GLY97 4.3 34.1 1.0
CG D:GLU112 4.3 60.2 1.0
C D:GLY97 4.8 39.1 1.0
OE1 D:GLU116 4.8 41.4 1.0
CG D:GLU116 4.8 41.0 1.0
O D:HOH429 4.9 36.0 1.0
N D:LEU98 5.0 42.2 1.0
CG D:GLU166 5.0 80.5 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 02:15:18 2024

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