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Magnesium in PDB 5qjv: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z281802060

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z281802060

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 Z281802060:
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 Z281802060, PDB code: 5qjv 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) 78.15 / 1.61
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.684, 59.551, 79.794, 79.84, 82.09, 76.39
R / Rfree (%) 21.3 / 24.7

Other elements in 5qjv:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z281802060 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 Z281802060 (pdb code 5qjv). 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 Z281802060, PDB code: 5qjv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjv

Go back to Magnesium Binding Sites List in 5qjv
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 Z281802060


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 Z281802060 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:28.6
occ:1.00
 O A:ALA96 2.0 23.2 1.0
OE2 A:GLU116 2.0 27.5 1.0
O A:HOH447 2.1 25.6 1.0
O A:HOH452 2.1 26.2 1.0
O A:HOH415 2.2 24.0 1.0
O A:HOH433 2.2 30.4 1.0
CD A:GLU116 3.1 27.5 1.0
MG A:MG302 3.1 48.3 1.0
C A:ALA96 3.2 25.5 1.0
OE1 A:GLU116 3.4 26.2 1.0
OE2 A:GLU166 3.7 56.4 1.0
OE2 A:GLU112 3.9 32.0 1.0
N A:GLY97 4.0 23.8 1.0
CA A:GLY97 4.1 25.5 1.0
N A:ALA96 4.1 20.8 1.0
CA A:ALA96 4.2 22.8 1.0
O A:HOH442 4.2 31.3 1.0
O A:HOH467 4.3 36.8 1.0
NH2 A:ARG84 4.3 26.6 1.0
O A:HOH422 4.4 22.3 1.0
CG A:GLU116 4.4 26.8 1.0
NE2 A:GLN82 4.4 28.3 1.0
O A:HOH460 4.5 38.8 1.0
OE1 A:GLN82 4.5 29.5 1.0
CB A:ALA96 4.6 21.6 1.0
O A:HOH471 4.7 50.4 1.0
CD A:GLU112 4.7 32.6 1.0
CD A:GLN82 4.8 33.6 1.0
O A:HOH405 5.0 40.3 1.0
CD A:GLU166 5.0 70.9 1.0

Magnesium binding site 2 out of 8 in 5qjv

Go back to Magnesium Binding Sites List in 5qjv
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 Z281802060


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 Z281802060 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:48.3
occ:1.00
 O A:HOH447 2.0 25.6 1.0
O A:HOH405 2.0 40.3 1.0
OE2 A:GLU112 2.1 32.0 1.0
OE2 A:GLU166 2.3 56.4 1.0
OE2 A:GLU116 2.4 27.5 1.0
O A:HOH410 2.6 47.1 1.0
CD A:GLU112 3.1 32.6 1.0
CD A:GLU166 3.1 70.9 1.0
MG A:MG301 3.1 28.6 1.0
OE1 A:GLU112 3.3 34.6 1.0
CD A:GLU116 3.4 27.5 1.0
OE1 A:GLU166 3.4 56.5 1.0
O A:HOH433 3.6 30.4 1.0
CG A:GLU116 3.7 26.8 1.0
O A:ALA96 3.8 23.2 1.0
OE2 A:GLU115 4.1 40.3 1.0
O A:HOH460 4.3 38.8 1.0
CG A:GLU166 4.3 67.4 1.0
OE1 A:GLU116 4.4 26.2 1.0
CG A:GLU112 4.5 29.4 1.0
O A:HOH452 4.8 26.2 1.0
C A:ALA96 4.8 25.5 1.0
CA A:GLY97 4.8 25.5 1.0
CB A:GLU112 4.9 27.8 1.0
O A:HOH415 4.9 24.0 1.0

Magnesium binding site 3 out of 8 in 5qjv

Go back to Magnesium Binding Sites List in 5qjv
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 Z281802060


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 Z281802060 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:32.5
occ:1.00
 OE2 B:GLU116 2.0 34.0 1.0
O B:ALA96 2.0 30.1 1.0
O B:HOH411 2.1 31.9 1.0
O B:HOH447 2.1 28.6 1.0
O B:HOH427 2.1 31.4 1.0
O B:HOH451 2.2 32.2 1.0
CD B:GLU116 3.0 34.8 1.0
C B:ALA96 3.2 26.9 1.0
OE1 B:GLU116 3.4 31.8 1.0
OE2 B:GLU166 3.7 63.0 1.0
N B:GLY97 4.1 28.0 1.0
CA B:GLY97 4.1 30.9 1.0
O B:HOH429 4.2 28.6 1.0
OE2 B:GLU112 4.2 40.1 1.0
N B:ALA96 4.2 26.8 1.0
NH2 B:ARG84 4.2 28.3 1.0
CA B:ALA96 4.2 26.4 1.0
CG B:GLU116 4.4 32.1 1.0
NE2 B:GLN82 4.4 34.2 1.0
O B:HOH464 4.4 43.8 1.0
O B:HOH402 4.4 43.8 1.0
OE1 B:GLN82 4.4 32.4 1.0
CD B:GLU166 4.6 76.5 1.0
MG B:MG303 4.6 89.8 1.0
O B:HOH469 4.6 45.7 1.0
CB B:ALA96 4.7 29.1 1.0
CD B:GLN82 4.8 39.8 1.0
CD B:GLU112 5.0 41.8 1.0

Magnesium binding site 4 out of 8 in 5qjv

Go back to Magnesium Binding Sites List in 5qjv
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 Z281802060


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 Z281802060 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:89.8
occ:1.00
 O B:HOH426 1.6 51.8 1.0
O B:HOH402 2.0 43.8 1.0
OE2 B:GLU112 2.8 40.1 1.0
O B:HOH451 2.8 32.2 1.0
OE1 B:GLU166 2.9 75.3 1.0
OE1 B:GLU112 3.1 41.5 1.0
OE2 B:GLU166 3.2 63.0 1.0
OE2 B:GLU115 3.3 51.4 1.0
CD B:GLU112 3.3 41.8 1.0
CD B:GLU166 3.4 76.5 1.0
O B:HOH464 3.8 43.8 1.0
OE2 B:GLU116 4.1 34.0 1.0
CD B:GLU115 4.5 44.7 1.0
MG B:MG302 4.6 32.5 1.0
NH1 B:ARG111 4.7 37.8 1.0
CG B:GLU112 4.8 37.3 1.0
CG B:GLU166 4.9 72.0 1.0
CD B:GLU116 5.0 34.8 1.0

Magnesium binding site 5 out of 8 in 5qjv

Go back to Magnesium Binding Sites List in 5qjv
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 Z281802060


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 Z281802060 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:45.9
occ:1.00
 MG C:MG303 2.1 32.9 1.0
O C:HOH402 2.6 38.8 1.0
OE2 C:GLU116 2.7 29.8 1.0
OE2 C:GLU166 3.0 48.4 1.0
O C:HOH445 3.0 26.6 1.0
O C:ALA96 3.0 27.4 1.0
O C:HOH412 3.0 31.6 1.0
O C:HOH454 3.0 45.2 1.0
OE2 C:GLU112 3.1 34.9 1.0
O C:HOH456 3.5 59.4 1.0
OE1 C:GLU112 3.7 48.6 1.0
CD C:GLU112 3.7 38.0 1.0
CA C:GLY97 3.8 33.4 1.0
CD C:GLU166 3.9 63.1 1.0
CD C:GLU116 3.9 31.5 1.0
C C:ALA96 4.0 32.4 1.0
O C:HOH449 4.1 40.4 1.0
O C:HOH423 4.3 27.3 1.0
N C:GLY97 4.4 29.0 1.0
OE1 C:GLU166 4.5 72.5 1.0
OE1 C:GLU116 4.7 33.4 1.0
CG C:GLU166 4.8 56.8 1.0
CG C:GLU116 4.8 30.9 1.0
O C:HOH453 4.9 61.4 1.0

Magnesium binding site 6 out of 8 in 5qjv

Go back to Magnesium Binding Sites List in 5qjv
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 Z281802060


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 Z281802060 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:32.9
occ:1.00
 O C:HOH445 1.9 26.6 1.0
O C:ALA96 2.1 27.4 1.0
OE2 C:GLU116 2.1 29.8 1.0
MG C:MG302 2.1 45.9 1.0
O C:HOH423 2.2 27.3 1.0
O C:HOH412 2.3 31.6 1.0
CD C:GLU116 3.1 31.5 1.0
C C:ALA96 3.3 32.4 1.0
OE1 C:GLU116 3.4 33.4 1.0
O C:HOH402 3.7 38.8 1.0
OE2 C:GLU166 3.8 48.4 1.0
O C:HOH449 4.0 40.4 1.0
OE2 C:GLU112 4.1 34.9 1.0
N C:GLY97 4.1 29.0 1.0
CA C:GLY97 4.2 33.4 1.0
N C:ALA96 4.2 26.2 1.0
CA C:ALA96 4.2 26.9 1.0
O C:HOH413 4.3 27.9 1.0
O C:HOH466 4.4 38.8 1.0
NH2 C:ARG84 4.4 33.8 1.0
NE2 C:GLN82 4.4 35.1 1.0
CG C:GLU116 4.5 30.9 1.0
O C:HOH454 4.5 45.2 1.0
OE1 C:GLN82 4.5 31.0 1.0
CB C:ALA96 4.7 27.4 1.0
CD C:GLU112 4.8 38.0 1.0
CD C:GLN82 4.9 43.0 1.0
CD C:GLU166 4.9 63.1 1.0

Magnesium binding site 7 out of 8 in 5qjv

Go back to Magnesium Binding Sites List in 5qjv
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 Z281802060


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 Z281802060 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:28.1
occ:1.00
 O D:HOH409 1.8 31.0 1.0
O D:HOH415 2.0 29.9 1.0
OE2 D:GLU116 2.0 30.3 1.0
O D:HOH416 2.0 32.2 1.0
MG D:MG302 2.1 40.5 1.0
O D:ALA96 2.1 27.4 1.0
CD D:GLU116 3.1 36.2 1.0
C D:ALA96 3.3 27.4 1.0
OE1 D:GLU116 3.4 32.2 1.0
OE2 D:GLU166 3.6 86.4 1.0
OE2 D:GLU112 3.8 51.2 1.0
N D:ALA96 4.1 29.9 1.0
CA D:GLY97 4.2 30.1 1.0
N D:GLY97 4.2 29.1 1.0
CA D:ALA96 4.2 28.2 1.0
O D:HOH430 4.3 34.5 1.0
O D:HOH412 4.3 26.1 0.9
NH2 D:ARG84 4.4 32.3 1.0
CG D:GLU116 4.4 32.5 1.0
NE2 D:GLN82 4.4 32.6 1.0
OE1 D:GLN82 4.4 34.8 1.0
CD D:GLU112 4.5 45.0 1.0
O D:HOH435 4.5 40.3 0.9
CG D:GLU112 4.6 51.9 1.0
CB D:ALA96 4.6 30.7 1.0
CD D:GLU166 4.8 82.8 1.0
CD D:GLN82 4.9 37.3 1.0
O D:HOH401 4.9 45.2 1.0

Magnesium binding site 8 out of 8 in 5qjv

Go back to Magnesium Binding Sites List in 5qjv
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 Z281802060


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 Z281802060 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:40.5
occ:1.00
 MG D:MG301 2.1 28.1 1.0
O D:HOH409 2.5 31.0 1.0
OE2 D:GLU166 2.7 86.4 1.0
OE2 D:GLU112 2.7 51.2 1.0
OE2 D:GLU116 2.8 30.3 1.0
O D:HOH416 2.9 32.2 1.0
O D:ALA96 3.0 27.4 1.0
O D:HOH407 3.2 45.9 1.0
CD D:GLU112 3.5 45.0 1.0
CA D:GLY97 3.6 30.1 1.0
CD D:GLU166 3.9 82.8 1.0
C D:ALA96 3.9 27.4 1.0
O D:HOH401 4.0 45.2 1.0
OE1 D:GLU112 4.0 46.5 1.0
CD D:GLU116 4.0 36.2 1.0
O D:HOH415 4.1 29.9 1.0
O D:HOH430 4.1 34.5 1.0
N D:GLY97 4.3 29.1 1.0
CG D:GLU112 4.3 51.9 1.0
OE1 D:GLU166 4.8 78.7 1.0
CG D:GLU166 4.8 71.7 1.0
O D:HOH435 4.8 40.3 0.9
OE1 D:GLU116 4.8 32.2 1.0
C D:GLY97 4.8 32.8 1.0
CG D:GLU116 4.9 32.5 1.0
N D:LEU98 5.0 35.3 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 02:23:10 2024

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