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Magnesium in PDB 5qj9: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z768399682

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z768399682

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 Z768399682:
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 Z768399682, PDB code: 5qj9 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) 77.83 / 1.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.594, 59.884, 79.674, 79.45, 81.18, 75.37
R / Rfree (%) 24.2 / 28.8

Other elements in 5qj9:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z768399682 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 Z768399682 (pdb code 5qj9). 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 Z768399682, PDB code: 5qj9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qj9

Go back to Magnesium Binding Sites List in 5qj9
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 Z768399682


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 Z768399682 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:29.5
occ:1.00
 O A:HOH453 2.0 21.6 1.0
O A:HOH445 2.1 22.3 1.0
O A:ALA96 2.1 22.9 1.0
OE2 A:GLU116 2.2 27.5 1.0
O A:HOH444 2.2 24.2 1.0
O A:HOH413 2.3 26.0 1.0
CD A:GLU116 3.2 26.4 1.0
C A:ALA96 3.3 21.2 1.0
OE1 A:GLU116 3.5 26.9 1.0
MG A:MG302 3.6 52.2 1.0
O A:HOH448 4.0 17.8 0.7
N A:ALA96 4.1 18.5 1.0
O A:HOH414 4.1 18.8 1.0
NH2 A:ARG84 4.2 28.6 1.0
CA A:ALA96 4.2 19.7 1.0
N A:GLY97 4.2 21.7 1.0
CA A:GLY97 4.2 25.6 1.0
NE2 A:GLN82 4.2 28.4 1.0
OE2 A:GLU112 4.2 37.1 1.0
OE2 A:GLU166 4.3 62.1 1.0
O A:HOH468 4.4 27.3 1.0
OE1 A:GLN82 4.4 26.1 1.0
CG A:GLU116 4.5 26.6 1.0
CB A:ALA96 4.7 17.7 1.0
CD A:GLN82 4.7 31.2 1.0
O A:HOH465 4.7 26.9 1.0
O A:HOH473 4.9 44.8 1.0
CZ A:ARG84 5.0 27.3 1.0

Magnesium binding site 2 out of 8 in 5qj9

Go back to Magnesium Binding Sites List in 5qj9
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 Z768399682


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 Z768399682 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:52.2
occ:1.00
 O A:HOH409 1.7 39.5 1.0
OE2 A:GLU112 2.0 37.1 1.0
O A:HOH444 2.2 24.2 1.0
O A:HOH443 2.6 45.6 1.0
OE2 A:GLU116 2.6 27.5 1.0
OE2 A:GLU166 2.6 62.1 1.0
CD A:GLU112 3.0 31.6 1.0
OE1 A:GLU166 3.2 73.0 1.0
CD A:GLU166 3.2 68.2 1.0
OE1 A:GLU112 3.3 33.0 1.0
CD A:GLU116 3.5 26.4 1.0
MG A:MG301 3.6 29.5 1.0
CG A:GLU116 3.7 26.6 1.0
OE2 A:GLU115 4.0 33.5 1.0
O A:HOH413 4.0 26.0 1.0
O A:ALA96 4.1 22.9 1.0
O A:HOH465 4.3 26.9 1.0
CG A:GLU112 4.4 27.0 1.0
OE1 A:GLU116 4.6 26.9 1.0
CG A:GLU166 4.7 62.2 1.0
CB A:GLU112 4.7 24.3 1.0
CA A:GLY97 4.8 25.6 1.0
C A:ALA96 4.9 21.2 1.0
O A:HOH453 5.0 21.6 1.0

Magnesium binding site 3 out of 8 in 5qj9

Go back to Magnesium Binding Sites List in 5qj9
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 Z768399682


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 Z768399682 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:30.8
occ:1.00
 O B:ALA96 1.9 22.5 1.0
O B:HOH422 1.9 35.6 1.0
OE2 B:GLU116 2.1 37.6 1.0
O B:HOH420 2.2 33.1 1.0
O B:HOH458 2.2 26.3 1.0
O B:HOH411 2.3 34.4 1.0
C B:ALA96 3.0 23.9 1.0
CD B:GLU116 3.1 38.6 1.0
OE1 B:GLU116 3.3 39.4 1.0
MG B:MG303 3.7 61.8 1.0
N B:ALA96 3.8 25.9 1.0
CA B:ALA96 3.9 25.4 1.0
O B:HOH423 3.9 32.1 1.0
N B:GLY97 4.0 25.4 1.0
CA B:GLY97 4.0 27.2 1.0
OE2 B:GLU112 4.1 44.8 1.0
NE2 B:GLN82 4.1 44.5 1.0
OE2 B:GLU166 4.2 58.1 1.0
CB B:ALA96 4.3 26.7 1.0
NH2 B:ARG84 4.4 26.8 1.0
O B:HOH468 4.4 38.3 1.0
CG B:GLU116 4.5 34.2 1.0
OE1 B:GLN82 4.5 41.1 1.0
CD B:GLN82 4.7 45.1 1.0

Magnesium binding site 4 out of 8 in 5qj9

Go back to Magnesium Binding Sites List in 5qj9
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 Z768399682


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 Z768399682 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:61.8
occ:1.00
 OE2 B:GLU112 1.9 44.8 1.0
O B:HOH405 2.4 43.8 1.0
OE2 B:GLU116 2.4 37.6 1.0
O B:HOH420 2.7 33.1 1.0
CD B:GLU112 2.8 36.8 1.0
OE2 B:GLU166 3.0 58.1 1.0
OE1 B:GLU112 3.1 34.4 1.0
CD B:GLU116 3.3 38.6 1.0
OE1 B:GLU166 3.3 64.2 1.0
O B:HOH410 3.4 60.0 1.0
CG B:GLU116 3.5 34.2 1.0
OE2 B:GLU115 3.5 47.4 1.0
CD B:GLU166 3.5 65.4 1.0
MG B:MG302 3.7 30.8 1.0
O B:ALA96 3.8 22.5 1.0
CG B:GLU112 4.2 34.2 1.0
O B:HOH422 4.3 35.6 1.0
OE1 B:GLU116 4.5 39.4 1.0
CB B:GLU112 4.6 34.0 1.0
CA B:GLY97 4.6 27.2 1.0
CB B:GLU115 4.6 39.0 1.0
C B:ALA96 4.6 23.9 1.0
CD B:GLU115 4.7 49.3 1.0
CA B:GLU112 4.8 30.9 1.0
O B:HOH441 4.8 40.1 0.9
O B:GLU112 4.9 28.4 1.0
N B:GLY97 5.0 25.4 1.0
CG B:GLU166 5.0 62.1 1.0
CB B:GLU116 5.0 33.8 1.0

Magnesium binding site 5 out of 8 in 5qj9

Go back to Magnesium Binding Sites List in 5qj9
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 Z768399682


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 Z768399682 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:50.2
occ:1.00
 O C:HOH402 2.3 49.6 1.0
MG C:MG303 2.4 27.5 1.0
OE2 C:GLU166 2.4 65.9 1.0
OE2 C:GLU116 2.9 34.4 1.0
O C:HOH405 3.0 40.2 1.0
O C:ALA96 3.1 25.4 1.0
OE2 C:GLU112 3.2 31.3 1.0
O C:HOH451 3.2 24.7 1.0
O C:HOH450 3.3 44.4 1.0
O C:HOH445 3.4 52.6 1.0
CD C:GLU166 3.6 67.2 1.0
CA C:GLY97 3.7 29.5 1.0
CD C:GLU112 3.9 39.1 1.0
O C:HOH406 3.9 57.9 1.0
OE1 C:GLU112 4.0 46.3 1.0
OE1 C:GLU166 4.1 65.3 1.0
C C:ALA96 4.1 27.2 1.0
CD C:GLU116 4.1 32.2 1.0
O C:HOH419 4.3 30.5 1.0
N C:GLY97 4.4 27.4 1.0
CG C:GLU166 4.7 64.0 1.0
O C:HOH465 4.7 40.7 1.0
CG C:GLU116 4.8 29.9 1.0
C C:GLY97 5.0 32.0 1.0

Magnesium binding site 6 out of 8 in 5qj9

Go back to Magnesium Binding Sites List in 5qj9
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 Z768399682


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 Z768399682 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:27.5
occ:1.00
 O C:HOH451 1.9 24.7 1.0
O C:HOH419 2.0 30.5 1.0
OE2 C:GLU116 2.0 34.4 1.0
O C:HOH405 2.1 40.2 1.0
O C:ALA96 2.2 25.4 1.0
MG C:MG302 2.4 50.2 1.0
CD C:GLU116 3.1 32.2 1.0
C C:ALA96 3.3 27.2 1.0
OE1 C:GLU116 3.5 38.0 1.0
OE2 C:GLU166 3.5 65.9 1.0
O C:HOH402 3.8 49.6 1.0
NH2 C:ARG84 4.2 29.7 1.0
N C:GLY97 4.2 27.4 1.0
CA C:ALA96 4.3 24.7 1.0
N C:ALA96 4.3 25.2 1.0
CA C:GLY97 4.3 29.5 1.0
NE2 C:GLN82 4.4 31.9 1.0
OE1 C:GLN82 4.4 32.8 1.0
OE2 C:GLU112 4.4 31.3 1.0
CG C:GLU116 4.4 29.9 1.0
O C:HOH460 4.6 38.4 1.0
CD C:GLU166 4.7 67.2 1.0
CB C:ALA96 4.7 25.1 1.0
CD C:GLN82 4.8 36.4 1.0
O C:HOH450 4.9 44.4 1.0
NH1 C:ARG84 5.0 34.6 1.0
CZ C:ARG84 5.0 33.4 1.0

Magnesium binding site 7 out of 8 in 5qj9

Go back to Magnesium Binding Sites List in 5qj9
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 Z768399682


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 Z768399682 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:37.1
occ:1.00
 OE2 D:GLU116 2.1 48.2 1.0
O D:HOH407 2.3 28.5 1.0
O D:HOH405 2.3 30.8 1.0
MG D:MG302 2.4 50.7 1.0
O D:HOH428 2.6 34.6 1.0
O D:ALA96 3.1 53.4 1.0
CD D:GLU116 3.3 56.3 1.0
NE2 D:GLN82 3.7 58.2 1.0
OE1 D:GLU116 3.8 53.6 1.0
OE1 D:GLN82 3.8 55.7 1.0
OE2 D:GLU112 4.0 57.8 1.0
C D:ALA96 4.1 56.8 1.0
CD D:GLN82 4.2 58.4 1.0
NH2 D:ARG84 4.3 48.3 1.0
O D:HOH403 4.4 61.7 1.0
CG D:GLU116 4.5 52.7 1.0
N D:ALA96 4.8 49.7 1.0
CA D:GLY97 4.8 59.3 1.0
N D:GLY97 4.9 56.5 1.0
CA D:ALA96 4.9 53.0 1.0
CG1 D:VAL168 4.9 74.8 1.0
CD D:GLU112 5.0 61.1 1.0
NH1 D:ARG84 5.0 51.9 1.0

Magnesium binding site 8 out of 8 in 5qj9

Go back to Magnesium Binding Sites List in 5qj9
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 Z768399682


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 Z768399682 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:50.7
occ:1.00
 OE2 D:GLU112 2.1 57.8 1.0
O D:HOH428 2.1 34.6 1.0
MG D:MG301 2.4 37.1 1.0
OE2 D:GLU116 2.8 48.2 1.0
O D:HOH403 3.0 61.7 1.0
CD D:GLU112 3.2 61.1 1.0
O D:HOH407 3.2 28.5 1.0
O D:ALA96 3.3 53.4 1.0
O D:HOH413 3.4 36.7 1.0
OE2 D:GLU166 3.9 90.5 1.0
OE1 D:GLU112 3.9 60.5 1.0
CA D:GLY97 3.9 59.3 1.0
CD D:GLU116 4.0 56.3 1.0
CD D:GLU166 4.1 86.6 1.0
CG D:GLU112 4.1 60.1 1.0
C D:ALA96 4.3 56.8 1.0
O D:HOH405 4.3 30.8 1.0
OE1 D:GLU166 4.5 84.6 1.0
N D:GLY97 4.6 56.5 1.0
CG D:GLU166 4.6 81.8 1.0
CG D:GLU116 4.7 52.7 1.0
OE2 D:GLU115 4.8 53.6 1.0
OE1 D:GLU116 4.8 53.6 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 02:11:41 2024

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