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Magnesium in PDB 5qjh: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z375990520

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z375990520

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 Z375990520:
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 Z375990520, PDB code: 5qjh 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) 78.03 / 2.03
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.010, 59.630, 79.830, 79.41, 81.64, 75.79
R / Rfree (%) 22.4 / 27.3

Other elements in 5qjh:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z375990520 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 Z375990520 (pdb code 5qjh). 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 Z375990520, PDB code: 5qjh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjh

Go back to Magnesium Binding Sites List in 5qjh
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 Z375990520


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 Z375990520 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:36.4
occ:1.00
 O A:HOH429 2.0 29.5 1.0
OE2 A:GLU116 2.0 33.6 1.0
O A:HOH417 2.1 30.2 1.0
O A:ALA96 2.1 26.0 1.0
O A:HOH448 2.2 26.2 1.0
O A:HOH409 2.4 36.0 1.0
CD A:GLU116 3.0 32.8 1.0
C A:ALA96 3.3 24.5 1.0
OE1 A:GLU116 3.4 31.9 1.0
MG A:MG302 3.6 65.6 1.0
OE2 A:GLU166 3.9 69.3 1.0
O A:HOH443 4.1 16.0 0.7
OE2 A:GLU112 4.1 35.9 1.0
N A:GLY97 4.2 24.1 1.0
O A:HOH426 4.2 19.8 1.0
N A:ALA96 4.2 22.6 1.0
CA A:GLY97 4.2 26.4 1.0
NH2 A:ARG84 4.2 30.9 1.0
CA A:ALA96 4.2 22.6 1.0
NE2 A:GLN82 4.3 29.8 1.0
CG A:GLU116 4.3 35.3 1.0
O A:HOH464 4.4 29.6 1.0
OE1 A:GLN82 4.4 27.5 1.0
O A:HOH458 4.5 33.3 1.0
CB A:ALA96 4.6 20.7 1.0
CD A:GLN82 4.7 35.0 1.0
O A:HOH468 4.8 67.0 1.0
CD A:GLU112 4.8 35.3 1.0
CD A:GLU166 5.0 81.7 1.0

Magnesium binding site 2 out of 8 in 5qjh

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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 Z375990520


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 Z375990520 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:65.6
occ:1.00
 O A:HOH410 1.9 64.1 1.0
O A:HOH453 2.0 60.8 1.0
O A:HOH429 2.2 29.5 1.0
OE2 A:GLU112 2.3 35.9 1.0
OE2 A:GLU166 2.4 69.3 1.0
OE2 A:GLU116 2.8 33.6 1.0
CD A:GLU166 3.0 81.7 1.0
OE1 A:GLU166 3.0 74.3 1.0
CD A:GLU112 3.1 35.3 1.0
OE1 A:GLU112 3.3 32.3 1.0
MG A:MG301 3.6 36.4 1.0
CD A:GLU116 3.7 32.8 1.0
CG A:GLU116 3.8 35.3 1.0
O A:HOH409 4.0 36.0 1.0
O A:ALA96 4.2 26.0 1.0
OE2 A:GLU115 4.2 39.4 1.0
CG A:GLU166 4.3 77.1 1.0
O A:HOH458 4.6 33.3 1.0
CG A:GLU112 4.6 33.5 1.0
OE1 A:GLU116 4.9 31.9 1.0
O A:HOH414 5.0 65.6 1.0
O A:HOH468 5.0 67.0 1.0

Magnesium binding site 3 out of 8 in 5qjh

Go back to Magnesium Binding Sites List in 5qjh
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 Z375990520


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 Z375990520 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:31.5
occ:1.00
 O B:HOH404 1.8 29.1 1.0
OE2 B:GLU116 2.0 39.4 1.0
O B:HOH415 2.0 31.8 1.0
O B:ALA96 2.1 29.7 1.0
O B:HOH441 2.1 21.9 1.0
O B:HOH442 2.2 34.5 1.0
CD B:GLU116 3.1 42.8 1.0
C B:ALA96 3.3 28.9 1.0
OE1 B:GLU116 3.4 41.9 1.0
MG B:MG303 3.7 67.7 1.0
OE2 B:GLU166 4.0 74.5 1.0
NE2 B:GLN82 4.1 41.2 1.0
O B:HOH421 4.1 31.3 1.0
CA B:GLY97 4.1 33.5 1.0
N B:GLY97 4.1 30.6 1.0
OE2 B:GLU112 4.2 44.6 1.0
NH2 B:ARG84 4.2 31.7 1.0
N B:ALA96 4.2 28.8 1.0
CA B:ALA96 4.2 29.9 1.0
OE1 B:GLN82 4.2 42.8 1.0
CG B:GLU116 4.4 38.9 1.0
O B:HOH462 4.5 35.4 1.0
CD B:GLN82 4.6 43.1 1.0
CB B:ALA96 4.6 29.4 1.0
CD B:GLU112 5.0 39.3 1.0

Magnesium binding site 4 out of 8 in 5qjh

Go back to Magnesium Binding Sites List in 5qjh
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 Z375990520


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 Z375990520 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:67.7
occ:1.00
 O B:HOH405 2.0 62.5 1.0
OE2 B:GLU112 2.1 44.6 1.0
OE2 B:GLU116 2.6 39.4 1.0
OE2 B:GLU166 2.6 74.5 1.0
O B:HOH442 2.7 34.5 1.0
O B:HOH446 2.7 47.1 1.0
CD B:GLU112 3.1 39.3 1.0
CG B:GLU116 3.2 38.9 1.0
CD B:GLU116 3.3 42.8 1.0
OE1 B:GLU112 3.4 42.0 1.0
OE2 B:GLU115 3.5 48.8 1.0
CD B:GLU166 3.6 75.5 1.0
MG B:MG302 3.7 31.5 1.0
OE1 B:GLU166 3.8 69.3 1.0
O B:ALA96 4.1 29.7 1.0
O B:HOH404 4.4 29.1 1.0
CB B:GLU115 4.4 40.5 1.0
CG B:GLU112 4.5 34.5 1.0
OE1 B:GLU116 4.5 41.9 1.0
CD B:GLU115 4.7 48.3 1.0
O B:GLU112 4.7 32.1 1.0
CB B:GLU116 4.7 40.0 1.0
CA B:GLU112 4.7 32.4 1.0
CB B:GLU112 4.7 36.4 1.0
C B:ALA96 4.9 28.9 1.0
CG B:GLU166 4.9 74.3 1.0
CA B:GLY97 5.0 33.5 1.0

Magnesium binding site 5 out of 8 in 5qjh

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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 Z375990520


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 Z375990520 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:74.9
occ:1.00
 O C:HOH440 2.0 38.8 1.0
OE2 C:GLU112 2.2 36.0 1.0
O C:HOH418 2.4 60.1 1.0
OE2 C:GLU166 2.6 79.1 1.0
O C:HOH430 2.8 55.6 1.0
OE2 C:GLU116 2.8 35.9 1.0
OE1 C:GLU166 2.9 78.4 1.0
CD C:GLU166 3.1 79.5 1.0
CD C:GLU112 3.2 40.4 1.0
O C:HOH449 3.4 58.2 1.0
MG C:MG303 3.4 30.7 1.0
OE1 C:GLU112 3.5 49.2 1.0
CD C:GLU116 3.7 35.6 1.0
O C:HOH432 3.8 43.1 1.0
CG C:GLU116 3.9 33.6 1.0
O C:ALA96 4.1 32.6 1.0
OE2 C:GLU115 4.4 45.0 1.0
CG C:GLU166 4.5 71.2 1.0
CG C:GLU112 4.6 38.0 1.0
O C:HOH436 4.7 28.6 1.0
CA C:GLY97 4.8 36.4 1.0
OE1 C:GLU116 4.9 47.1 1.0
C C:ALA96 5.0 32.1 1.0

Magnesium binding site 6 out of 8 in 5qjh

Go back to Magnesium Binding Sites List in 5qjh
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 Z375990520


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 Z375990520 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:30.7
occ:1.00
 O C:HOH432 1.9 43.1 1.0
O C:HOH436 2.0 28.6 1.0
OE2 C:GLU116 2.0 35.9 1.0
O C:HOH416 2.1 29.1 1.0
O C:ALA96 2.2 32.6 1.0
O C:HOH440 2.3 38.8 1.0
CD C:GLU116 3.1 35.6 1.0
C C:ALA96 3.3 32.1 1.0
MG C:MG302 3.4 74.9 1.0
OE1 C:GLU116 3.5 47.1 1.0
OE2 C:GLU166 4.2 79.1 1.0
N C:GLY97 4.2 34.0 1.0
OE2 C:GLU112 4.2 36.0 1.0
N C:ALA96 4.2 29.6 1.0
OE1 C:GLN82 4.3 39.2 1.0
CA C:GLY97 4.3 36.4 1.0
NE2 C:GLN82 4.3 38.8 1.0
CA C:ALA96 4.3 29.9 1.0
NH2 C:ARG84 4.3 34.7 1.0
CG C:GLU116 4.4 33.6 1.0
CB C:ALA96 4.7 28.6 1.0
CD C:GLN82 4.7 43.1 1.0
CD C:GLU166 5.0 79.5 1.0
NH1 C:ARG84 5.0 37.9 1.0

Magnesium binding site 7 out of 8 in 5qjh

Go back to Magnesium Binding Sites List in 5qjh
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 Z375990520


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 Z375990520 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:41.5
occ:1.00
 OE2 D:GLU116 2.0 37.6 1.0
O D:HOH402 2.1 31.5 1.0
MG D:MG302 2.2 47.2 1.0
O D:HOH405 2.2 32.9 1.0
O D:ALA96 2.8 44.1 1.0
CD D:GLU116 3.1 43.4 1.0
OE2 D:GLU166 3.4 93.1 1.0
OE1 D:GLU116 3.5 43.0 1.0
NE2 D:GLN82 3.7 46.4 1.0
OE2 D:GLU112 4.0 61.6 1.0
C D:ALA96 4.0 44.8 1.0
OE1 D:GLN82 4.1 44.8 1.0
O D:HOH420 4.2 47.9 1.0
NH2 D:ARG84 4.3 44.6 1.0
CG D:GLU116 4.3 40.9 1.0
CD D:GLN82 4.3 47.5 1.0
O D:HOH401 4.5 40.4 1.0
CD D:GLU166 4.5 95.7 1.0
CA D:GLY97 4.7 48.5 1.0
N D:ALA96 4.8 41.7 1.0
N D:GLY97 4.8 46.4 1.0
CD D:GLU112 4.9 56.6 1.0
CA D:ALA96 4.9 43.5 1.0

Magnesium binding site 8 out of 8 in 5qjh

Go back to Magnesium Binding Sites List in 5qjh
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 Z375990520


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 Z375990520 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:47.2
occ:1.00
 MG D:MG301 2.2 41.5 1.0
OE2 D:GLU112 2.2 61.6 1.0
OE2 D:GLU166 2.7 93.1 1.0
OE2 D:GLU116 2.8 37.6 1.0
O D:HOH402 2.9 31.5 1.0
O D:ALA96 3.1 44.1 1.0
O D:HOH418 3.1 57.1 1.0
CD D:GLU112 3.3 56.6 1.0
O D:HOH401 3.5 40.4 1.0
CA D:GLY97 3.7 48.5 1.0
CD D:GLU116 4.0 43.4 1.0
CD D:GLU166 4.0 95.7 1.0
CG D:GLU112 4.0 56.0 1.0
C D:ALA96 4.0 44.8 1.0
OE1 D:GLU112 4.1 60.6 1.0
O D:HOH405 4.2 32.9 1.0
O D:HOH420 4.3 47.9 1.0
N D:GLY97 4.3 46.4 1.0
OE1 D:GLU166 4.7 92.5 1.0
OE1 D:GLU116 4.8 43.0 1.0
CG D:GLU116 4.8 40.9 1.0
C D:GLY97 4.9 46.4 1.0
CG D:GLU166 5.0 87.8 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 02:15:31 2024

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