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Magnesium in PDB 5qj4: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1827602749

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1827602749

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 Z1827602749:
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 Z1827602749, PDB code: 5qj4 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) 78.33 / 1.89
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.382, 59.834, 80.137, 79.36, 81.67, 75.75
R / Rfree (%) 21.3 / 25.3

Other elements in 5qj4:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1827602749 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 Z1827602749 (pdb code 5qj4). 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 Z1827602749, PDB code: 5qj4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qj4

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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 Z1827602749


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 Z1827602749 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:26.2
occ:1.00
 OE2 A:GLU116 2.0 23.4 1.0
O A:ALA96 2.1 19.8 1.0
O A:HOH449 2.1 23.5 1.0
O A:HOH421 2.2 21.2 1.0
O A:HOH457 2.2 18.9 1.0
O A:HOH414 2.3 22.6 1.0
CD A:GLU116 3.1 23.6 1.0
C A:ALA96 3.2 18.0 1.0
OE1 A:GLU116 3.4 24.7 1.0
MG A:MG302 3.4 54.3 1.0
OE2 A:GLU166 4.1 67.5 1.0
N A:GLY97 4.1 20.9 1.0
CA A:GLY97 4.1 22.3 1.0
CA A:ALA96 4.2 16.8 1.0
O A:HOH439 4.2 17.3 0.8
OE2 A:GLU112 4.2 31.4 1.0
N A:ALA96 4.2 16.6 1.0
O A:HOH424 4.3 19.4 1.0
NH2 A:ARG84 4.3 23.4 1.0
NE2 A:GLN82 4.4 22.3 1.0
O A:HOH469 4.4 21.3 1.0
CG A:GLU116 4.4 24.2 1.0
OE1 A:GLN82 4.5 21.0 1.0
O A:HOH476 4.5 48.8 1.0
O A:HOH464 4.6 29.2 1.0
CB A:ALA96 4.6 14.6 1.0
CD A:GLN82 4.8 26.6 1.0
CD A:GLU112 4.9 27.8 1.0

Magnesium binding site 2 out of 8 in 5qj4

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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 Z1827602749


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 Z1827602749 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:54.3
occ:1.00
 O A:HOH403 2.0 38.9 1.0
O A:HOH449 2.2 23.5 1.0
OE2 A:GLU112 2.2 31.4 1.0
O A:HOH422 2.2 46.2 1.0
OE2 A:GLU166 2.4 67.5 1.0
OE2 A:GLU116 2.6 23.4 1.0
CD A:GLU112 3.2 27.8 1.0
CD A:GLU166 3.2 72.1 1.0
OE1 A:GLU166 3.4 68.4 1.0
MG A:MG301 3.4 26.2 1.0
OE1 A:GLU112 3.4 30.6 1.0
CD A:GLU116 3.4 23.6 1.0
CG A:GLU116 3.6 24.2 1.0
O A:ALA96 4.0 19.8 1.0
O A:HOH414 4.0 22.6 1.0
OE2 A:GLU115 4.1 32.2 1.0
O A:HOH464 4.3 29.2 1.0
CG A:GLU166 4.5 67.0 1.0
CG A:GLU112 4.6 24.5 1.0
OE1 A:GLU116 4.6 24.7 1.0
CA A:GLY97 4.8 22.3 1.0
CB A:GLU112 4.9 23.8 1.0
C A:ALA96 4.9 18.0 1.0

Magnesium binding site 3 out of 8 in 5qj4

Go back to Magnesium Binding Sites List in 5qj4
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 Z1827602749


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 Z1827602749 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:32.5
occ:1.00
 O B:ALA96 2.0 25.1 1.0
O B:HOH408 2.1 30.8 1.0
O B:HOH411 2.1 29.9 1.0
O B:HOH449 2.2 18.5 1.0
OE2 B:GLU116 2.2 35.2 1.0
O B:HOH445 2.2 29.2 1.0
CD B:GLU116 3.1 33.0 1.0
C B:ALA96 3.2 23.9 1.0
OE1 B:GLU116 3.4 30.3 1.0
OE2 B:GLU166 4.0 57.5 1.0
N B:GLY97 4.1 24.6 1.0
N B:ALA96 4.1 24.0 1.0
CA B:ALA96 4.1 24.2 1.0
O B:HOH420 4.1 30.9 1.0
CA B:GLY97 4.1 27.7 1.0
OE2 B:GLU112 4.2 42.7 1.0
NH2 B:ARG84 4.3 26.8 1.0
NE2 B:GLN82 4.3 36.3 1.0
MG B:MG304 4.3 65.8 1.0
O B:HOH464 4.4 38.7 0.9
CG B:GLU116 4.5 31.7 1.0
OE1 B:GLN82 4.5 35.9 1.0
O B:HOH465 4.5 30.9 1.0
CB B:ALA96 4.5 24.7 1.0
CD B:GLU166 4.7 72.0 1.0
CD B:GLN82 4.8 38.0 1.0
CD B:GLU112 5.0 37.8 1.0

Magnesium binding site 4 out of 8 in 5qj4

Go back to Magnesium Binding Sites List in 5qj4
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 Z1827602749


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 Z1827602749 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:65.8
occ:1.00
 O B:HOH435 2.2 59.9 1.0
OE2 B:GLU166 2.4 57.5 1.0
OE2 B:GLU112 2.5 42.7 1.0
O B:HOH424 2.6 37.2 1.0
OE1 B:GLU166 3.0 73.9 1.0
OE2 B:GLU116 3.1 35.2 1.0
CD B:GLU166 3.1 72.0 1.0
OE2 B:GLU115 3.2 46.1 1.0
O B:HOH445 3.3 29.2 1.0
CD B:GLU112 3.4 37.8 1.0
CG B:GLU116 3.4 31.7 1.0
CD B:GLU116 3.7 33.0 1.0
OE1 B:GLU112 3.7 36.6 1.0
CB B:GLU115 4.1 36.8 1.0
CD B:GLU115 4.3 44.3 1.0
MG B:MG303 4.3 32.5 1.0
CG B:GLU166 4.6 67.6 1.0
CG B:GLU112 4.8 35.6 1.0
O B:ALA96 4.8 25.1 1.0
O B:HOH408 4.8 30.8 1.0
CG B:GLU115 4.9 40.5 1.0
O B:GLU112 4.9 31.4 1.0
CB B:GLU116 4.9 33.7 1.0
OE1 B:GLU116 4.9 30.3 1.0
N B:GLU116 5.0 35.4 1.0

Magnesium binding site 5 out of 8 in 5qj4

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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 Z1827602749


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 Z1827602749 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:61.0
occ:1.00
 O C:HOH438 2.0 36.9 1.0
OE2 C:GLU112 2.2 30.7 1.0
OE2 C:GLU166 2.3 83.2 1.0
O C:HOH404 2.4 47.5 1.0
O C:HOH420 2.5 53.0 1.0
OE2 C:GLU116 2.6 28.3 1.0
MG C:MG303 3.1 29.8 1.0
CD C:GLU112 3.1 38.1 1.0
OE1 C:GLU112 3.4 43.5 1.0
CD C:GLU166 3.4 79.1 1.0
O C:HOH461 3.4 56.3 1.0
O C:ALA96 3.4 24.1 1.0
CD C:GLU116 3.6 26.5 1.0
OE1 C:GLU166 3.7 78.2 1.0
O C:HOH414 3.8 31.4 1.0
O C:HOH457 3.8 38.2 0.9
CG C:GLU116 4.0 25.5 1.0
CA C:GLY97 4.4 30.9 1.0
C C:ALA96 4.5 26.7 1.0
OE2 C:GLU115 4.5 37.4 1.0
CG C:GLU112 4.5 33.4 1.0
O C:HOH454 4.5 23.0 1.0
OE1 C:GLU116 4.6 34.9 1.0
CG C:GLU166 4.7 69.9 1.0
N C:GLY97 4.8 27.8 1.0
O C:HOH425 4.8 25.4 1.0

Magnesium binding site 6 out of 8 in 5qj4

Go back to Magnesium Binding Sites List in 5qj4
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 Z1827602749


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 Z1827602749 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:29.8
occ:1.00
 O C:HOH438 2.0 36.9 1.0
O C:HOH425 2.1 25.4 1.0
O C:HOH454 2.1 23.0 1.0
OE2 C:GLU116 2.1 28.3 1.0
O C:HOH414 2.2 31.4 1.0
O C:ALA96 2.2 24.1 1.0
MG C:MG302 3.1 61.0 1.0
CD C:GLU116 3.2 26.5 1.0
C C:ALA96 3.3 26.7 1.0
OE1 C:GLU116 3.5 34.9 1.0
OE2 C:GLU166 3.8 83.2 1.0
N C:ALA96 4.2 23.4 1.0
O C:HOH411 4.2 26.4 0.9
OE2 C:GLU112 4.2 30.7 1.0
CA C:ALA96 4.2 22.6 1.0
N C:GLY97 4.3 27.8 1.0
NE2 C:GLN82 4.3 31.9 1.0
OE1 C:GLN82 4.3 28.8 1.0
CA C:GLY97 4.3 30.9 1.0
NH2 C:ARG84 4.4 30.1 1.0
O C:HOH457 4.4 38.2 0.9
O C:HOH462 4.5 33.3 0.9
CG C:GLU116 4.6 25.5 1.0
CB C:ALA96 4.6 23.7 1.0
CD C:GLN82 4.8 35.7 1.0
CD C:GLU166 4.9 79.1 1.0

Magnesium binding site 7 out of 8 in 5qj4

Go back to Magnesium Binding Sites List in 5qj4
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 Z1827602749


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 Z1827602749 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:35.7
occ:1.00
 OE2 D:GLU116 2.0 33.7 1.0
O D:HOH407 2.2 26.0 1.0
O D:HOH405 2.3 27.1 1.0
MG D:MG302 2.5 34.9 1.0
O D:HOH428 2.5 43.7 1.0
O D:ALA96 3.1 32.8 1.0
CD D:GLU116 3.2 38.5 1.0
OE2 D:GLU166 3.4 89.0 1.0
NE2 D:GLN82 3.5 42.5 1.0
OE1 D:GLU116 3.7 34.0 1.0
NH2 D:ARG84 4.0 37.8 1.0
OE1 D:GLN82 4.2 39.5 1.0
OE2 D:GLU112 4.2 45.2 1.0
O D:HOH414 4.2 34.9 0.9
C D:ALA96 4.2 36.2 1.0
CD D:GLN82 4.3 43.8 1.0
CG D:GLU116 4.4 37.1 1.0
CD D:GLU166 4.5 86.7 1.0
O D:HOH402 4.7 45.2 1.0
O D:HOH408 4.8 44.2 1.0
NH1 D:ARG84 4.9 32.3 1.0
CZ D:ARG84 4.9 37.8 1.0
CG D:GLU166 4.9 79.7 1.0
N D:ALA96 4.9 34.7 1.0
CA D:GLY97 4.9 38.2 1.0

Magnesium binding site 8 out of 8 in 5qj4

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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 Z1827602749


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 Z1827602749 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:34.9
occ:1.00
 O D:HOH428 2.0 43.7 1.0
OE2 D:GLU112 2.3 45.2 1.0
O D:HOH408 2.4 44.2 1.0
MG D:MG301 2.5 35.7 1.0
OE2 D:GLU166 2.8 89.0 1.0
OE2 D:GLU116 2.8 33.7 1.0
O D:HOH407 3.0 26.0 1.0
O D:ALA96 3.0 32.8 1.0
CD D:GLU112 3.3 48.8 1.0
O D:HOH402 3.5 45.2 1.0
CA D:GLY97 3.6 38.2 1.0
OE1 D:GLU112 3.9 54.1 1.0
CD D:GLU166 4.0 86.7 1.0
CD D:GLU116 4.0 38.5 1.0
C D:ALA96 4.0 36.2 1.0
CG D:GLU112 4.1 53.9 1.0
N D:GLY97 4.2 35.6 1.0
O D:HOH405 4.3 27.1 1.0
OE1 D:GLU166 4.7 81.9 1.0
O D:HOH414 4.8 34.9 0.9
CG D:GLU116 4.8 37.1 1.0
C D:GLY97 4.8 38.1 1.0
OE1 D:GLU116 4.8 34.0 1.0
CG D:GLU166 4.9 79.7 1.0
N D:LEU98 5.0 40.2 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 02:11:14 2024

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