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Magnesium in PDB 5qjk: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060

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 Z373221060:
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 Z373221060, PDB code: 5qjk 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) 78.39 / 1.65
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.961, 59.772, 80.215, 79.30, 81.69, 75.95
R / Rfree (%) 20.7 / 23.7

Other elements in 5qjk:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z373221060 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 Z373221060 (pdb code 5qjk). 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 Z373221060, PDB code: 5qjk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjk

Go back to Magnesium Binding Sites List in 5qjk
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 Z373221060


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 Z373221060 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:24.8
occ:1.00
 OE2 A:GLU116 2.1 23.2 1.0
O A:ALA96 2.1 20.6 1.0
O A:HOH432 2.1 21.9 1.0
O A:HOH448 2.2 23.0 1.0
O A:HOH428 2.2 25.8 1.0
O A:HOH462 2.2 22.5 1.0
CD A:GLU116 3.1 24.0 1.0
C A:ALA96 3.3 19.5 1.0
MG A:MG302 3.4 52.5 1.0
OE1 A:GLU116 3.4 23.1 1.0
OE2 A:GLU166 3.9 44.1 1.0
OE2 A:GLU112 4.0 30.0 1.0
CA A:GLY97 4.1 20.0 1.0
N A:GLY97 4.1 20.0 1.0
N A:ALA96 4.2 18.2 1.0
NH2 A:ARG84 4.2 24.2 1.0
CA A:ALA96 4.2 17.6 1.0
O A:HOH471 4.3 47.9 1.0
O A:HOH416 4.3 20.8 1.0
NE2 A:GLN82 4.4 25.0 1.0
OE1 A:GLN82 4.4 26.3 1.0
O A:HOH470 4.4 28.1 1.0
CG A:GLU116 4.5 23.1 1.0
O A:HOH469 4.5 23.1 0.9
CB A:ALA96 4.7 16.3 1.0
CD A:GLN82 4.8 29.7 1.0
O A:HOH463 4.8 31.4 1.0
CD A:GLU112 4.8 28.9 1.0

Magnesium binding site 2 out of 8 in 5qjk

Go back to Magnesium Binding Sites List in 5qjk
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 Z373221060


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 Z373221060 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:52.5
occ:1.00
 O A:HOH407 1.9 34.6 1.0
O A:HOH448 2.0 23.0 1.0
OE2 A:GLU112 2.2 30.0 1.0
O A:HOH415 2.4 46.4 1.0
OE2 A:GLU166 2.5 44.1 1.0
OE2 A:GLU116 2.6 23.2 1.0
CD A:GLU112 3.0 28.9 1.0
CD A:GLU166 3.1 62.6 1.0
OE1 A:GLU112 3.2 31.4 1.0
OE1 A:GLU166 3.2 51.5 1.0
MG A:MG301 3.4 24.8 1.0
CD A:GLU116 3.6 24.0 1.0
CG A:GLU116 3.8 23.1 1.0
O A:HOH428 3.9 25.8 1.0
O A:ALA96 4.0 20.6 1.0
O A:HOH471 4.0 47.9 1.0
OE2 A:GLU115 4.2 34.1 1.0
CG A:GLU166 4.4 56.6 1.0
CG A:GLU112 4.5 26.9 1.0
OE1 A:GLU116 4.7 23.1 1.0
O A:HOH463 4.7 31.4 1.0
CA A:GLY97 4.9 20.0 1.0
CB A:GLU112 5.0 26.5 1.0
C A:ALA96 5.0 19.5 1.0

Magnesium binding site 3 out of 8 in 5qjk

Go back to Magnesium Binding Sites List in 5qjk
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 Z373221060


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 Z373221060 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:27.1
occ:1.00
 O B:ALA96 2.0 24.6 1.0
OE2 B:GLU116 2.1 28.5 1.0
O B:HOH438 2.1 28.0 1.0
O B:HOH418 2.1 27.6 1.0
O B:HOH450 2.1 25.9 1.0
O B:HOH414 2.2 27.1 1.0
CD B:GLU116 3.1 29.5 1.0
C B:ALA96 3.2 21.1 1.0
OE1 B:GLU116 3.4 28.1 1.0
OE2 B:GLU166 3.9 48.0 1.0
CA B:GLY97 4.1 22.2 1.0
N B:GLY97 4.1 23.5 1.0
OE2 B:GLU112 4.1 34.2 1.0
NH2 B:ARG84 4.2 26.9 1.0
O B:HOH425 4.2 25.8 1.0
N B:ALA96 4.2 22.4 1.0
CA B:ALA96 4.2 23.2 1.0
NE2 B:GLN82 4.4 32.2 1.0
O B:HOH467 4.4 34.4 0.9
OE1 B:GLN82 4.4 34.4 1.0
CG B:GLU116 4.5 28.6 1.0
O B:HOH470 4.5 40.8 1.0
O B:HOH468 4.7 23.5 0.9
CD B:GLU166 4.7 65.8 1.0
CB B:ALA96 4.7 24.9 1.0
CD B:GLN82 4.8 36.2 1.0
MG B:MG303 4.8 65.3 1.0
CD B:GLU112 4.9 36.2 1.0
O B:HOH404 4.9 40.8 1.0

Magnesium binding site 4 out of 8 in 5qjk

Go back to Magnesium Binding Sites List in 5qjk
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 Z373221060


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 Z373221060 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:65.3
occ:1.00
 O B:HOH411 1.6 41.8 1.0
OE1 B:GLU166 2.1 66.3 1.0
O B:HOH404 2.3 40.8 1.0
CD B:GLU166 2.9 65.8 1.0
O B:HOH438 3.0 28.0 1.0
OE2 B:GLU166 3.1 48.0 1.0
OE2 B:GLU112 3.3 34.2 1.0
OE1 B:GLU112 3.5 36.5 1.0
OE2 B:GLU115 3.8 40.1 1.0
CD B:GLU112 3.8 36.2 1.0
O B:HOH467 4.3 34.4 0.9
OE2 B:GLU116 4.3 28.5 1.0
CG B:GLU166 4.3 59.9 1.0
MG B:MG302 4.8 27.1 1.0
O B:HOH414 5.0 27.1 1.0

Magnesium binding site 5 out of 8 in 5qjk

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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 Z373221060


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 Z373221060 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:38.2
occ:1.00
 MG C:MG303 2.1 29.0 1.0
OE2 C:GLU116 2.8 27.3 1.0
O C:ALA96 3.0 25.0 1.0
O C:HOH460 3.0 25.5 1.0
O C:HOH412 3.0 29.8 1.0
O C:HOH461 3.1 41.8 1.0
OE2 C:GLU166 3.2 56.7 1.0
OE2 C:GLU112 3.2 31.7 1.0
O C:HOH429 3.2 51.0 1.0
CA C:GLY97 3.6 28.2 1.0
OE1 C:GLU112 3.6 40.9 1.0
O C:HOH403 3.7 44.1 1.0
CD C:GLU112 3.7 33.9 1.0
C C:ALA96 4.0 25.9 1.0
CD C:GLU116 4.1 29.2 1.0
CD C:GLU166 4.1 65.5 1.0
O C:HOH424 4.2 24.8 1.0
N C:GLY97 4.3 25.3 1.0
O C:HOH469 4.5 27.9 1.0
OE1 C:GLU166 4.7 67.9 1.0
C C:GLY97 4.8 28.7 1.0
OE1 C:GLU116 4.9 32.6 1.0
CG C:GLU116 5.0 27.4 1.0
N C:LEU98 5.0 29.8 1.0

Magnesium binding site 6 out of 8 in 5qjk

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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 Z373221060


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 Z373221060 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:29.0
occ:1.00
 O C:HOH460 2.0 25.5 1.0
OE2 C:GLU116 2.0 27.3 1.0
O C:HOH424 2.1 24.8 1.0
MG C:MG302 2.1 38.2 1.0
O C:ALA96 2.1 25.0 1.0
O C:HOH412 2.2 29.8 1.0
CD C:GLU116 3.1 29.2 1.0
C C:ALA96 3.3 25.9 1.0
OE1 C:GLU116 3.5 32.6 1.0
OE2 C:GLU166 3.8 56.7 1.0
OE2 C:GLU112 4.1 31.7 1.0
CA C:GLY97 4.1 28.2 1.0
N C:GLY97 4.2 25.3 1.0
N C:ALA96 4.2 21.8 1.0
CA C:ALA96 4.2 22.0 1.0
O C:HOH417 4.2 25.0 0.9
NH2 C:ARG84 4.2 28.2 1.0
NE2 C:GLN82 4.4 30.7 1.0
OE1 C:GLN82 4.5 30.0 1.0
O C:HOH473 4.5 32.2 0.9
O C:HOH461 4.5 41.8 1.0
CG C:GLU116 4.5 27.4 1.0
O C:HOH469 4.7 27.9 1.0
CB C:ALA96 4.7 21.8 1.0
O C:HOH403 4.8 44.1 1.0
CD C:GLU112 4.8 33.9 1.0
CD C:GLN82 4.9 35.5 1.0

Magnesium binding site 7 out of 8 in 5qjk

Go back to Magnesium Binding Sites List in 5qjk
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 Z373221060


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 Z373221060 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:27.5
occ:1.00
 O D:HOH429 1.9 30.7 0.9
OE2 D:GLU116 2.0 28.1 1.0
O D:HOH409 2.0 25.3 1.0
O D:HOH434 2.1 28.1 1.0
O D:ALA96 2.2 28.4 1.0
MG D:MG302 2.2 44.2 1.0
O D:HOH436 2.3 33.6 1.0
CD D:GLU116 3.1 34.5 1.0
C D:ALA96 3.3 27.9 1.0
OE1 D:GLU116 3.4 31.9 1.0
OE2 D:GLU112 4.2 39.5 1.0
N D:GLY97 4.2 28.1 1.0
N D:ALA96 4.2 25.1 1.0
CA D:GLY97 4.2 28.4 1.0
CA D:ALA96 4.2 26.6 1.0
NH2 D:ARG84 4.3 29.8 1.0
O D:HOH416 4.4 26.2 0.9
CG D:GLU116 4.4 32.3 1.0
NE2 D:GLN82 4.4 32.9 1.0
OE1 D:GLN82 4.5 30.3 1.0
O D:HOH445 4.6 29.4 0.9
OE2 D:GLU166 4.6 71.2 1.0
O D:HOH442 4.7 26.8 0.9
O D:HOH405 4.7 45.5 1.0
CB D:ALA96 4.7 27.1 1.0
CD D:GLU112 4.7 41.4 1.0
CD D:GLN82 4.9 32.5 1.0
CG D:GLU112 5.0 46.6 1.0

Magnesium binding site 8 out of 8 in 5qjk

Go back to Magnesium Binding Sites List in 5qjk
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 Z373221060


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 Z373221060 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:44.2
occ:1.00
 O D:HOH436 1.4 33.6 1.0
MG D:MG301 2.2 27.5 1.0
OE2 D:GLU112 2.6 39.5 1.0
OE2 D:GLU116 2.6 28.1 1.0
O D:ALA96 2.7 28.4 1.0
CD D:GLU112 3.2 41.4 1.0
O D:HOH429 3.2 30.7 0.9
O D:HOH430 3.2 50.3 1.0
O D:HOH405 3.3 45.5 1.0
O D:HOH434 3.3 28.1 1.0
OE2 D:GLU166 3.3 71.2 1.0
CA D:GLY97 3.4 28.4 1.0
OE1 D:GLU112 3.6 45.4 1.0
C D:ALA96 3.7 27.9 1.0
CD D:GLU116 3.8 34.5 1.0
N D:GLY97 4.0 28.1 1.0
CG D:GLU112 4.0 46.6 1.0
O D:HOH409 4.2 25.3 1.0
CD D:GLU166 4.4 72.8 1.0
OE1 D:GLU116 4.6 31.9 1.0
CG D:GLU116 4.6 32.3 1.0
C D:GLY97 4.7 27.4 1.0
OE1 D:GLU166 4.8 73.9 1.0
N D:LEU98 4.9 30.2 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 02:18:47 2024

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