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Magnesium in PDB 5qjr: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z220816104

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z220816104

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 Z220816104:
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 Z220816104, PDB code: 5qjr 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) 78.08 / 1.62
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.540, 60.030, 79.990, 79.25, 81.06, 75.33
R / Rfree (%) 24.2 / 27.7

Other elements in 5qjr:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z220816104 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 Z220816104 (pdb code 5qjr). 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 Z220816104, PDB code: 5qjr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjr

Go back to Magnesium Binding Sites List in 5qjr
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 Z220816104


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 Z220816104 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:26.1
occ:1.00
 OE2 A:GLU116 2.0 23.4 1.0
O A:HOH416 2.0 22.7 1.0
O A:HOH438 2.0 22.1 1.0
O A:ALA96 2.1 22.8 1.0
O A:HOH456 2.1 20.8 1.0
O A:HOH422 2.2 25.2 1.0
CD A:GLU116 3.0 26.5 1.0
C A:ALA96 3.3 22.8 1.0
OE1 A:GLU116 3.4 25.7 1.0
MG A:MG302 3.4 60.0 1.0
OE2 A:GLU166 3.9 61.6 1.0
O A:HOH436 4.1 21.8 0.7
CA A:GLY97 4.1 24.9 1.0
N A:GLY97 4.1 22.8 1.0
OE2 A:GLU112 4.1 36.4 1.0
N A:ALA96 4.2 18.7 1.0
CA A:ALA96 4.2 20.8 1.0
NH2 A:ARG84 4.3 26.1 1.0
O A:HOH421 4.3 23.2 1.0
NE2 A:GLN82 4.3 28.6 1.0
CG A:GLU116 4.4 26.1 1.0
O A:HOH468 4.4 26.8 1.0
OE1 A:GLN82 4.5 26.1 1.0
O A:HOH460 4.6 30.2 1.0
CB A:ALA96 4.7 19.2 1.0
CD A:GLN82 4.7 30.8 1.0
O A:HOH473 4.9 52.6 1.0
CD A:GLU112 4.9 31.2 1.0

Magnesium binding site 2 out of 8 in 5qjr

Go back to Magnesium Binding Sites List in 5qjr
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 Z220816104


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 Z220816104 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:60.0
occ:1.00
 O A:HOH406 1.9 45.9 1.0
OE2 A:GLU112 2.0 36.4 1.0
O A:HOH438 2.1 22.1 1.0
OE2 A:GLU166 2.5 61.6 1.0
OE2 A:GLU116 2.7 23.4 1.0
O A:HOH417 2.7 44.8 1.0
CD A:GLU112 2.9 31.2 1.0
OE1 A:GLU112 3.2 32.4 1.0
CD A:GLU166 3.2 67.4 1.0
OE1 A:GLU166 3.4 60.8 1.0
MG A:MG301 3.4 26.1 1.0
CD A:GLU116 3.6 26.5 1.0
CG A:GLU116 3.7 26.1 1.0
OE2 A:GLU115 4.0 34.1 1.0
O A:ALA96 4.1 22.8 1.0
O A:HOH422 4.1 25.2 1.0
CG A:GLU112 4.4 28.9 1.0
O A:HOH460 4.5 30.2 1.0
CG A:GLU166 4.5 63.0 1.0
OE1 A:GLU116 4.7 25.7 1.0
CA A:GLY97 4.7 24.9 1.0
CB A:GLU112 4.8 27.3 1.0
C A:ALA96 4.9 22.8 1.0

Magnesium binding site 3 out of 8 in 5qjr

Go back to Magnesium Binding Sites List in 5qjr
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 Z220816104


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 Z220816104 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:27.3
occ:1.00
 O B:HOH440 2.0 31.3 1.0
O B:ALA96 2.0 28.1 1.0
O B:HOH413 2.0 31.2 1.0
O B:HOH435 2.1 26.3 1.0
OE2 B:GLU116 2.1 37.1 1.0
O B:HOH436 2.1 28.4 1.0
CD B:GLU116 3.1 36.6 1.0
C B:ALA96 3.2 24.9 1.0
OE1 B:GLU116 3.4 31.7 1.0
MG B:MG304 4.0 73.2 1.0
OE2 B:GLU166 4.0 57.8 1.0
N B:GLY97 4.1 27.6 1.0
CA B:ALA96 4.2 25.8 1.0
OE2 B:GLU112 4.2 39.1 1.0
N B:ALA96 4.2 25.4 1.0
CA B:GLY97 4.2 27.9 1.0
O B:HOH437 4.2 28.5 1.0
NH2 B:ARG84 4.3 29.8 1.0
NE2 B:GLN82 4.4 36.6 1.0
OE1 B:GLN82 4.4 37.0 1.0
O B:HOH466 4.4 44.7 1.0
CG B:GLU116 4.5 33.0 1.0
CD B:GLU166 4.6 69.3 1.0
CB B:ALA96 4.6 28.5 1.0
CD B:GLN82 4.8 40.9 1.0
OE1 B:GLU166 4.9 70.2 1.0
O B:HOH410 5.0 48.8 1.0

Magnesium binding site 4 out of 8 in 5qjr

Go back to Magnesium Binding Sites List in 5qjr
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 Z220816104


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 Z220816104 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:73.2
occ:1.00
 OE2 B:GLU112 2.0 39.1 1.0
O B:HOH410 2.4 48.8 1.0
OE2 B:GLU166 2.7 57.8 1.0
OE2 B:GLU116 2.8 37.1 1.0
O B:HOH420 2.9 66.4 1.0
O B:HOH436 3.0 28.4 1.0
CD B:GLU112 3.1 38.2 1.0
OE1 B:GLU166 3.2 70.2 1.0
OE2 B:GLU115 3.3 51.8 1.0
CG B:GLU116 3.3 33.0 1.0
CD B:GLU166 3.4 69.3 1.0
CD B:GLU116 3.4 36.6 1.0
OE1 B:GLU112 3.5 37.0 1.0
MG B:MG303 4.0 27.3 1.0
CB B:GLU115 4.3 34.8 1.0
O B:ALA96 4.3 28.1 1.0
CG B:GLU112 4.4 35.7 1.0
CD B:GLU115 4.4 43.8 1.0
CB B:GLU112 4.6 35.8 1.0
OE1 B:GLU116 4.6 31.7 1.0
O B:GLU112 4.6 29.2 1.0
CA B:GLU112 4.6 33.2 1.0
O B:HOH440 4.6 31.3 1.0
CB B:GLU116 4.8 30.3 1.0
CG B:GLU166 4.9 64.6 1.0

Magnesium binding site 5 out of 8 in 5qjr

Go back to Magnesium Binding Sites List in 5qjr
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 Z220816104


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 Z220816104 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:59.0
occ:1.00
 MG C:MG303 2.3 35.2 1.0
OE2 C:GLU166 2.6 70.5 1.0
OE2 C:GLU116 2.8 32.0 1.0
O C:ALA96 2.9 28.0 1.0
O C:HOH442 3.0 45.8 1.0
OE2 C:GLU112 3.0 35.9 1.0
O C:HOH427 3.1 35.1 1.0
O C:HOH445 3.2 28.5 1.0
O C:HOH409 3.4 52.4 1.0
CA C:GLY97 3.6 33.8 1.0
O C:HOH404 3.7 52.2 1.0
CD C:GLU166 3.7 71.3 1.0
CD C:GLU112 3.8 37.4 1.0
OE1 C:GLU112 3.9 45.5 1.0
C C:ALA96 3.9 31.6 1.0
CD C:GLU116 4.0 31.7 1.0
N C:GLY97 4.2 33.3 1.0
O C:HOH425 4.2 25.1 1.0
OE1 C:GLU166 4.4 74.5 1.0
CG C:GLU166 4.7 65.3 1.0
C C:GLY97 4.8 35.4 1.0
OE1 C:GLU116 4.8 33.8 1.0
CG C:GLU116 4.9 30.1 1.0
CG C:GLU112 5.0 33.4 1.0
N C:LEU98 5.0 39.7 1.0

Magnesium binding site 6 out of 8 in 5qjr

Go back to Magnesium Binding Sites List in 5qjr
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 Z220816104


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 Z220816104 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:35.2
occ:1.00
 O C:HOH445 2.0 28.5 1.0
O C:HOH425 2.0 25.1 1.0
OE2 C:GLU116 2.1 32.0 1.0
O C:ALA96 2.1 28.0 1.0
O C:HOH427 2.2 35.1 1.0
MG C:MG302 2.3 59.0 1.0
CD C:GLU116 3.2 31.7 1.0
C C:ALA96 3.2 31.6 1.0
OE1 C:GLU116 3.5 33.8 1.0
OE2 C:GLU166 3.7 70.5 1.0
N C:GLY97 4.1 33.3 1.0
CA C:GLY97 4.1 33.8 1.0
NH2 C:ARG84 4.1 30.3 1.0
N C:ALA96 4.2 24.9 1.0
CA C:ALA96 4.2 26.2 1.0
OE2 C:GLU112 4.3 35.9 1.0
NE2 C:GLN82 4.3 33.4 1.0
OE1 C:GLN82 4.4 33.3 1.0
O C:HOH460 4.5 42.1 1.0
O C:HOH442 4.5 45.8 1.0
CG C:GLU116 4.5 30.1 1.0
CB C:ALA96 4.6 24.8 1.0
O C:HOH409 4.8 52.4 1.0
CD C:GLN82 4.8 36.8 1.0
CD C:GLU166 4.9 71.3 1.0

Magnesium binding site 7 out of 8 in 5qjr

Go back to Magnesium Binding Sites List in 5qjr
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 Z220816104


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 Z220816104 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:38.8
occ:1.00
 OE2 D:GLU116 1.9 43.9 1.0
O D:HOH404 2.1 32.0 1.0
O D:HOH418 2.1 27.2 1.0
MG D:MG302 2.3 40.6 1.0
O D:HOH423 2.4 36.9 1.0
O D:ALA96 2.8 39.4 1.0
CD D:GLU116 3.0 53.7 1.0
OE1 D:GLU116 3.5 50.3 1.0
OE2 D:GLU166 3.8 78.6 1.0
OE2 D:GLU112 3.8 51.7 1.0
C D:ALA96 3.8 46.0 1.0
NE2 D:GLN82 3.9 42.8 1.0
NH2 D:ARG84 4.1 44.7 1.0
OE1 D:GLN82 4.2 46.5 1.0
O D:HOH402 4.3 49.7 1.0
CG D:GLU116 4.3 50.8 1.0
N D:ALA96 4.5 44.8 1.0
CD D:GLN82 4.5 45.8 1.0
CA D:GLY97 4.5 45.2 1.0
N D:GLY97 4.6 45.2 1.0
CA D:ALA96 4.7 47.2 1.0
O D:HOH401 4.8 37.6 1.0
CD D:GLU112 4.8 54.1 1.0
CD D:GLU166 4.9 78.7 1.0
CG D:GLU112 5.0 53.7 1.0

Magnesium binding site 8 out of 8 in 5qjr

Go back to Magnesium Binding Sites List in 5qjr
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 Z220816104


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 Z220816104 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:40.6
occ:1.00
 O D:HOH423 1.7 36.9 1.0
OE2 D:GLU112 2.0 51.7 1.0
MG D:MG301 2.3 38.8 1.0
O D:HOH401 2.5 37.6 1.0
OE2 D:GLU116 2.9 43.9 1.0
O D:ALA96 2.9 39.4 1.0
OE2 D:GLU166 3.0 78.6 1.0
O D:HOH402 3.1 49.7 1.0
O D:HOH418 3.1 27.2 1.0
CD D:GLU112 3.1 54.1 1.0
CA D:GLY97 3.4 45.2 1.0
C D:ALA96 3.9 46.0 1.0
OE1 D:GLU112 4.0 56.8 1.0
CD D:GLU116 4.0 53.7 1.0
CG D:GLU112 4.0 53.7 1.0
N D:GLY97 4.1 45.2 1.0
O D:HOH404 4.2 32.0 1.0
CD D:GLU166 4.3 78.7 1.0
C D:GLY97 4.7 44.8 1.0
OE1 D:GLU116 4.7 50.3 1.0
CG D:GLU116 4.8 50.8 1.0
N D:LEU98 4.9 43.6 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 02:21:12 2024

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