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Magnesium in PDB 5qk3: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z239136710

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z239136710

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 Z239136710:
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 Z239136710, PDB code: 5qk3 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) 78.23 / 1.71
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.490, 60.020, 80.130, 79.15, 81.35, 75.43
R / Rfree (%) 22.8 / 26.6

Other elements in 5qk3:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z239136710 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 Z239136710 (pdb code 5qk3). 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 Z239136710, PDB code: 5qk3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qk3

Go back to Magnesium Binding Sites List in 5qk3
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 Z239136710


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 Z239136710 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:29.6
occ:1.00
 OE2 A:GLU116 2.0 23.5 1.0
O A:HOH450 2.1 23.3 1.0
O A:HOH457 2.1 19.8 1.0
O A:HOH412 2.1 25.6 1.0
O A:ALA96 2.2 22.6 1.0
O A:HOH425 2.2 25.9 1.0
CD A:GLU116 3.1 26.3 1.0
C A:ALA96 3.3 23.1 1.0
OE1 A:GLU116 3.4 26.7 1.0
MG A:MG302 3.4 67.6 1.0
OE2 A:GLU166 4.0 59.6 1.0
O A:HOH449 4.1 27.3 1.0
CA A:GLY97 4.1 23.4 1.0
OE2 A:GLU112 4.1 35.6 1.0
N A:GLY97 4.2 21.4 1.0
N A:ALA96 4.2 17.6 1.0
CA A:ALA96 4.2 20.3 1.0
NH2 A:ARG84 4.3 23.2 1.0
O A:HOH411 4.3 19.9 1.0
NE2 A:GLN82 4.4 27.0 1.0
CG A:GLU116 4.4 24.5 1.0
O A:HOH466 4.4 26.6 1.0
OE1 A:GLN82 4.5 24.8 1.0
O A:HOH463 4.5 32.5 1.0
CB A:ALA96 4.7 19.4 1.0
CD A:GLN82 4.8 32.5 1.0
CD A:GLU112 4.9 32.0 1.0

Magnesium binding site 2 out of 8 in 5qk3

Go back to Magnesium Binding Sites List in 5qk3
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 Z239136710


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 Z239136710 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:67.6
occ:1.00
 O A:HOH406 1.9 43.1 1.0
O A:HOH450 2.1 23.3 1.0
OE2 A:GLU112 2.1 35.6 1.0
O A:HOH404 2.4 45.2 1.0
OE2 A:GLU166 2.5 59.6 1.0
OE2 A:GLU116 2.8 23.5 1.0
CD A:GLU112 3.0 32.0 1.0
OE1 A:GLU112 3.1 33.4 1.0
CD A:GLU166 3.2 71.2 1.0
MG A:MG301 3.4 29.6 1.0
OE1 A:GLU166 3.5 61.6 1.0
CD A:GLU116 3.7 26.3 1.0
CG A:GLU116 3.8 24.5 1.0
O A:ALA96 4.1 22.6 1.0
OE2 A:GLU115 4.1 34.2 1.0
O A:HOH425 4.1 25.9 1.0
O A:HOH463 4.3 32.5 1.0
CG A:GLU112 4.4 29.6 1.0
CG A:GLU166 4.4 67.2 1.0
CA A:GLY97 4.7 23.4 1.0
OE1 A:GLU116 4.7 26.7 1.0
CB A:GLU112 4.9 29.0 1.0
C A:ALA96 5.0 23.1 1.0
O A:HOH457 5.0 19.8 1.0

Magnesium binding site 3 out of 8 in 5qk3

Go back to Magnesium Binding Sites List in 5qk3
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 Z239136710


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 Z239136710 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:30.6
occ:1.00
 OE2 B:GLU116 2.0 32.5 1.0
O B:ALA96 2.0 25.3 1.0
O B:HOH414 2.0 29.3 1.0
O B:HOH408 2.1 27.4 1.0
O B:HOH437 2.2 33.8 1.0
O B:HOH451 2.2 25.3 1.0
CD B:GLU116 3.0 32.7 1.0
C B:ALA96 3.2 22.5 1.0
OE1 B:GLU116 3.4 28.9 1.0
OE2 B:GLU166 3.7 46.5 1.0
MG B:MG304 4.0 80.1 1.0
N B:GLY97 4.1 25.3 1.0
OE2 B:GLU112 4.1 37.2 1.0
CA B:GLY97 4.1 25.0 1.0
CA B:ALA96 4.2 24.2 1.0
N B:ALA96 4.2 23.0 1.0
O B:HOH430 4.2 28.5 1.0
NE2 B:GLN82 4.2 38.2 1.0
NH2 B:ARG84 4.3 26.9 1.0
OE1 B:GLN82 4.4 31.3 1.0
CG B:GLU116 4.4 33.6 1.0
O B:HOH472 4.4 41.4 1.0
O B:HOH464 4.5 37.1 0.8
CD B:GLU166 4.6 67.5 1.0
CB B:ALA96 4.6 26.9 1.0
CD B:GLN82 4.7 40.5 1.0
CD B:GLU112 5.0 36.9 1.0

Magnesium binding site 4 out of 8 in 5qk3

Go back to Magnesium Binding Sites List in 5qk3
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 Z239136710


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 Z239136710 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:80.1
occ:1.00
 OE2 B:GLU112 2.1 37.2 1.0
O B:HOH424 2.6 63.2 1.0
OE2 B:GLU166 2.6 46.5 1.0
O B:HOH410 2.7 44.6 1.0
OE2 B:GLU116 2.9 32.5 1.0
O B:HOH437 3.1 33.8 1.0
CD B:GLU112 3.1 36.9 1.0
OE1 B:GLU166 3.2 71.8 1.0
CD B:GLU166 3.3 67.5 1.0
CG B:GLU116 3.4 33.6 1.0
OE1 B:GLU112 3.5 34.4 1.0
OE2 B:GLU115 3.5 48.3 1.0
CD B:GLU116 3.6 32.7 1.0
MG B:MG303 4.0 30.6 1.0
CB B:GLU115 4.3 35.7 1.0
O B:ALA96 4.4 25.3 1.0
CG B:GLU112 4.5 34.3 1.0
CD B:GLU115 4.7 45.2 1.0
O B:HOH408 4.8 27.4 1.0
OE1 B:GLU116 4.8 28.9 1.0
CA B:GLU112 4.8 31.5 1.0
CG B:GLU166 4.8 61.0 1.0
CB B:GLU112 4.8 36.3 1.0
O B:GLU112 4.8 30.2 1.0
CB B:GLU116 4.9 33.2 1.0

Magnesium binding site 5 out of 8 in 5qk3

Go back to Magnesium Binding Sites List in 5qk3
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 Z239136710


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 Z239136710 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:67.8
occ:1.00
 O C:HOH440 1.7 41.2 1.0
OE2 C:GLU112 2.2 34.1 1.0
O C:HOH405 2.4 54.5 1.0
OE2 C:GLU166 2.6 67.2 1.0
O C:HOH451 2.6 54.1 1.0
OE2 C:GLU116 2.6 33.1 1.0
MG C:MG303 2.9 33.3 1.0
CD C:GLU112 3.1 39.4 1.0
OE1 C:GLU112 3.2 45.0 1.0
O C:ALA96 3.4 25.3 1.0
CD C:GLU166 3.5 74.1 1.0
O C:HOH403 3.6 54.5 1.0
CD C:GLU116 3.7 33.7 1.0
O C:HOH413 3.8 33.8 1.0
OE1 C:GLU166 3.8 82.1 1.0
CA C:GLY97 4.1 30.7 1.0
CG C:GLU116 4.2 31.3 1.0
O C:HOH445 4.3 26.9 1.0
C C:ALA96 4.3 27.8 1.0
CG C:GLU112 4.5 35.9 1.0
N C:GLY97 4.6 29.4 1.0
OE2 C:GLU115 4.7 39.4 1.0
OE1 C:GLU116 4.7 35.3 1.0
CG C:GLU166 4.7 65.6 1.0
O C:HOH432 4.8 29.0 1.0

Magnesium binding site 6 out of 8 in 5qk3

Go back to Magnesium Binding Sites List in 5qk3
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 Z239136710


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 Z239136710 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:33.3
occ:1.00
 OE2 C:GLU116 2.0 33.1 1.0
O C:HOH432 2.0 29.0 1.0
O C:HOH445 2.1 26.9 1.0
O C:HOH440 2.1 41.2 1.0
O C:ALA96 2.1 25.3 1.0
O C:HOH413 2.1 33.8 1.0
MG C:MG302 2.9 67.8 1.0
CD C:GLU116 3.1 33.7 1.0
C C:ALA96 3.3 27.8 1.0
OE1 C:GLU116 3.4 35.3 1.0
OE2 C:GLU166 3.5 67.2 1.0
OE2 C:GLU112 4.1 34.1 1.0
N C:ALA96 4.2 24.2 1.0
CA C:GLY97 4.2 30.7 1.0
N C:GLY97 4.2 29.4 1.0
CA C:ALA96 4.2 23.5 1.0
NE2 C:GLN82 4.4 29.3 1.0
NH2 C:ARG84 4.4 31.2 1.0
CG C:GLU116 4.4 31.3 1.0
OE1 C:GLN82 4.4 31.0 1.0
O C:HOH405 4.6 54.5 1.0
CB C:ALA96 4.7 23.6 1.0
CD C:GLU166 4.7 74.1 1.0
CD C:GLN82 4.9 36.2 1.0

Magnesium binding site 7 out of 8 in 5qk3

Go back to Magnesium Binding Sites List in 5qk3
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 Z239136710


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 Z239136710 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:40.4
occ:1.00
 O D:HOH416 1.9 32.9 1.0
OE2 D:GLU116 1.9 43.3 1.0
O D:HOH401 2.2 29.7 1.0
MG D:MG302 2.3 41.9 1.0
O D:HOH422 2.4 39.2 1.0
O D:ALA96 2.8 37.7 1.0
CD D:GLU116 3.0 51.1 1.0
OE1 D:GLU116 3.5 43.1 1.0
OE2 D:GLU112 3.8 53.1 1.0
NE2 D:GLN82 3.8 39.3 1.0
C D:ALA96 3.8 42.8 1.0
OE2 D:GLU166 3.9 84.6 1.0
O D:HOH402 4.2 53.5 1.0
OE1 D:GLN82 4.3 41.3 1.0
CG D:GLU116 4.3 44.8 1.0
NH2 D:ARG84 4.3 38.8 1.0
N D:ALA96 4.5 44.0 1.0
CD D:GLN82 4.5 46.4 1.0
CA D:GLY97 4.6 42.1 1.0
N D:GLY97 4.7 42.4 1.0
CA D:ALA96 4.7 43.1 1.0
O D:HOH403 4.8 43.4 1.0
CD D:GLU112 4.8 53.3 1.0
CD D:GLU166 5.0 88.1 1.0

Magnesium binding site 8 out of 8 in 5qk3

Go back to Magnesium Binding Sites List in 5qk3
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 Z239136710


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 Z239136710 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:41.9
occ:1.00
 O D:HOH422 1.7 39.2 1.0
OE2 D:GLU112 2.1 53.1 1.0
MG D:MG301 2.3 40.4 1.0
O D:HOH403 2.5 43.4 1.0
OE2 D:GLU116 2.8 43.3 1.0
O D:ALA96 2.8 37.7 1.0
O D:HOH416 2.9 32.9 1.0
CD D:GLU112 3.1 53.3 1.0
OE2 D:GLU166 3.2 84.6 1.0
O D:HOH402 3.2 53.5 1.0
CA D:GLY97 3.4 42.1 1.0
OE1 D:GLU112 3.7 55.6 1.0
C D:ALA96 3.8 42.8 1.0
CD D:GLU116 3.9 51.1 1.0
CG D:GLU112 4.0 55.5 1.0
N D:GLY97 4.1 42.4 1.0
O D:HOH401 4.2 29.7 1.0
CD D:GLU166 4.4 88.1 1.0
C D:GLY97 4.7 41.9 1.0
OE1 D:GLU116 4.7 43.1 1.0
CG D:GLU116 4.7 44.8 1.0
N D:LEU98 4.9 41.2 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 02:27:04 2024

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