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Magnesium in PDB 5qka: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2377835233

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2377835233

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 Z2377835233:
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 Z2377835233, PDB code: 5qka 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) 77.61 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.753, 60.122, 79.520, 79.24, 81.03, 75.23
R / Rfree (%) 24.6 / 28.6

Other elements in 5qka:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2377835233 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 Z2377835233 (pdb code 5qka). 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 Z2377835233, PDB code: 5qka:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qka

Go back to Magnesium Binding Sites List in 5qka
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 Z2377835233


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 Z2377835233 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:32.6
occ:1.00
 O A:ALA96 2.0 26.2 1.0
O A:HOH420 2.1 25.8 1.0
O A:HOH425 2.1 24.5 1.0
OE2 A:GLU116 2.1 31.5 1.0
O A:HOH448 2.1 25.5 1.0
O A:HOH405 2.4 31.1 1.0
CD A:GLU116 3.1 32.3 1.0
C A:ALA96 3.2 25.9 1.0
MG A:MG302 3.4 71.9 1.0
OE1 A:GLU116 3.4 28.9 1.0
OE2 A:GLU112 3.9 39.3 1.0
O A:HOH453 4.0 29.4 0.8
OE2 A:GLU166 4.0 57.5 1.0
CA A:GLY97 4.1 27.7 1.0
N A:GLY97 4.1 27.2 1.0
N A:ALA96 4.1 21.9 1.0
CA A:ALA96 4.1 25.4 1.0
O A:HOH427 4.2 27.1 1.0
NH2 A:ARG84 4.2 27.9 1.0
O A:HOH466 4.3 34.5 1.0
NE2 A:GLN82 4.4 31.9 1.0
CG A:GLU116 4.4 30.3 1.0
OE1 A:GLN82 4.5 29.3 1.0
CB A:ALA96 4.6 23.4 1.0
O A:HOH470 4.6 54.4 1.0
CD A:GLN82 4.8 34.5 1.0
O A:HOH461 4.8 35.7 1.0
CD A:GLU112 4.8 37.3 1.0

Magnesium binding site 2 out of 8 in 5qka

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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 Z2377835233


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 Z2377835233 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:71.9
occ:1.00
 O A:HOH425 2.0 24.5 1.0
OE2 A:GLU112 2.0 39.3 1.0
O A:HOH401 2.1 54.6 1.0
OE2 A:GLU166 2.4 57.5 1.0
OE2 A:GLU116 2.5 31.5 1.0
O A:HOH412 2.9 45.7 1.0
CD A:GLU112 3.0 37.3 1.0
CD A:GLU166 3.2 70.7 1.0
OE1 A:GLU112 3.2 34.9 1.0
MG A:MG301 3.4 32.6 1.0
CD A:GLU116 3.5 32.3 1.0
OE1 A:GLU166 3.5 71.0 1.0
CG A:GLU116 3.7 30.3 1.0
O A:ALA96 4.0 26.2 1.0
O A:HOH405 4.1 31.1 1.0
OE2 A:GLU115 4.2 39.7 1.0
CG A:GLU166 4.4 67.9 1.0
CG A:GLU112 4.4 33.7 1.0
O A:HOH461 4.5 35.7 1.0
OE1 A:GLU116 4.5 28.9 1.0
CA A:GLY97 4.8 27.7 1.0
CB A:GLU112 4.8 31.5 1.0
C A:ALA96 4.9 25.9 1.0
O A:HOH448 5.0 25.5 1.0
O A:HOH470 5.0 54.4 1.0

Magnesium binding site 3 out of 8 in 5qka

Go back to Magnesium Binding Sites List in 5qka
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 Z2377835233


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 Z2377835233 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:37.0
occ:1.00
 O B:HOH408 1.9 37.7 1.0
O B:HOH406 2.0 37.5 1.0
O B:HOH444 2.0 31.3 1.0
O B:HOH424 2.1 40.5 1.0
O B:ALA96 2.1 34.6 1.0
OE2 B:GLU116 2.2 37.8 1.0
CD B:GLU116 3.1 43.5 1.0
OE1 B:GLU116 3.3 36.3 1.0
C B:ALA96 3.3 33.2 1.0
MG B:MG303 3.9 68.8 1.0
NE2 B:GLN82 4.0 43.4 1.0
OE2 B:GLU166 4.0 53.8 1.0
O B:HOH429 4.0 33.4 1.0
NH2 B:ARG84 4.1 37.6 1.0
N B:ALA96 4.2 30.8 1.0
OE1 B:GLN82 4.2 46.6 1.0
N B:GLY97 4.2 33.3 1.0
CA B:ALA96 4.2 30.7 1.0
CA B:GLY97 4.3 36.7 1.0
OE2 B:GLU112 4.3 46.8 1.0
O B:HOH458 4.4 51.0 1.0
CG B:GLU116 4.5 37.8 1.0
CD B:GLN82 4.5 50.8 1.0
CB B:ALA96 4.6 33.2 1.0
CD B:GLU166 4.7 71.2 1.0
CZ B:ARG84 5.0 34.9 1.0

Magnesium binding site 4 out of 8 in 5qka

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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 Z2377835233


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 Z2377835233 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:68.8
occ:1.00
 OE2 B:GLU112 1.9 46.8 1.0
O B:HOH417 2.1 69.2 1.0
OE2 B:GLU116 2.4 37.8 1.0
O B:HOH424 2.8 40.5 1.0
OE2 B:GLU166 2.9 53.8 1.0
CD B:GLU112 2.9 47.0 1.0
CD B:GLU116 3.3 43.5 1.0
OE1 B:GLU112 3.3 48.5 1.0
CG B:GLU116 3.3 37.8 1.0
OE2 B:GLU115 3.5 62.6 1.0
OE1 B:GLU166 3.6 70.3 1.0
CD B:GLU166 3.7 71.2 1.0
O B:HOH420 3.8 71.5 1.0
MG B:MG302 3.9 37.0 1.0
O B:ALA96 4.0 34.6 1.0
CG B:GLU112 4.3 45.8 1.0
OE1 B:GLU116 4.5 36.3 1.0
O B:HOH406 4.5 37.5 1.0
CB B:GLU112 4.5 46.3 1.0
CA B:GLU112 4.6 40.7 1.0
CB B:GLU115 4.6 50.8 1.0
O B:GLU112 4.7 33.4 1.0
CD B:GLU115 4.7 58.9 1.0
CB B:GLU116 4.8 40.4 1.0
C B:ALA96 4.8 33.2 1.0
CA B:GLY97 4.9 36.7 1.0

Magnesium binding site 5 out of 8 in 5qka

Go back to Magnesium Binding Sites List in 5qka
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 Z2377835233


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 Z2377835233 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:85.9
occ:1.00
 O C:HOH443 1.9 70.8 1.0
O C:HOH462 2.7 54.1 1.0
O C:HOH422 2.7 55.1 1.0
OE1 C:GLU112 2.9 49.5 1.0
OE2 C:GLU166 3.0 66.7 1.0
O C:HOH408 3.2 39.2 1.0
OE2 C:GLU112 3.4 43.6 1.0
OE2 C:GLU115 3.5 42.4 1.0
CD C:GLU112 3.6 44.5 1.0
CD C:GLU166 3.7 73.7 1.0
OE1 C:GLU166 3.8 68.9 1.0
O C:HOH442 4.0 52.0 1.0
NH1 C:ARG111 4.4 44.4 1.0
CD C:GLU115 4.8 43.9 1.0
OE2 C:GLU116 4.9 37.2 1.0

Magnesium binding site 6 out of 8 in 5qka

Go back to Magnesium Binding Sites List in 5qka
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 Z2377835233


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 Z2377835233 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:36.2
occ:1.00
 O C:HOH444 1.9 32.3 1.0
OE2 C:GLU116 2.1 37.2 1.0
O C:HOH420 2.1 31.1 1.0
O C:HOH419 2.2 36.6 1.0
O C:ALA96 2.2 34.0 1.0
O C:HOH408 2.3 39.2 1.0
CD C:GLU116 3.1 36.3 1.0
C C:ALA96 3.4 30.2 1.0
OE1 C:GLU116 3.4 37.0 1.0
OE1 C:GLU166 3.9 68.9 1.0
CA C:GLY97 4.2 32.1 1.0
NH2 C:ARG84 4.2 35.8 1.0
OE2 C:GLU166 4.2 66.7 1.0
N C:GLY97 4.2 31.9 1.0
OE2 C:GLU112 4.2 43.6 1.0
CD C:GLU166 4.3 73.7 1.0
CA C:ALA96 4.3 28.3 1.0
N C:ALA96 4.3 27.4 1.0
NE2 C:GLN82 4.3 41.1 1.0
CG C:GLU116 4.5 33.4 1.0
OE1 C:GLN82 4.5 37.0 1.0
CB C:ALA96 4.8 28.1 1.0
CD C:GLN82 4.9 40.6 1.0
NH1 C:ARG84 4.9 36.5 1.0
CZ C:ARG84 4.9 37.1 1.0
O C:HOH443 5.0 70.8 1.0

Magnesium binding site 7 out of 8 in 5qka

Go back to Magnesium Binding Sites List in 5qka
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 Z2377835233


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 Z2377835233 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:45.5
occ:1.00
 OE2 D:GLU116 1.9 69.5 1.0
O D:HOH401 2.4 37.0 1.0
O D:HOH417 2.4 36.6 1.0
MG D:MG302 2.5 50.8 1.0
O D:HOH423 2.6 42.4 1.0
CD D:GLU116 3.2 73.0 1.0
OE1 D:GLU116 3.8 71.9 1.0
O D:ALA96 3.9 56.3 1.0
OE2 D:GLU166 4.0 0.7 1.0
OE2 D:GLU112 4.1 71.0 1.0
CG D:GLU116 4.3 70.6 1.0
C D:ALA96 4.4 60.3 1.0
CG1 D:VAL168 4.4 77.5 1.0
CD D:GLU166 4.6 0.1 1.0
N D:ALA96 4.7 47.8 1.0
NE2 D:GLN82 4.7 41.5 1.0
OE1 D:GLN82 4.8 45.7 1.0
N D:GLY97 4.9 60.8 1.0
CD D:GLU112 4.9 66.8 1.0
CA D:GLY97 4.9 63.6 1.0
CG D:GLU166 5.0 0.3 1.0

Magnesium binding site 8 out of 8 in 5qka

Go back to Magnesium Binding Sites List in 5qka
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 Z2377835233


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 Z2377835233 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:50.8
occ:1.00
 O D:HOH423 1.8 42.4 1.0
OE2 D:GLU112 2.1 71.0 1.0
MG D:MG301 2.5 45.5 1.0
O D:HOH417 2.8 36.6 1.0
O D:HOH406 2.8 51.4 1.0
CD D:GLU112 3.0 66.8 1.0
OE2 D:GLU166 3.2 0.7 1.0
O D:ALA96 3.3 56.3 1.0
OE2 D:GLU116 3.3 69.5 1.0
CA D:GLY97 3.3 63.6 1.0
OE1 D:GLU112 3.7 68.6 1.0
C D:ALA96 3.9 60.3 1.0
N D:GLY97 3.9 60.8 1.0
CG D:GLU112 3.9 67.6 1.0
O D:HOH401 4.2 37.0 1.0
CD D:GLU116 4.2 73.0 1.0
CD D:GLU166 4.3 0.1 1.0
OE1 D:GLU116 4.5 71.9 1.0
C D:GLY97 4.6 65.0 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 02:29:47 2024

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