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Magnesium in PDB 5qj7: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z32327641

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z32327641

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 Z32327641:
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 Z32327641, PDB code: 5qj7 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 / 1.56
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.345, 59.789, 79.913, 79.38, 81.48, 75.77
R / Rfree (%) 23.7 / 27.4

Other elements in 5qj7:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z32327641 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 Z32327641 (pdb code 5qj7). 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 Z32327641, PDB code: 5qj7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qj7

Go back to Magnesium Binding Sites List in 5qj7
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 Z32327641


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 Z32327641 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:28.1
occ:1.00
 O A:ALA96 2.0 21.2 1.0
O A:HOH451 2.0 21.5 1.0
O A:HOH420 2.1 23.1 1.0
OE2 A:GLU116 2.1 24.1 1.0
O A:HOH459 2.2 21.7 1.0
O A:HOH422 2.2 24.5 1.0
CD A:GLU116 3.1 26.2 1.0
C A:ALA96 3.2 19.7 1.0
MG A:MG302 3.4 46.0 1.0
OE1 A:GLU116 3.4 25.4 1.0
OE2 A:GLU166 3.7 57.2 1.0
N A:GLY97 4.1 22.5 1.0
OE2 A:GLU112 4.1 27.4 1.0
O A:HOH452 4.2 21.7 0.7
CA A:ALA96 4.2 18.2 1.0
CA A:GLY97 4.2 25.2 1.0
N A:ALA96 4.2 18.3 1.0
NH2 A:ARG84 4.3 24.6 1.0
O A:HOH419 4.3 19.1 1.0
NE2 A:GLN82 4.3 34.0 1.0
CG A:GLU116 4.4 25.6 1.0
O A:HOH474 4.4 28.1 1.0
OE1 A:GLN82 4.4 26.8 1.0
CB A:ALA96 4.6 16.9 1.0
O A:HOH472 4.7 32.3 1.0
CD A:GLN82 4.8 31.8 1.0
CD A:GLU112 4.9 24.9 1.0
CD A:GLU166 4.9 64.5 1.0

Magnesium binding site 2 out of 8 in 5qj7

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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 Z32327641


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 Z32327641 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:46.0
occ:1.00
 O A:HOH407 2.0 36.7 1.0
OE2 A:GLU112 2.0 27.4 1.0
O A:HOH451 2.2 21.5 1.0
O A:HOH417 2.2 42.0 1.0
OE2 A:GLU166 2.5 57.2 1.0
OE2 A:GLU116 2.6 24.1 1.0
CD A:GLU112 3.0 24.9 1.0
CD A:GLU166 3.1 64.5 1.0
OE1 A:GLU112 3.2 26.6 1.0
OE1 A:GLU166 3.2 59.3 1.0
MG A:MG301 3.4 28.1 1.0
CD A:GLU116 3.5 26.2 1.0
CG A:GLU116 3.7 25.6 1.0
O A:HOH422 3.9 24.5 1.0
O A:ALA96 4.0 21.2 1.0
OE2 A:GLU115 4.0 33.5 1.0
CG A:GLU112 4.4 24.6 1.0
O A:HOH472 4.4 32.3 1.0
CG A:GLU166 4.5 60.3 1.0
OE1 A:GLU116 4.6 25.4 1.0
CA A:GLY97 4.8 25.2 1.0
CB A:GLU112 4.8 22.9 1.0
C A:ALA96 4.9 19.7 1.0

Magnesium binding site 3 out of 8 in 5qj7

Go back to Magnesium Binding Sites List in 5qj7
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 Z32327641


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 Z32327641 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:29.9
occ:1.00
 O B:ALA96 1.9 24.1 1.0
OE2 B:GLU116 2.1 33.2 1.0
O B:HOH408 2.2 30.2 1.0
O B:HOH439 2.2 28.9 1.0
O B:HOH416 2.2 28.8 1.0
O B:HOH438 2.3 26.8 1.0
CD B:GLU116 3.1 32.8 1.0
C B:ALA96 3.1 20.1 1.0
OE1 B:GLU116 3.4 30.1 1.0
OE2 B:GLU166 3.8 47.7 1.0
N B:GLY97 4.0 24.4 1.0
OE2 B:GLU112 4.0 33.5 1.0
CA B:GLY97 4.0 25.2 1.0
N B:ALA96 4.1 23.4 1.0
CA B:ALA96 4.1 23.9 1.0
O B:HOH420 4.2 26.5 1.0
NE2 B:GLN82 4.3 37.0 1.0
NH2 B:ARG84 4.4 28.1 1.0
CG B:GLU116 4.4 31.7 1.0
OE1 B:GLN82 4.5 33.0 1.0
MG B:MG304 4.5 80.8 1.0
O B:HOH467 4.5 38.1 1.0
CB B:ALA96 4.5 25.5 1.0
CD B:GLU166 4.8 66.6 1.0
CD B:GLN82 4.8 40.7 1.0
CD B:GLU112 4.9 31.0 1.0
O B:HOH452 5.0 42.3 1.0

Magnesium binding site 4 out of 8 in 5qj7

Go back to Magnesium Binding Sites List in 5qj7
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 Z32327641


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 Z32327641 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:80.8
occ:1.00
 OE2 B:GLU112 2.3 33.5 1.0
OE2 B:GLU166 2.5 47.7 1.0
O B:HOH433 2.8 71.8 1.0
O B:HOH452 2.8 42.3 1.0
OE2 B:GLU115 3.0 40.5 1.0
OE1 B:GLU166 3.2 71.3 1.0
CD B:GLU166 3.2 66.6 1.0
OE2 B:GLU116 3.3 33.2 1.0
CD B:GLU112 3.4 31.0 1.0
O B:HOH439 3.4 28.9 1.0
CG B:GLU116 3.5 31.7 1.0
OE1 B:GLU112 3.8 31.9 1.0
CD B:GLU116 3.8 32.8 1.0
CB B:GLU115 3.9 33.6 1.0
CD B:GLU115 4.1 43.7 1.0
MG B:MG303 4.5 29.9 1.0
CG B:GLU115 4.7 38.5 1.0
CG B:GLU112 4.7 28.4 1.0
CG B:GLU166 4.7 56.4 1.0
O B:GLU112 4.8 27.0 1.0
CA B:GLU112 4.8 26.8 1.0
N B:GLU116 4.9 33.9 1.0
O B:HOH408 4.9 30.2 1.0
CB B:GLU116 4.9 29.1 1.0
CB B:GLU112 4.9 28.7 1.0
O B:ALA96 5.0 24.1 1.0
OE1 B:GLU116 5.0 30.1 1.0

Magnesium binding site 5 out of 8 in 5qj7

Go back to Magnesium Binding Sites List in 5qj7
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 Z32327641


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 Z32327641 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:46.4
occ:1.00
 MG C:MG303 2.2 36.1 1.0
OE2 C:GLU166 2.7 51.2 1.0
OE2 C:GLU116 2.9 37.3 1.0
OE2 C:GLU112 2.9 37.1 1.0
O C:HOH462 2.9 53.1 1.0
O C:ALA96 3.0 25.8 1.0
O C:HOH445 3.2 50.5 1.0
O C:HOH406 3.2 37.9 1.0
O C:HOH451 3.2 28.3 1.0
O C:HOH405 3.2 31.3 1.0
OE1 C:GLU112 3.5 44.4 1.0
CD C:GLU112 3.5 38.3 1.0
CD C:GLU166 3.7 64.8 1.0
CA C:GLY97 3.7 30.6 1.0
C C:ALA96 4.0 30.9 1.0
CD C:GLU116 4.1 33.8 1.0
O C:HOH476 4.2 46.6 1.0
O C:HOH411 4.3 29.9 1.0
OE1 C:GLU166 4.3 68.5 1.0
N C:GLY97 4.4 27.4 1.0
CG C:GLU116 4.7 30.9 1.0
CG C:GLU166 4.8 55.7 1.0
CG C:GLU112 4.9 35.2 1.0
OE1 C:GLU116 4.9 38.2 1.0
O C:HOH480 5.0 53.2 1.0
C C:GLY97 5.0 33.5 1.0

Magnesium binding site 6 out of 8 in 5qj7

Go back to Magnesium Binding Sites List in 5qj7
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 Z32327641


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 Z32327641 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:36.1
occ:1.00
 OE2 C:GLU116 1.9 37.3 1.0
O C:HOH451 2.0 28.3 1.0
O C:HOH411 2.1 29.9 1.0
O C:ALA96 2.2 25.8 1.0
MG C:MG302 2.2 46.4 1.0
O C:HOH405 2.3 31.3 1.0
CD C:GLU116 3.1 33.8 1.0
OE2 C:GLU166 3.3 51.2 1.0
C C:ALA96 3.3 30.9 1.0
OE1 C:GLU116 3.5 38.2 1.0
OE2 C:GLU112 4.1 37.1 1.0
N C:GLY97 4.2 27.4 1.0
CA C:GLY97 4.2 30.6 1.0
N C:ALA96 4.2 25.0 1.0
CA C:ALA96 4.3 22.9 1.0
O C:HOH416 4.3 28.2 1.0
CG C:GLU116 4.3 30.9 1.0
NE2 C:GLN82 4.4 35.1 1.0
NH2 C:ARG84 4.5 33.9 1.0
O C:HOH406 4.5 37.9 1.0
OE1 C:GLN82 4.5 31.3 1.0
CD C:GLU166 4.6 64.8 1.0
O C:HOH468 4.7 42.1 1.0
CB C:ALA96 4.7 22.7 1.0
O C:HOH476 4.7 46.6 1.0
CD C:GLN82 4.9 38.2 1.0
CD C:GLU112 4.9 38.3 1.0

Magnesium binding site 7 out of 8 in 5qj7

Go back to Magnesium Binding Sites List in 5qj7
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 Z32327641


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 Z32327641 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:31.0
occ:1.00
 OE2 D:GLU116 1.9 31.9 1.0
O D:HOH428 2.0 25.9 1.0
O D:HOH415 2.0 26.7 1.0
MG D:MG302 2.3 37.0 1.0
O D:ALA96 2.4 33.9 1.0
O D:HOH433 2.4 37.1 1.0
CD D:GLU116 3.0 40.2 1.0
OE1 D:GLU116 3.4 38.5 1.0
C D:ALA96 3.5 33.3 1.0
OE2 D:GLU166 3.6 80.5 1.0
OE2 D:GLU112 3.8 48.4 1.0
NE2 D:GLN82 4.2 32.5 1.0
N D:ALA96 4.2 31.9 1.0
NH2 D:ARG84 4.2 35.2 1.0
CG D:GLU116 4.3 37.4 1.0
OE1 D:GLN82 4.4 45.8 1.0
CA D:ALA96 4.4 32.9 1.0
N D:GLY97 4.4 30.7 1.0
CA D:GLY97 4.4 34.1 1.0
O D:HOH414 4.6 46.3 1.0
CD D:GLU112 4.6 47.0 1.0
O D:HOH402 4.6 46.3 1.0
CD D:GLN82 4.7 41.8 1.0
CB D:ALA96 4.7 30.9 1.0
CG D:GLU112 4.8 52.1 1.0
CD D:GLU166 4.8 80.4 1.0

Magnesium binding site 8 out of 8 in 5qj7

Go back to Magnesium Binding Sites List in 5qj7
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 Z32327641


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 Z32327641 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:37.0
occ:1.00
 O D:HOH433 1.6 37.1 1.0
OE2 D:GLU112 2.3 48.4 1.0
MG D:MG301 2.3 31.0 1.0
O D:HOH414 2.4 46.3 1.0
O D:ALA96 2.8 33.9 1.0
OE2 D:GLU116 2.8 31.9 1.0
OE2 D:GLU166 3.0 80.5 1.0
CD D:GLU112 3.0 47.0 1.0
O D:HOH428 3.1 25.9 1.0
CA D:GLY97 3.4 34.1 1.0
O D:HOH402 3.5 46.3 1.0
OE1 D:GLU112 3.6 52.2 1.0
C D:ALA96 3.7 33.3 1.0
CG D:GLU112 3.9 52.1 1.0
CD D:GLU116 3.9 40.2 1.0
N D:GLY97 4.0 30.7 1.0
CD D:GLU166 4.2 80.4 1.0
O D:HOH415 4.3 26.7 1.0
C D:GLY97 4.7 38.9 1.0
CG D:GLU116 4.7 37.4 1.0
OE1 D:GLU116 4.8 38.5 1.0
OE1 D:GLU166 4.9 75.0 1.0
N D:LEU98 4.9 37.4 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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