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Magnesium in PDB 5qk1: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2027049478

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2027049478

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 Z2027049478:
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 Z2027049478, PDB code: 5qk1 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) 78.50 / 1.49
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.295, 59.894, 80.357, 79.21, 81.58, 75.63
R / Rfree (%) 21.8 / 25.2

Other elements in 5qk1:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2027049478 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 Z2027049478 (pdb code 5qk1). 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 Z2027049478, PDB code: 5qk1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qk1

Go back to Magnesium Binding Sites List in 5qk1
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 Z2027049478


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 Z2027049478 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:27.3
occ:1.00
 OE2 A:GLU116 2.0 27.4 1.0
O A:HOH413 2.0 23.6 1.0
O A:HOH447 2.1 23.8 1.0
O A:HOH435 2.1 27.3 1.0
O A:ALA96 2.1 23.9 1.0
O A:HOH467 2.2 23.1 1.0
CD A:GLU116 3.0 28.4 1.0
C A:ALA96 3.3 24.4 1.0
OE1 A:GLU116 3.4 27.0 1.0
MG A:MG302 3.5 66.0 1.0
OE2 A:GLU166 3.9 60.8 1.0
O A:HOH476 4.1 51.2 1.0
OE2 A:GLU112 4.1 36.4 1.0
CA A:GLY97 4.2 22.9 1.0
N A:GLY97 4.2 24.4 1.0
O A:HOH450 4.2 23.9 0.7
N A:ALA96 4.2 19.6 1.0
CA A:ALA96 4.3 21.5 1.0
O A:HOH428 4.3 21.5 1.0
NH2 A:ARG84 4.3 25.8 1.0
NE2 A:GLN82 4.3 21.9 0.7
CG A:GLU116 4.4 28.6 1.0
O A:HOH480 4.5 30.2 1.0
OE1 A:GLN82 4.5 24.0 0.7
O A:HOH471 4.6 34.2 1.0
CB A:ALA96 4.7 19.8 1.0
CD A:GLU112 4.8 31.5 1.0
CD A:GLN82 4.9 23.1 0.7
CD A:GLU166 5.0 75.9 1.0

Magnesium binding site 2 out of 8 in 5qk1

Go back to Magnesium Binding Sites List in 5qk1
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 Z2027049478


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 Z2027049478 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:66.0
occ:1.00
 O A:HOH447 1.9 23.8 1.0
O A:HOH409 2.1 41.0 1.0
OE2 A:GLU112 2.3 36.4 1.0
O A:HOH423 2.5 48.9 1.0
OE2 A:GLU166 2.6 60.8 1.0
CD A:GLU112 3.0 31.5 1.0
OE1 A:GLU112 3.0 35.2 1.0
OE2 A:GLU116 3.0 27.4 1.0
CD A:GLU166 3.1 75.9 1.0
OE1 A:GLU166 3.2 64.4 1.0
MG A:MG301 3.5 27.3 1.0
O A:HOH476 3.6 51.2 1.0
CD A:GLU116 3.9 28.4 1.0
O A:HOH435 4.0 27.3 1.0
O A:HOH471 4.1 34.2 1.0
O A:ALA96 4.1 23.9 1.0
OE2 A:GLU115 4.2 38.3 1.0
CG A:GLU116 4.2 28.6 1.0
CG A:GLU166 4.3 67.5 1.0
CG A:GLU112 4.5 28.2 1.0
CA A:GLY97 4.7 22.9 1.0
O A:HOH401 4.7 49.6 1.0
O A:HOH467 5.0 23.1 1.0

Magnesium binding site 3 out of 8 in 5qk1

Go back to Magnesium Binding Sites List in 5qk1
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 Z2027049478


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 Z2027049478 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:30.8
occ:1.00
 O B:ALA96 2.0 26.6 1.0
OE2 B:GLU116 2.1 33.5 1.0
O B:HOH409 2.1 30.7 1.0
O B:HOH434 2.1 28.8 1.0
O B:HOH412 2.1 29.6 1.0
O B:HOH446 2.1 28.9 1.0
CD B:GLU116 3.1 35.1 1.0
C B:ALA96 3.2 22.9 1.0
OE1 B:GLU116 3.4 30.3 1.0
OE2 B:GLU166 3.9 56.6 1.0
OE2 B:GLU112 4.0 38.1 1.0
N B:GLY97 4.1 27.2 1.0
CA B:GLY97 4.1 28.5 1.0
CA B:ALA96 4.2 24.4 1.0
N B:ALA96 4.2 24.5 1.0
O B:HOH411 4.3 26.8 1.0
NE2 B:GLN82 4.3 34.5 1.0
NH2 B:ARG84 4.4 28.2 1.0
O B:HOH426 4.4 36.2 0.9
CG B:GLU116 4.4 34.6 1.0
OE1 B:GLN82 4.5 34.0 1.0
O B:HOH461 4.5 37.0 0.9
O B:HOH471 4.5 38.9 1.0
CD B:GLU166 4.6 70.1 1.0
CB B:ALA96 4.6 27.9 1.0
O B:HOH403 4.6 49.1 1.0
CD B:GLN82 4.8 40.0 1.0
CD B:GLU112 4.9 41.2 1.0

Magnesium binding site 4 out of 8 in 5qk1

Go back to Magnesium Binding Sites List in 5qk1
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 Z2027049478


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 Z2027049478 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:62.7
occ:1.00
 O B:HOH475 2.3 57.7 1.0
O B:HOH403 2.6 49.1 1.0
OE1 B:GLU166 2.8 68.4 1.0
OE1 B:GLU112 2.9 38.4 1.0
O B:HOH446 3.0 28.9 1.0
OE2 B:GLU112 3.2 38.1 1.0
CD B:GLU112 3.5 41.2 1.0
CD B:GLU166 3.6 70.1 1.0
O B:HOH461 3.7 37.0 0.9
OE2 B:GLU166 3.8 56.6 1.0
OE2 B:GLU115 3.8 42.9 1.0
NH1 B:ARG111 4.4 36.4 1.0
OE2 B:GLU116 4.7 33.5 1.0
CG B:GLU112 5.0 36.6 1.0
CD B:GLU115 5.0 46.5 1.0

Magnesium binding site 5 out of 8 in 5qk1

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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 Z2027049478


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 Z2027049478 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:48.7
occ:1.00
 MG C:MG303 2.1 33.1 1.0
OE2 C:GLU116 2.9 34.7 1.0
O C:ALA96 2.9 28.8 1.0
O C:HOH454 3.0 28.9 1.0
O C:HOH429 3.0 33.9 1.0
OE1 C:GLU166 3.1 59.6 1.0
OE2 C:GLU112 3.1 35.8 1.0
O C:HOH445 3.2 42.3 1.0
O C:HOH426 3.5 62.0 1.0
OE1 C:GLU112 3.6 45.5 1.0
OE2 C:GLU166 3.6 68.2 1.0
CA C:GLY97 3.6 32.1 1.0
CD C:GLU112 3.7 35.9 1.0
CD C:GLU166 3.7 69.9 1.0
O C:HOH404 3.9 56.7 1.0
C C:ALA96 4.0 29.7 1.0
CD C:GLU116 4.1 33.2 1.0
O C:HOH437 4.1 41.9 0.9
O C:HOH436 4.2 28.8 1.0
N C:GLY97 4.3 30.5 1.0
O C:HOH422 4.3 59.8 1.0
OE1 C:GLU116 4.9 33.9 1.0
C C:GLY97 4.9 32.5 1.0
CG C:GLU116 4.9 29.1 1.0

Magnesium binding site 6 out of 8 in 5qk1

Go back to Magnesium Binding Sites List in 5qk1
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 Z2027049478


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 Z2027049478 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:33.1
occ:1.00
 OE2 C:GLU116 2.0 34.7 1.0
O C:HOH436 2.1 28.8 1.0
O C:HOH454 2.1 28.9 1.0
MG C:MG302 2.1 48.7 1.0
O C:HOH429 2.1 33.9 1.0
O C:ALA96 2.2 28.8 1.0
CD C:GLU116 3.1 33.2 1.0
C C:ALA96 3.3 29.7 1.0
OE1 C:GLU116 3.4 33.9 1.0
OE2 C:GLU112 4.0 35.8 1.0
O C:HOH437 4.1 41.9 0.9
N C:ALA96 4.1 24.5 1.0
O C:HOH410 4.2 27.3 0.9
CA C:GLY97 4.2 32.1 1.0
CA C:ALA96 4.2 24.8 1.0
N C:GLY97 4.3 30.5 1.0
OE2 C:GLU166 4.3 68.2 1.0
NE2 C:GLN82 4.4 34.5 1.0
CG C:GLU116 4.4 29.1 1.0
NH2 C:ARG84 4.4 31.9 1.0
OE1 C:GLN82 4.5 34.9 1.0
OE1 C:GLU166 4.6 59.6 1.0
O C:HOH468 4.6 38.0 0.9
CB C:ALA96 4.7 24.6 1.0
O C:HOH445 4.7 42.3 1.0
CD C:GLU166 4.8 69.9 1.0
CD C:GLU112 4.8 35.9 1.0
CD C:GLN82 4.9 40.0 1.0
O C:HOH404 5.0 56.7 1.0

Magnesium binding site 7 out of 8 in 5qk1

Go back to Magnesium Binding Sites List in 5qk1
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 Z2027049478


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 Z2027049478 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:33.0
occ:1.00
 O D:HOH417 2.0 30.8 1.0
OE2 D:GLU116 2.0 33.1 1.0
O D:HOH404 2.1 30.1 1.0
O D:ALA96 2.2 29.9 1.0
MG D:MG302 2.2 43.7 1.0
O D:HOH429 2.5 44.9 1.0
CD D:GLU116 3.0 43.7 1.0
C D:ALA96 3.3 31.9 1.0
OE1 D:GLU116 3.4 39.9 1.0
OE2 D:GLU112 3.9 49.8 1.0
OE2 D:GLU166 4.0 88.9 1.0
N D:ALA96 4.1 31.7 1.0
CA D:GLY97 4.2 34.3 1.0
N D:GLY97 4.2 32.5 1.0
CA D:ALA96 4.2 31.0 1.0
NH2 D:ARG84 4.3 32.2 1.0
NE2 D:GLN82 4.4 35.0 1.0
CG D:GLU116 4.4 39.5 1.0
OE1 D:GLN82 4.4 36.4 1.0
O D:HOH406 4.5 28.9 0.9
CB D:ALA96 4.6 32.6 1.0
CD D:GLU112 4.6 51.4 1.0
O D:HOH412 4.7 58.0 1.0
CG D:GLU112 4.8 56.8 1.0
O D:HOH402 4.8 53.6 1.0
CD D:GLN82 4.9 38.9 1.0

Magnesium binding site 8 out of 8 in 5qk1

Go back to Magnesium Binding Sites List in 5qk1
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 Z2027049478


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 Z2027049478 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:43.7
occ:1.00
 O D:HOH429 1.6 44.9 1.0
MG D:MG301 2.2 33.0 1.0
OE2 D:GLU112 2.5 49.8 1.0
O D:HOH412 2.6 58.0 1.0
OE2 D:GLU116 2.8 33.1 1.0
OE2 D:GLU166 2.9 88.9 1.0
O D:ALA96 3.0 29.9 1.0
O D:HOH417 3.1 30.8 1.0
CD D:GLU112 3.4 51.4 1.0
O D:HOH402 3.5 53.6 1.0
CA D:GLY97 3.5 34.3 1.0
C D:ALA96 3.9 31.9 1.0
CD D:GLU116 3.9 43.7 1.0
OE1 D:GLU112 4.0 60.9 1.0
CD D:GLU166 4.1 92.7 1.0
N D:GLY97 4.2 32.5 1.0
O D:HOH404 4.3 30.1 1.0
CG D:GLU112 4.3 56.8 1.0
OE1 D:GLU116 4.8 39.9 1.0
CG D:GLU116 4.8 39.5 1.0
OE1 D:GLU166 4.8 0.5 1.0
C D:GLY97 4.8 35.5 1.0
N D:LEU98 5.0 37.7 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 02:27:01 2024

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