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Magnesium in PDB 5qtp: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227:
2.7.7.96; 3.6.1.13; 3.6.1.58;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227, PDB code: 5qtp was solved by Y.Dubianok, T.Krojer, H.Kovacs, F.Moriaud, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.67 / 1.73
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.246, 59.826, 80.052, 79.42, 81.55, 75.70
R / Rfree (%) 22.9 / 26.1

Other elements in 5qtp:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227 also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227 (pdb code 5qtp). 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 -- Crystal Structure of NUDT5 in Complex with Ae-0227, PDB code: 5qtp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qtp

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Magnesium binding site 1 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 -- Crystal Structure of NUDT5 in Complex with Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:29.8
occ:1.00
 OE2 A:GLU116 2.0 24.3 1.0
O A:HOH453 2.1 28.1 1.0
O A:HOH454 2.1 21.5 1.0
O A:ALA96 2.1 23.5 1.0
O A:HOH420 2.1 23.1 1.0
O A:HOH418 2.2 23.4 1.0
CD A:GLU116 3.1 26.4 1.0
MG A:MG302 3.3 65.3 1.0
C A:ALA96 3.3 23.0 1.0
OE1 A:GLU116 3.5 24.6 1.0
OE2 A:GLU166 3.8 50.5 1.0
OE2 A:GLU112 4.1 26.2 1.0
N A:GLY97 4.1 24.8 1.0
CA A:GLY97 4.2 22.6 1.0
NE2 A:GLN82 4.2 22.8 1.0
N A:ALA96 4.2 19.2 1.0
NH2 A:ARG84 4.3 24.8 1.0
CA A:ALA96 4.3 20.8 1.0
O A:HOH422 4.3 21.7 1.0
O A:HOH447 4.3 19.6 0.7
CG A:GLU116 4.4 26.1 1.0
OE1 A:GLN82 4.4 24.1 1.0
O A:HOH470 4.5 28.6 1.0
O A:HOH465 4.5 36.8 1.0
CD A:GLN82 4.7 27.5 1.0
CB A:ALA96 4.7 17.2 1.0
CD A:GLU112 4.8 27.8 1.0
CD A:GLU166 5.0 67.9 1.0

Magnesium binding site 2 out of 8 in 5qtp

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Magnesium binding site 2 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 -- Crystal Structure of NUDT5 in Complex with Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:65.3
occ:1.00
 O A:HOH414 2.0 37.2 1.0
O A:HOH453 2.1 28.1 1.0
OE2 A:GLU112 2.1 26.2 1.0
OE2 A:GLU166 2.4 50.5 1.0
O A:HOH411 2.5 46.7 1.0
OE2 A:GLU116 2.6 24.3 1.0
CD A:GLU112 3.1 27.8 1.0
CD A:GLU166 3.1 67.9 1.0
MG A:MG301 3.3 29.8 1.0
OE1 A:GLU166 3.3 61.4 1.0
OE1 A:GLU112 3.3 31.1 1.0
CD A:GLU116 3.5 26.4 1.0
CG A:GLU116 3.7 26.1 1.0
O A:ALA96 3.9 23.5 1.0
O A:HOH420 4.0 23.1 1.0
OE2 A:GLU115 4.3 33.2 1.0
CG A:GLU112 4.4 25.9 1.0
CG A:GLU166 4.4 62.6 1.0
O A:HOH465 4.5 36.8 1.0
OE1 A:GLU116 4.6 24.6 1.0
CA A:GLY97 4.8 22.6 1.0
O A:HOH454 4.9 21.5 1.0
C A:ALA96 4.9 23.0 1.0
CB A:GLU112 4.9 23.9 1.0

Magnesium binding site 3 out of 8 in 5qtp

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Magnesium binding site 3 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 -- Crystal Structure of NUDT5 in Complex with Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:31.6
occ:1.00
 O B:HOH407 2.0 28.9 1.0
O B:ALA96 2.0 25.3 1.0
O B:HOH440 2.2 26.5 1.0
O B:HOH447 2.2 28.8 1.0
OE2 B:GLU116 2.2 35.3 1.0
O B:HOH409 2.3 26.7 1.0
CD B:GLU116 3.1 32.8 1.0
C B:ALA96 3.2 22.9 1.0
OE1 B:GLU116 3.4 31.0 1.0
OE2 B:GLU166 4.0 44.4 1.0
O B:HOH436 4.1 35.5 1.0
N B:GLY97 4.1 24.7 1.0
CA B:GLY97 4.1 23.9 1.0
OE2 B:GLU112 4.2 39.6 1.0
CA B:ALA96 4.2 24.0 1.0
N B:ALA96 4.2 24.9 1.0
NH2 B:ARG84 4.3 24.4 1.0
NE2 B:GLN82 4.3 35.6 1.0
MG B:MG304 4.4 59.5 1.0
OE1 B:GLN82 4.4 37.5 1.0
CG B:GLU116 4.5 32.4 1.0
CB B:ALA96 4.5 24.8 1.0
O B:HOH456 4.6 29.7 0.8
O B:HOH460 4.7 42.7 1.0
CD B:GLN82 4.8 40.8 1.0
CD B:GLU166 4.8 61.8 1.0
OE1 B:GLU166 4.8 61.9 1.0

Magnesium binding site 4 out of 8 in 5qtp

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Magnesium binding site 4 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 -- Crystal Structure of NUDT5 in Complex with Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:59.5
occ:1.00
 O B:HOH410 2.2 62.9 1.0
OE2 B:GLU112 2.4 39.6 1.0
O B:HOH402 2.7 38.4 1.0
OE2 B:GLU166 2.7 44.4 1.0
OE1 B:GLU166 2.9 61.9 1.0
CD B:GLU166 3.0 61.8 1.0
OE2 B:GLU116 3.1 35.3 1.0
OE2 B:GLU115 3.2 50.9 1.0
CG B:GLU116 3.4 32.4 1.0
CD B:GLU112 3.4 38.5 1.0
CD B:GLU116 3.6 32.8 1.0
O B:HOH440 3.7 26.5 1.0
OE1 B:GLU112 3.8 40.9 1.0
CB B:GLU115 3.9 38.7 1.0
CD B:GLU115 4.3 45.9 1.0
CG B:GLU166 4.4 59.6 1.0
MG B:MG303 4.4 31.6 1.0
O B:GLU112 4.7 32.2 1.0
CG B:GLU112 4.7 34.2 1.0
CG B:GLU115 4.7 45.3 1.0
CA B:GLU112 4.8 32.4 1.0
CB B:GLU116 4.8 30.9 1.0
OE1 B:GLU116 4.8 31.0 1.0
O B:ALA96 4.8 25.3 1.0
N B:GLU116 4.9 33.0 1.0
CB B:GLU112 5.0 36.7 1.0
C B:GLU115 5.0 33.9 1.0

Magnesium binding site 5 out of 8 in 5qtp

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Magnesium binding site 5 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 -- Crystal Structure of NUDT5 in Complex with Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:55.5
occ:1.00
 O C:HOH461 1.5 42.9 1.0
O C:HOH401 2.1 38.9 1.0
OE2 C:GLU112 2.5 30.7 1.0
MG C:MG303 2.6 31.5 1.0
OE2 C:GLU116 2.6 32.6 1.0
OE2 C:GLU166 2.6 58.3 0.5
O C:HOH440 2.6 45.5 1.0
O C:HOH459 2.9 45.9 1.0
OE1 C:GLU112 3.1 45.3 1.0
CD C:GLU112 3.1 37.2 1.0
O C:ALA96 3.2 27.3 1.0
O C:HOH421 3.6 30.3 1.0
CD C:GLU116 3.8 34.2 1.0
CA C:GLY97 3.8 27.8 1.0
O C:HOH452 3.8 25.5 1.0
CD C:GLU166 3.8 60.4 0.5
C C:ALA96 4.2 26.6 1.0
CG C:GLU116 4.5 28.2 1.0
N C:GLY97 4.5 28.6 1.0
CG C:GLU112 4.5 34.0 1.0
OE1 C:GLU166 4.5 60.3 0.5
O C:HOH420 4.6 25.6 1.0
OE1 C:GLU116 4.7 34.0 1.0
CG C:GLU166 4.9 57.1 0.5

Magnesium binding site 6 out of 8 in 5qtp

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Magnesium binding site 6 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 -- Crystal Structure of NUDT5 in Complex with Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:31.5
occ:1.00
 O C:HOH452 2.0 25.5 1.0
OE2 C:GLU116 2.1 32.6 1.0
O C:HOH461 2.1 42.9 1.0
O C:HOH421 2.1 30.3 1.0
O C:HOH420 2.2 25.6 1.0
O C:ALA96 2.3 27.3 1.0
MG C:MG302 2.6 55.5 1.0
CD C:GLU116 3.1 34.2 1.0
C C:ALA96 3.4 26.6 1.0
OE1 C:GLU116 3.5 34.0 1.0
OE2 C:GLU166 3.8 58.3 0.5
O C:HOH401 3.8 38.9 1.0
OE2 C:GLU112 4.1 30.7 1.0
CA C:GLY97 4.2 27.8 1.0
N C:GLY97 4.3 28.6 1.0
O C:HOH426 4.3 28.1 0.9
NH2 C:ARG84 4.3 31.5 1.0
NE2 C:GLN82 4.3 30.9 1.0
N C:ALA96 4.4 25.1 1.0
CA C:ALA96 4.4 24.1 1.0
O1 C:EDO304 4.4 34.3 0.9
OE1 C:GLN82 4.4 31.9 1.0
CG C:GLU116 4.5 28.2 1.0
O C:HOH435 4.6 33.0 0.9
CB C:ALA96 4.8 23.8 1.0
CD C:GLN82 4.9 33.9 1.0
CD C:GLU112 4.9 37.2 1.0
CD C:GLU166 4.9 60.4 0.5

Magnesium binding site 7 out of 8 in 5qtp

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Magnesium binding site 7 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 -- Crystal Structure of NUDT5 in Complex with Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:30.4
occ:1.00
 O D:HOH608 1.9 24.5 1.0
O D:HOH619 1.9 31.5 0.8
OE2 D:GLU116 1.9 32.4 1.0
O D:HOH610 2.1 31.0 1.0
MG D:MG503 2.2 36.6 1.0
O D:ALA96 2.3 34.6 1.0
O D:HOH634 2.7 47.1 1.0
CD D:GLU116 2.9 39.2 1.0
OE1 D:GLU116 3.2 36.2 1.0
C D:ALA96 3.4 34.5 1.0
OE2 D:GLU166 3.7 71.1 1.0
OE2 D:GLU112 3.7 58.8 1.0
NE2 D:GLN82 4.2 42.6 1.0
CG D:GLU116 4.2 39.5 1.0
N D:ALA96 4.3 31.9 1.0
NH2 D:ARG84 4.3 33.2 1.0
N D:GLY97 4.3 34.2 1.0
O D:HOH604 4.3 46.9 1.0
OE1 D:GLN82 4.4 41.0 1.0
CA D:GLY97 4.4 35.6 1.0
CA D:ALA96 4.4 33.1 1.0
CD D:GLU112 4.7 53.9 1.0
CD D:GLN82 4.8 44.1 1.0
CG D:GLU112 4.8 55.9 1.0
O D:HOH632 4.8 48.0 1.0
CD D:GLU166 4.8 73.8 1.0
CB D:ALA96 4.9 31.8 1.0
O D:HOH636 5.0 27.6 0.8
NH1 D:ARG84 5.0 34.5 1.0

Magnesium binding site 8 out of 8 in 5qtp

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Magnesium binding site 8 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 -- Crystal Structure of NUDT5 in Complex with Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:36.6
occ:1.00
 O D:HOH634 2.0 47.1 1.0
MG D:MG502 2.2 30.4 1.0
OE2 D:GLU112 2.3 58.8 1.0
O D:HOH632 2.8 48.0 1.0
OE2 D:GLU166 2.8 71.1 1.0
OE2 D:GLU116 2.8 32.4 1.0
O D:HOH608 2.8 24.5 1.0
O D:ALA96 2.9 34.6 1.0
O D:HOH619 3.1 31.5 0.8
O D:HOH604 3.3 46.9 1.0
CD D:GLU112 3.4 53.9 1.0
CA D:GLY97 3.5 35.6 1.0
C D:ALA96 3.8 34.5 1.0
CD D:GLU116 4.0 39.2 1.0
CD D:GLU166 4.1 73.8 1.0
N D:GLY97 4.1 34.2 1.0
CG D:GLU112 4.2 55.9 1.0
OE1 D:GLU112 4.3 59.5 1.0
O D:HOH610 4.3 31.0 1.0
OE1 D:GLU116 4.7 36.2 1.0
C D:GLY97 4.8 35.0 1.0
CG D:GLU116 4.8 39.5 1.0
OE1 D:GLU166 4.9 67.5 1.0
N D:LEU98 4.9 33.8 1.0

Reference:

Y.Dubianok, T.Krojer, H.Kovacs, F.Moriaud, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft. Pandda Analysis Group Deposition To Be Published.
Page generated: Tue Aug 12 18:42:03 2025

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