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Magnesium in PDB 5qtl: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804, PDB code: 5qtl 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) 78.34 / 1.73
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.330, 59.820, 80.180, 79.34, 81.47, 75.65
R / Rfree (%) 22.1 / 25.3

Other elements in 5qtl:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804 also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804 (pdb code 5qtl). 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 Gb-0804, PDB code: 5qtl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qtl

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Magnesium binding site 1 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


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 Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:33.4
occ:1.00
 OE2 A:GLU116 2.1 26.4 1.0
O A:HOH456 2.1 25.0 1.0
O A:HOH435 2.1 27.5 1.0
O A:ALA96 2.2 25.4 1.0
O A:HOH425 2.2 27.7 1.0
O A:HOH459 2.2 25.8 1.0
CD A:GLU116 3.1 27.1 1.0
C A:ALA96 3.3 24.8 1.0
MG A:MG302 3.4 52.9 1.0
OE1 A:GLU116 3.5 26.6 1.0
OE2 A:GLU166 3.6 54.5 1.0
O A:HOH439 4.1 26.4 0.7
NH2 A:ARG84 4.2 26.4 1.0
N A:GLY97 4.2 24.8 1.0
OE2 A:GLU112 4.2 33.3 1.0
CA A:GLY97 4.2 23.4 1.0
N A:ALA96 4.3 20.7 1.0
CA A:ALA96 4.3 21.9 1.0
NE2 A:GLN82 4.3 29.8 1.0
OE1 A:GLN82 4.3 28.5 1.0
O A:HOH429 4.3 23.1 1.0
O A:HOH479 4.4 31.5 0.7
CG A:GLU116 4.4 25.9 1.0
O A:HOH481 4.5 27.6 1.0
CD A:GLN82 4.7 33.4 1.0
CB A:ALA96 4.8 18.8 1.0
CD A:GLU166 4.8 65.2 1.0
CD A:GLU112 4.9 30.5 1.0
NH1 A:ARG84 5.0 28.7 1.0
CZ A:ARG84 5.0 25.6 1.0

Magnesium binding site 2 out of 8 in 5qtl

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Magnesium binding site 2 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


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 Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:52.9
occ:1.00
 O A:HOH404 1.9 39.4 1.0
O A:HOH456 2.1 25.0 1.0
OE2 A:GLU112 2.1 33.3 1.0
OE2 A:GLU166 2.4 54.5 1.0
OE2 A:GLU116 2.7 26.4 1.0
CD A:GLU166 3.0 65.2 1.0
CD A:GLU112 3.0 30.5 1.0
OE1 A:GLU166 3.2 59.4 1.0
OE1 A:GLU112 3.3 33.0 1.0
MG A:MG301 3.4 33.4 1.0
CD A:GLU116 3.6 27.1 1.0
CG A:GLU116 3.8 25.9 1.0
O A:HOH479 4.0 31.5 0.7
O A:ALA96 4.0 25.4 1.0
O A:HOH425 4.1 27.7 1.0
OE2 A:GLU115 4.2 33.3 1.0
CG A:GLU166 4.3 58.9 1.0
CG A:GLU112 4.4 28.8 1.0
OE1 A:GLU116 4.7 26.6 1.0
CA A:GLY97 4.8 23.4 1.0
CB A:GLU112 4.8 26.0 1.0
C A:ALA96 5.0 24.8 1.0

Magnesium binding site 3 out of 8 in 5qtl

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Magnesium binding site 3 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


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 Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:34.8
occ:1.00
 OE2 B:GLU116 2.0 35.0 1.0
O B:ALA96 2.0 29.6 1.0
O B:HOH611 2.1 30.1 1.0
O B:HOH614 2.1 31.4 1.0
O B:HOH653 2.2 28.5 1.0
CD B:GLU116 3.0 34.4 1.0
C B:ALA96 3.2 25.2 1.0
MG B:MG504 3.3 70.4 1.0
OE1 B:GLU116 3.4 33.3 1.0
OE2 B:GLU166 3.8 54.7 1.0
N B:GLY97 4.1 28.7 1.0
CA B:GLY97 4.2 30.1 1.0
N B:ALA96 4.2 27.4 1.0
O B:HOH620 4.2 33.0 1.0
NH2 B:ARG84 4.2 29.5 1.0
CA B:ALA96 4.2 28.4 1.0
OE2 B:GLU112 4.3 43.9 1.0
NE2 B:GLN82 4.3 37.5 1.0
OE1 B:GLN82 4.4 35.7 1.0
CG B:GLU116 4.4 32.0 1.0
O B:HOH665 4.4 50.1 1.0
O B:HOH673 4.5 37.8 1.0
CD B:GLU166 4.6 65.2 1.0
CD B:GLN82 4.7 43.0 1.0
CB B:ALA96 4.8 29.3 1.0

Magnesium binding site 4 out of 8 in 5qtl

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Magnesium binding site 4 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


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 Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:70.4
occ:1.00
 OE2 B:GLU112 1.8 43.9 1.0
O B:HOH613 2.3 53.9 1.0
OE2 B:GLU116 2.6 35.0 1.0
OE2 B:GLU166 2.7 54.7 1.0
O B:HOH605 2.8 31.4 0.5
CD B:GLU112 2.8 39.6 1.0
OE1 B:GLU112 3.2 39.1 1.0
MG B:MG503 3.3 34.8 1.0
CD B:GLU116 3.4 34.4 1.0
CD B:GLU166 3.5 65.2 1.0
OE1 B:GLU166 3.6 63.0 1.0
O B:ALA96 3.6 29.6 1.0
CG B:GLU116 3.7 32.0 1.0
O B:HOH665 3.8 50.1 1.0
OE2 B:GLU115 4.0 45.5 1.0
CG B:GLU112 4.1 37.0 1.0
O B:HOH614 4.2 31.4 1.0
CA B:GLY97 4.4 30.1 1.0
OE1 B:GLU116 4.5 33.3 1.0
C B:ALA96 4.5 25.2 1.0
CB B:GLU112 4.6 35.2 1.0
N B:GLY97 4.8 28.7 1.0
CA B:GLU112 4.8 32.3 1.0
CG B:GLU166 4.9 61.0 1.0
O B:HOH653 5.0 28.5 1.0
O B:HOH611 5.0 30.1 1.0

Magnesium binding site 5 out of 8 in 5qtl

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Magnesium binding site 5 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


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 Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:52.5
occ:1.00
 O C:HOH412 2.0 48.6 1.0
O C:HOH447 2.0 32.5 1.0
OE2 C:GLU112 2.1 36.5 1.0
OE2 C:GLU166 2.3 59.8 1.0
OE2 C:GLU116 2.3 31.8 1.0
O C:HOH455 2.4 55.5 1.0
CD C:GLU112 3.1 39.5 1.0
MG C:MG303 3.1 34.1 1.0
CD C:GLU166 3.2 62.9 1.0
CD C:GLU116 3.3 34.4 1.0
OE1 C:GLU112 3.5 47.6 1.0
OE1 C:GLU166 3.6 72.2 1.0
O C:ALA96 3.7 28.6 1.0
CG C:GLU116 3.7 30.8 1.0
O C:HOH429 3.8 32.5 1.0
O C:HOH452 3.9 59.1 1.0
OE2 C:GLU115 4.1 43.1 1.0
OE1 C:GLU116 4.4 35.1 1.0
CG C:GLU112 4.5 35.0 1.0
CG C:GLU166 4.5 58.9 1.0
CA C:GLY97 4.6 32.9 1.0
O C:HOH456 4.6 28.6 1.0
C C:ALA96 4.6 29.5 1.0
CB C:GLU112 4.9 34.9 1.0

Magnesium binding site 6 out of 8 in 5qtl

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Magnesium binding site 6 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


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 Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:34.1
occ:1.00
 O C:HOH456 2.0 28.6 1.0
OE2 C:GLU116 2.1 31.8 1.0
O C:HOH447 2.1 32.5 1.0
O C:HOH429 2.1 32.5 1.0
O C:ALA96 2.1 28.6 1.0
O C:HOH451 2.1 27.0 1.0
CD C:GLU116 3.1 34.4 1.0
MG C:MG302 3.1 52.5 1.0
C C:ALA96 3.3 29.5 1.0
OE1 C:GLU116 3.4 35.1 1.0
OE2 C:GLU166 3.8 59.8 1.0
OE2 C:GLU112 4.2 36.5 1.0
N C:GLY97 4.2 32.5 1.0
N C:ALA96 4.2 27.0 1.0
CA C:ALA96 4.2 26.1 1.0
CA C:GLY97 4.3 32.9 1.0
NE2 C:GLN82 4.3 38.6 1.0
O C:HOH416 4.3 26.7 0.8
NH2 C:ARG84 4.4 32.9 1.0
CG C:GLU116 4.4 30.8 1.0
OE1 C:GLN82 4.5 32.6 1.0
CB C:ALA96 4.7 25.5 1.0
O C:HOH470 4.7 39.0 0.8
O C:HOH412 4.8 48.6 1.0
CD C:GLN82 4.8 40.6 1.0

Magnesium binding site 7 out of 8 in 5qtl

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Magnesium binding site 7 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


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 Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:38.0
occ:1.00
 O D:HOH615 1.9 30.1 0.8
O D:HOH630 1.9 34.2 1.0
OE2 D:GLU116 2.0 38.1 1.0
O D:HOH613 2.1 30.9 1.0
MG D:MG503 2.2 45.2 1.0
O D:ALA96 2.2 35.3 1.0
CD D:GLU116 3.0 45.4 1.0
OE1 D:GLU116 3.3 40.3 1.0
C D:ALA96 3.3 34.7 1.0
OE2 D:GLU112 3.8 57.1 1.0
OE2 D:GLU166 3.9 67.0 1.0
N D:ALA96 4.2 34.4 1.0
N D:GLY97 4.2 35.4 1.0
CA D:ALA96 4.2 35.9 1.0
NH2 D:ARG84 4.3 37.5 1.0
CA D:GLY97 4.3 39.0 1.0
O D:HOH609 4.3 35.3 0.8
CG D:GLU116 4.3 43.3 1.0
NE2 D:GLN82 4.4 38.8 1.0
OE1 D:GLN82 4.4 38.0 1.0
O D:HOH637 4.4 35.1 0.8
CD D:GLU112 4.5 52.5 1.0
O D:HOH603 4.6 55.2 1.0
CB D:ALA96 4.6 36.2 1.0
CG D:GLU112 4.7 57.3 1.0
CD D:GLN82 4.8 42.8 1.0
O D:HOH645 4.9 35.5 0.8
CD D:GLU166 4.9 72.7 1.0
O D:HOH619 4.9 44.8 1.0

Magnesium binding site 8 out of 8 in 5qtl

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Magnesium binding site 8 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


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 Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:45.2
occ:1.00
 MG D:MG502 2.2 38.0 1.0
OE2 D:GLU112 2.5 57.1 1.0
OE2 D:GLU166 2.6 67.0 1.0
O D:HOH615 2.8 30.1 0.8
OE2 D:GLU116 2.9 38.1 1.0
O D:HOH630 3.0 34.2 1.0
O D:ALA96 3.1 35.3 1.0
O D:HOH619 3.1 44.8 1.0
CD D:GLU112 3.4 52.5 1.0
O D:HOH603 3.5 55.2 1.0
CA D:GLY97 3.6 39.0 1.0
CD D:GLU166 3.8 72.7 1.0
C D:ALA96 4.0 34.7 1.0
CD D:GLU116 4.0 45.4 1.0
OE1 D:GLU112 4.0 54.9 1.0
CG D:GLU112 4.2 57.3 1.0
O D:HOH613 4.3 30.9 1.0
N D:GLY97 4.3 35.4 1.0
O D:HOH637 4.4 35.1 0.8
OE1 D:GLU166 4.6 69.0 1.0
CG D:GLU166 4.8 66.3 1.0
OE1 D:GLU116 4.8 40.3 1.0
C D:GLY97 4.9 40.0 1.0
CG D:GLU116 4.9 43.3 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 18:40:29 2025

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