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Magnesium in PDB 5qjd: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z240297434

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z240297434

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 Z240297434:
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 Z240297434, PDB code: 5qjd 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) 78.48 / 1.61
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.728, 59.593, 80.188, 79.65, 82.00, 76.23
R / Rfree (%) 21 / 23.7

Other elements in 5qjd:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z240297434 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 Z240297434 (pdb code 5qjd). 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 Z240297434, PDB code: 5qjd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjd

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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 Z240297434


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 Z240297434 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:24.1
occ:1.00
 O A:ALA96 2.1 20.8 1.0
OE2 A:GLU116 2.1 22.1 1.0
O A:HOH461 2.1 21.4 1.0
O A:HOH452 2.1 21.4 1.0
O A:HOH410 2.2 20.9 1.0
O A:HOH432 2.2 23.7 1.0
CD A:GLU116 3.1 22.8 1.0
MG A:MG302 3.1 53.5 1.0
C A:ALA96 3.3 19.2 1.0
OE1 A:GLU116 3.4 20.5 1.0
OE2 A:GLU166 3.9 48.2 1.0
OE2 A:GLU112 4.0 26.5 1.0
N A:GLY97 4.1 20.2 1.0
CA A:GLY97 4.2 19.6 1.0
O A:HOH467 4.2 30.4 1.0
N A:ALA96 4.2 16.6 1.0
CA A:ALA96 4.2 17.7 1.0
NH2 A:ARG84 4.3 21.3 1.0
O A:HOH480 4.3 27.2 1.0
O A:HOH426 4.3 17.9 1.0
CG A:GLU116 4.4 24.2 1.0
OE1 A:GLN82 4.5 20.4 0.5
NE2 A:GLN82 4.5 20.3 0.5
O A:HOH484 4.5 44.6 1.0
O A:HOH474 4.7 33.2 1.0
CB A:ALA96 4.7 18.1 1.0
CD A:GLU112 4.8 25.3 1.0
CD A:GLN82 4.9 20.6 0.5
O A:HOH413 5.0 35.7 1.0

Magnesium binding site 2 out of 8 in 5qjd

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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 Z240297434


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 Z240297434 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:53.5
occ:1.00
 O A:HOH452 1.9 21.4 1.0
O A:HOH413 2.0 35.7 1.0
OE2 A:GLU112 2.1 26.5 1.0
OE2 A:GLU166 2.3 48.2 1.0
OE2 A:GLU116 2.4 22.1 1.0
O A:HOH408 2.6 47.4 1.0
CD A:GLU112 3.1 25.3 1.0
MG A:MG301 3.1 24.1 1.0
CD A:GLU166 3.2 63.1 1.0
OE1 A:GLU112 3.3 27.7 1.0
CD A:GLU116 3.4 22.8 1.0
OE1 A:GLU166 3.5 56.0 1.0
CG A:GLU116 3.7 24.2 1.0
O A:ALA96 3.8 20.8 1.0
O A:HOH432 3.8 23.7 1.0
CG A:GLU166 4.4 61.5 1.0
O A:HOH474 4.4 33.2 1.0
OE2 A:GLU115 4.4 34.1 1.0
OE1 A:GLU116 4.4 20.5 1.0
CG A:GLU112 4.5 22.9 1.0
O A:HOH484 4.6 44.6 1.0
CA A:GLY97 4.7 19.6 1.0
O A:HOH461 4.8 21.4 1.0
C A:ALA96 4.8 19.2 1.0
CB A:GLU112 4.8 22.8 1.0
O A:HOH410 4.9 20.9 1.0

Magnesium binding site 3 out of 8 in 5qjd

Go back to Magnesium Binding Sites List in 5qjd
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 Z240297434


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 Z240297434 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:26.7
occ:1.00
 O B:ALA96 2.0 25.4 1.0
O B:HOH442 2.0 27.1 1.0
OE2 B:GLU116 2.1 30.2 1.0
O B:HOH411 2.1 25.7 1.0
O B:HOH404 2.1 25.5 1.0
O B:HOH453 2.2 27.1 1.0
CD B:GLU116 3.1 30.3 1.0
C B:ALA96 3.2 22.6 1.0
OE1 B:GLU116 3.3 28.1 1.0
OE2 B:GLU166 3.8 55.1 1.0
N B:GLY97 4.1 23.8 1.0
CA B:GLY97 4.1 23.5 1.0
OE2 B:GLU112 4.2 33.5 1.0
NH2 B:ARG84 4.2 25.1 1.0
N B:ALA96 4.2 23.4 1.0
O B:HOH455 4.2 34.3 0.9
CA B:ALA96 4.2 23.2 1.0
O B:HOH417 4.2 23.5 1.0
NE2 B:GLN82 4.3 31.7 1.0
OE1 B:GLN82 4.4 33.9 1.0
CG B:GLU116 4.4 31.1 1.0
O B:HOH474 4.5 34.4 0.9
O B:HOH478 4.5 36.5 1.0
CB B:ALA96 4.7 24.8 1.0
CD B:GLN82 4.7 34.5 1.0
CD B:GLU166 4.8 71.2 1.0
CD B:GLU112 4.9 31.8 1.0

Magnesium binding site 4 out of 8 in 5qjd

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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 Z240297434


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 Z240297434 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:90.3
occ:1.00
 O B:HOH436 1.8 43.6 1.0
O B:HOH416 2.0 50.0 1.0
OE1 B:GLU166 2.5 74.0 1.0
OE2 B:GLU112 3.0 33.5 1.0
OE2 B:GLU166 3.1 55.1 1.0
CD B:GLU166 3.1 71.2 1.0
OE1 B:GLU112 3.1 33.7 1.0
OE2 B:GLU115 3.2 40.3 1.0
O B:HOH453 3.3 27.1 1.0
CD B:GLU112 3.5 31.8 1.0
OE2 B:GLU116 4.3 30.2 1.0
O B:HOH474 4.4 34.4 0.9
CG B:GLU166 4.4 68.0 1.0
CD B:GLU115 4.4 41.6 1.0
NH1 B:ARG111 4.6 32.2 1.0
CB B:GLU115 4.9 36.3 1.0
CG B:GLU112 5.0 30.9 1.0

Magnesium binding site 5 out of 8 in 5qjd

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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 Z240297434


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 Z240297434 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:39.7
occ:1.00
 MG C:MG303 2.1 27.7 1.0
O C:HOH403 2.8 37.8 1.0
OE2 C:GLU116 2.8 28.4 1.0
O C:ALA96 2.9 24.0 1.0
O C:HOH455 2.9 25.2 1.0
O C:HOH422 3.0 31.1 1.0
O C:HOH461 3.1 44.4 1.0
OE2 C:GLU166 3.2 50.9 1.0
OE2 C:GLU112 3.3 33.8 1.0
O C:HOH446 3.4 42.7 1.0
CA C:GLY97 3.6 27.1 1.0
OE1 C:GLU112 3.8 39.9 1.0
CD C:GLU112 3.8 34.1 1.0
C C:ALA96 3.9 24.7 1.0
CD C:GLU116 4.1 27.0 1.0
CD C:GLU166 4.1 63.8 1.0
O C:HOH436 4.2 24.6 1.0
N C:GLY97 4.3 25.4 1.0
O C:HOH479 4.5 54.4 1.0
O C:HOH462 4.5 37.8 1.0
OE1 C:GLU166 4.7 63.9 1.0
OE1 C:GLU116 4.8 32.4 1.0
C C:GLY97 4.9 27.3 1.0
O C:HOH475 4.9 26.8 0.8
CG C:GLU116 5.0 25.8 1.0

Magnesium binding site 6 out of 8 in 5qjd

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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 Z240297434


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 Z240297434 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:27.7
occ:1.00
 O C:HOH455 2.0 25.2 1.0
OE2 C:GLU116 2.0 28.4 1.0
O C:HOH436 2.1 24.6 1.0
MG C:MG302 2.1 39.7 1.0
O C:ALA96 2.1 24.0 1.0
O C:HOH422 2.2 31.1 1.0
CD C:GLU116 3.1 27.0 1.0
C C:ALA96 3.3 24.7 1.0
OE1 C:GLU116 3.4 32.4 1.0
OE2 C:GLU166 3.7 50.9 1.0
O C:HOH403 3.8 37.8 1.0
OE2 C:GLU112 4.1 33.8 1.0
N C:ALA96 4.2 21.1 1.0
CA C:ALA96 4.2 22.1 1.0
N C:GLY97 4.2 25.4 1.0
CA C:GLY97 4.2 27.1 1.0
NH2 C:ARG84 4.3 30.0 1.0
O C:HOH421 4.3 23.9 0.8
NE2 C:GLN82 4.4 30.1 1.0
CG C:GLU116 4.4 25.8 1.0
OE1 C:GLN82 4.4 29.5 1.0
O C:HOH475 4.5 26.8 0.8
O C:HOH462 4.6 37.8 1.0
O C:HOH461 4.7 44.4 1.0
CB C:ALA96 4.7 20.5 1.0
CD C:GLN82 4.9 36.3 1.0
CD C:GLU112 4.9 34.1 1.0
CD C:GLU166 4.9 63.8 1.0

Magnesium binding site 7 out of 8 in 5qjd

Go back to Magnesium Binding Sites List in 5qjd
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 Z240297434


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 Z240297434 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:24.0
occ:1.00
 O D:HOH414 2.0 25.9 1.0
O D:HOH446 2.0 26.9 0.8
O D:HOH440 2.1 23.4 1.0
MG D:MG302 2.1 33.6 1.0
O D:ALA96 2.1 22.3 1.0
OE2 D:GLU116 2.1 25.7 1.0
CD D:GLU116 3.1 29.8 1.0
C D:ALA96 3.2 22.9 1.0
OE1 D:GLU116 3.4 26.4 1.0
OE2 D:GLU166 3.8 61.8 0.8
OE2 D:GLU112 4.0 41.8 1.0
CA D:GLY97 4.1 25.2 1.0
N D:GLY97 4.1 23.2 1.0
N D:ALA96 4.2 21.9 1.0
CA D:ALA96 4.2 22.9 1.0
NH2 D:ARG84 4.3 24.8 1.0
O D:HOH409 4.4 22.1 0.8
O D:HOH450 4.4 30.6 0.8
O D:HOH456 4.4 25.9 0.8
CG D:GLU116 4.4 28.6 1.0
NE2 D:GLN82 4.5 27.5 1.0
OE1 D:GLN82 4.5 28.1 1.0
CD D:GLU112 4.6 41.2 1.0
CB D:ALA96 4.6 24.5 1.0
O D:HOH444 4.7 40.4 1.0
CG D:GLU112 4.7 44.0 1.0
CD D:GLN82 5.0 30.4 1.0
CD D:GLU166 5.0 61.5 0.8
O D:HOH402 5.0 43.1 1.0

Magnesium binding site 8 out of 8 in 5qjd

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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 Z240297434


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 Z240297434 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:33.6
occ:1.00
 MG D:MG301 2.1 24.0 1.0
O D:HOH446 2.8 26.9 0.8
OE2 D:GLU116 2.9 25.7 1.0
OE2 D:GLU112 3.0 41.8 1.0
O D:ALA96 3.0 22.3 1.0
O D:HOH440 3.0 23.4 1.0
O D:HOH444 3.0 40.4 1.0
OE2 D:GLU166 3.1 61.8 0.8
O D:HOH418 3.3 42.8 1.0
CA D:GLY97 3.5 25.2 1.0
CD D:GLU112 3.6 41.2 1.0
C D:ALA96 3.9 22.9 1.0
O D:HOH402 4.0 43.1 1.0
CD D:GLU116 4.1 29.8 1.0
O D:HOH414 4.1 25.9 1.0
OE1 D:GLU112 4.1 41.2 1.0
N D:GLY97 4.2 23.2 1.0
O D:HOH450 4.2 30.6 0.8
CD D:GLU166 4.3 61.5 0.8
CG D:GLU112 4.4 44.0 1.0
O D:HOH460 4.4 48.6 0.8
O D:HOH456 4.7 25.9 0.8
C D:GLY97 4.8 25.9 1.0
OE1 D:GLU116 4.8 26.4 1.0
N D:LEU98 4.9 29.4 1.0
CG D:GLU116 5.0 28.6 1.0
OE1 D:GLU166 5.0 61.6 0.8

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 02:15:16 2024

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