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Magnesium in PDB 5qjq: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z56791867

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z56791867

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 Z56791867:
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 Z56791867, PDB code: 5qjq 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) 78.14 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.923, 59.630, 79.839, 79.67, 82.01, 76.26
R / Rfree (%) 21.1 / 24

Other elements in 5qjq:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z56791867 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 Z56791867 (pdb code 5qjq). 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 Z56791867, PDB code: 5qjq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjq

Go back to Magnesium Binding Sites List in 5qjq
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 Z56791867


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 Z56791867 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:24.6
occ:1.00
 O A:ALA96 2.0 20.6 1.0
OE2 A:GLU116 2.1 23.9 1.0
O A:HOH418 2.1 20.6 1.0
O A:HOH453 2.1 21.8 1.0
O A:HOH445 2.1 23.6 1.0
O A:HOH459 2.1 22.6 1.0
CD A:GLU116 3.1 23.2 1.0
C A:ALA96 3.2 21.5 1.0
MG A:MG302 3.3 50.6 1.0
OE1 A:GLU116 3.4 23.2 1.0
OE2 A:GLU166 3.9 43.7 1.0
OE2 A:GLU112 4.1 28.3 1.0
N A:GLY97 4.1 21.4 1.0
CA A:GLY97 4.1 21.7 1.0
N A:ALA96 4.2 18.4 1.0
CA A:ALA96 4.2 18.6 1.0
NH2 A:ARG84 4.3 23.8 1.0
O A:HOH430 4.3 19.6 1.0
CG A:GLU116 4.4 24.0 1.0
OE1 A:GLN82 4.4 25.5 1.0
NE2 A:GLN82 4.4 25.4 1.0
O A:HOH477 4.5 33.0 1.0
O A:HOH483 4.6 41.1 1.0
O A:HOH472 4.6 27.5 0.9
CB A:ALA96 4.7 18.7 1.0
O A:HOH476 4.8 34.3 1.0
CD A:GLN82 4.8 29.6 1.0
CD A:GLU112 4.9 28.8 1.0

Magnesium binding site 2 out of 8 in 5qjq

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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 Z56791867


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 Z56791867 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:50.6
occ:1.00
 O A:HOH412 2.0 38.1 1.0
O A:HOH453 2.1 21.8 1.0
OE2 A:GLU112 2.1 28.3 1.0
OE2 A:GLU166 2.4 43.7 1.0
O A:HOH407 2.5 46.9 1.0
OE2 A:GLU116 2.5 23.9 1.0
CD A:GLU112 3.1 28.8 1.0
CD A:GLU166 3.2 64.3 1.0
MG A:MG301 3.3 24.6 1.0
OE1 A:GLU112 3.3 31.1 1.0
CD A:GLU116 3.4 23.2 1.0
OE1 A:GLU166 3.5 59.1 1.0
CG A:GLU116 3.7 24.0 1.0
O A:HOH424 3.7 59.3 1.0
O A:ALA96 3.9 20.6 1.0
O A:HOH445 3.9 23.6 1.0
OE2 A:GLU115 4.2 34.5 1.0
CG A:GLU112 4.5 24.7 1.0
CG A:GLU166 4.5 62.1 1.0
OE1 A:GLU116 4.5 23.2 1.0
O A:HOH476 4.7 34.3 1.0
CA A:GLY97 4.8 21.7 1.0
CB A:GLU112 4.8 25.8 1.0
C A:ALA96 4.9 21.5 1.0
O A:HOH483 4.9 41.1 1.0
O A:HOH459 4.9 22.6 1.0
O A:HOH418 5.0 20.6 1.0

Magnesium binding site 3 out of 8 in 5qjq

Go back to Magnesium Binding Sites List in 5qjq
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 Z56791867


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 Z56791867 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:28.1
occ:1.00
 O B:ALA96 2.0 27.3 1.0
OE2 B:GLU116 2.1 34.6 1.0
O B:HOH419 2.1 29.3 1.0
O B:HOH437 2.1 26.3 1.0
O B:HOH445 2.2 29.1 1.0
O B:HOH422 2.2 27.7 1.0
CD B:GLU116 3.1 34.0 1.0
C B:ALA96 3.2 23.8 1.0
OE1 B:GLU116 3.4 30.3 1.0
OE2 B:GLU166 3.9 56.6 1.0
N B:GLY97 4.1 24.2 1.0
CA B:GLY97 4.1 26.0 1.0
N B:ALA96 4.2 24.6 1.0
CA B:ALA96 4.2 22.4 1.0
NH2 B:ARG84 4.2 25.2 1.0
O B:HOH429 4.2 27.4 1.0
OE2 B:GLU112 4.2 33.2 1.0
NE2 B:GLN82 4.4 31.4 1.0
CG B:GLU116 4.4 30.9 1.0
OE1 B:GLN82 4.4 31.4 1.0
O B:HOH474 4.5 38.8 1.0
O B:HOH465 4.6 39.8 0.9
CB B:ALA96 4.7 26.4 1.0
CD B:GLU166 4.8 76.6 1.0
CD B:GLN82 4.8 36.2 1.0
O B:HOH470 4.8 26.4 0.9
O B:HOH413 4.9 46.6 1.0
MG B:MG303 4.9 68.6 1.0

Magnesium binding site 4 out of 8 in 5qjq

Go back to Magnesium Binding Sites List in 5qjq
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 Z56791867


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 Z56791867 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:68.6
occ:1.00
 O B:HOH415 1.7 42.7 1.0
O B:HOH413 2.2 46.6 1.0
OE1 B:GLU166 2.3 74.8 1.0
O B:HOH445 3.0 29.1 1.0
CD B:GLU166 3.1 76.6 1.0
OE2 B:GLU166 3.1 56.6 1.0
OE2 B:GLU112 3.3 33.2 1.0
OE1 B:GLU112 3.4 38.3 1.0
OE2 B:GLU115 3.6 43.9 1.0
CD B:GLU112 3.8 36.3 1.0
O B:HOH465 4.3 39.8 0.9
OE2 B:GLU116 4.4 34.6 1.0
CG B:GLU166 4.4 72.2 1.0
CD B:GLU115 4.8 44.8 1.0
MG B:MG302 4.9 28.1 1.0
NH1 B:ARG111 4.9 35.0 1.0

Magnesium binding site 5 out of 8 in 5qjq

Go back to Magnesium Binding Sites List in 5qjq
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 Z56791867


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 Z56791867 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:40.5
occ:1.00
 MG C:MG303 2.1 29.8 1.0
O C:HOH402 2.8 40.3 1.0
OE2 C:GLU116 2.8 28.5 1.0
O C:HOH418 2.8 57.9 1.0
O C:ALA96 2.9 23.1 1.0
O C:HOH413 3.0 28.1 1.0
O C:HOH457 3.0 25.8 1.0
O C:HOH468 3.2 45.5 0.9
OE2 C:GLU112 3.3 34.1 1.0
OE2 C:GLU166 3.3 57.2 1.0
O C:HOH432 3.5 42.8 1.0
CA C:GLY97 3.6 28.5 1.0
O C:HOH471 3.6 54.0 1.0
OE1 C:GLU112 3.8 42.9 1.0
CD C:GLU112 3.8 39.5 1.0
C C:ALA96 4.0 26.7 1.0
CD C:GLU116 4.0 29.1 1.0
CD C:GLU166 4.1 66.1 1.0
O C:HOH415 4.2 24.9 1.0
N C:GLY97 4.3 25.6 1.0
OE1 C:GLU166 4.6 67.5 1.0
O C:HOH469 4.8 23.2 1.0
OE1 C:GLU116 4.8 30.1 1.0
C C:GLY97 4.9 26.8 1.0
CG C:GLU116 5.0 26.0 1.0

Magnesium binding site 6 out of 8 in 5qjq

Go back to Magnesium Binding Sites List in 5qjq
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 Z56791867


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 Z56791867 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:29.8
occ:1.00
 OE2 C:GLU116 2.0 28.5 1.0
O C:HOH457 2.0 25.8 1.0
O C:HOH415 2.1 24.9 1.0
O C:ALA96 2.1 23.1 1.0
MG C:MG302 2.1 40.5 1.0
O C:HOH413 2.2 28.1 1.0
CD C:GLU116 3.1 29.1 1.0
C C:ALA96 3.3 26.7 1.0
OE1 C:GLU116 3.4 30.1 1.0
O C:HOH402 3.8 40.3 1.0
OE2 C:GLU166 3.9 57.2 1.0
O C:HOH471 3.9 54.0 1.0
CA C:GLY97 4.1 28.5 1.0
N C:GLY97 4.1 25.6 1.0
N C:ALA96 4.2 22.2 1.0
OE2 C:GLU112 4.2 34.1 1.0
CA C:ALA96 4.2 21.6 1.0
NH2 C:ARG84 4.3 28.9 1.0
O C:HOH417 4.3 25.8 0.9
NE2 C:GLN82 4.3 28.8 1.0
OE1 C:GLN82 4.4 29.4 1.0
CG C:GLU116 4.5 26.0 1.0
O C:HOH472 4.5 33.9 0.9
O C:HOH468 4.6 45.5 0.9
CB C:ALA96 4.7 22.7 1.0
O C:HOH469 4.8 23.2 1.0
CD C:GLN82 4.8 31.9 1.0
CD C:GLU112 4.9 39.5 1.0
O C:HOH418 4.9 57.9 1.0

Magnesium binding site 7 out of 8 in 5qjq

Go back to Magnesium Binding Sites List in 5qjq
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 Z56791867


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 Z56791867 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:26.8
occ:1.00
 O D:HOH425 1.9 31.2 0.9
MG D:MG302 2.0 36.2 1.0
OE2 D:GLU116 2.0 30.5 1.0
O D:HOH426 2.1 29.4 1.0
O D:ALA96 2.1 28.1 1.0
O D:HOH414 2.1 27.9 1.0
CD D:GLU116 3.1 34.0 1.0
C D:ALA96 3.2 26.4 1.0
O D:HOH445 3.4 64.0 1.0
OE1 D:GLU116 3.4 31.4 1.0
OE2 D:GLU166 4.0 80.5 1.0
OE2 D:GLU112 4.1 39.8 1.0
CA D:GLY97 4.1 28.6 1.0
N D:GLY97 4.1 27.9 1.0
N D:ALA96 4.2 25.0 1.0
CA D:ALA96 4.2 27.8 1.0
NH2 D:ARG84 4.3 29.7 1.0
O D:HOH413 4.4 26.0 0.9
CG D:GLU116 4.4 32.7 1.0
NE2 D:GLN82 4.5 31.2 1.0
OE1 D:GLN82 4.5 31.4 1.0
O D:HOH442 4.5 32.6 0.9
CB D:ALA96 4.6 29.0 1.0
O D:HOH438 4.8 35.1 0.9
O D:HOH408 4.9 47.7 1.0
CD D:GLN82 5.0 35.0 1.0
CD D:GLU112 5.0 39.3 1.0

Magnesium binding site 8 out of 8 in 5qjq

Go back to Magnesium Binding Sites List in 5qjq
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 Z56791867


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 Z56791867 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:36.2
occ:1.00
 MG D:MG301 2.0 26.8 1.0
O D:HOH445 2.2 64.0 1.0
O D:HOH425 2.6 31.2 0.9
OE2 D:GLU116 2.8 30.5 1.0
O D:HOH426 2.9 29.4 1.0
O D:ALA96 3.0 28.1 1.0
O D:HOH410 3.2 44.4 1.0
OE2 D:GLU166 3.2 80.5 1.0
OE2 D:GLU112 3.3 39.8 1.0
O D:HOH433 3.4 41.4 0.9
CA D:GLY97 3.6 28.6 1.0
O D:HOH408 3.9 47.7 1.0
C D:ALA96 4.0 26.4 1.0
CD D:GLU112 4.0 39.3 1.0
CD D:GLU116 4.1 34.0 1.0
OE1 D:GLU112 4.1 36.9 1.0
O D:HOH414 4.1 27.9 1.0
N D:GLY97 4.2 27.9 1.0
CD D:GLU166 4.4 80.5 1.0
O D:HOH438 4.6 35.1 0.9
OE1 D:GLU116 4.8 31.4 1.0
O D:HOH442 4.8 32.6 0.9
C D:GLY97 4.8 30.9 1.0
CG D:GLU116 4.9 32.7 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 02:19:41 2024

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