Atomistry » Magnesium » PDB 5prc-5qk5 » 5qji
Atomistry »
  Magnesium »
    PDB 5prc-5qk5 »
      5qji »

Magnesium in PDB 5qji: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1899842917

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1899842917

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 Z1899842917:
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 Z1899842917, PDB code: 5qji 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) 77.65 / 1.69
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.980, 59.770, 79.380, 79.84, 81.43, 75.99
R / Rfree (%) 25.7 / 30.1

Other elements in 5qji:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1899842917 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 Z1899842917 (pdb code 5qji). 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 Z1899842917, PDB code: 5qji:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qji

Go back to Magnesium Binding Sites List in 5qji
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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:39.2
occ:1.00
 O A:HOH424 1.9 38.4 1.0
OE2 A:GLU116 2.0 32.9 1.0
O A:HOH441 2.0 30.0 1.0
O A:ALA96 2.1 27.7 1.0
O A:HOH425 2.2 28.2 1.0
O A:HOH448 2.5 31.8 1.0
CD A:GLU116 3.0 33.4 1.0
MG A:MG302 3.3 61.2 1.0
C A:ALA96 3.3 27.1 1.0
OE1 A:GLU116 3.4 39.8 1.0
OE2 A:GLU166 3.8 72.5 1.0
OE2 A:GLU112 4.0 34.9 1.0
NE2 A:GLN82 4.2 37.7 1.0
N A:GLY97 4.2 28.4 1.0
CA A:GLY97 4.3 30.0 1.0
CA A:ALA96 4.3 24.4 1.0
CG A:GLU116 4.3 33.1 1.0
OE1 A:GLN82 4.3 38.2 1.0
O A:HOH444 4.3 34.1 0.7
N A:ALA96 4.4 24.3 1.0
NH2 A:ARG84 4.4 39.0 1.0
O A:HOH421 4.4 28.9 1.0
O A:HOH461 4.5 35.2 1.0
CD A:GLN82 4.6 37.3 1.0
O A:HOH456 4.7 40.7 1.0
O A:HOH466 4.8 49.2 1.0
CB A:ALA96 4.8 22.8 1.0
CD A:GLU112 4.8 36.0 1.0
O A:HOH411 4.9 47.6 1.0

Magnesium binding site 2 out of 8 in 5qji

Go back to Magnesium Binding Sites List in 5qji
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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:61.2
occ:1.00
 O A:HOH411 2.0 47.6 1.0
O A:HOH441 2.1 30.0 1.0
OE2 A:GLU112 2.2 34.9 1.0
OE2 A:GLU166 2.2 72.5 1.0
OE2 A:GLU116 2.6 32.9 1.0
O A:HOH413 2.6 43.3 1.0
CD A:GLU166 3.1 74.8 1.0
CD A:GLU112 3.2 36.0 1.0
MG A:MG301 3.3 39.2 1.0
OE1 A:GLU112 3.3 35.1 1.0
OE1 A:GLU166 3.4 73.8 1.0
CD A:GLU116 3.6 33.4 1.0
O A:HOH424 3.8 38.4 1.0
CG A:GLU116 3.8 33.1 1.0
O A:ALA96 4.0 27.7 1.0
OE2 A:GLU115 4.1 45.1 1.0
O A:HOH456 4.4 40.7 1.0
CG A:GLU166 4.5 69.5 1.0
CG A:GLU112 4.6 35.4 1.0
OE1 A:GLU116 4.7 39.8 1.0
CA A:GLY97 4.9 30.0 1.0
C A:ALA96 5.0 27.1 1.0

Magnesium binding site 3 out of 8 in 5qji

Go back to Magnesium Binding Sites List in 5qji
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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:39.5
occ:1.00
 O B:ALA96 1.9 33.7 1.0
O B:HOH433 1.9 39.0 1.0
OE2 B:GLU116 2.1 39.8 1.0
O B:HOH440 2.1 37.0 1.0
O B:HOH402 2.2 33.6 1.0
O B:HOH443 2.4 35.3 1.0
CD B:GLU116 3.0 41.5 1.0
C B:ALA96 3.0 30.3 1.0
OE1 B:GLU116 3.3 40.6 1.0
N B:ALA96 3.9 28.8 1.0
OE1 B:GLN82 3.9 45.5 1.0
N B:GLY97 3.9 32.1 1.0
CA B:ALA96 4.0 34.9 1.0
CA B:GLY97 4.0 33.5 1.0
O B:HOH422 4.0 34.4 1.0
OE2 B:GLU166 4.1 50.8 1.0
MG B:MG303 4.1 73.8 1.0
NE2 B:GLN82 4.1 42.5 1.0
OE2 B:GLU112 4.1 43.1 1.0
NH2 B:ARG84 4.2 39.9 1.0
CD B:GLN82 4.4 50.2 1.0
CG B:GLU116 4.4 37.3 1.0
CB B:ALA96 4.5 35.2 1.0
O B:HOH460 4.7 50.2 1.0

Magnesium binding site 4 out of 8 in 5qji

Go back to Magnesium Binding Sites List in 5qji
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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:73.8
occ:1.00
 OE2 B:GLU112 1.9 43.1 1.0
O B:HOH412 2.0 62.2 1.0
O B:HOH427 2.6 44.0 1.0
OE2 B:GLU166 2.7 50.8 1.0
OE2 B:GLU116 2.9 39.8 1.0
CD B:GLU112 3.0 41.3 1.0
O B:HOH443 3.0 35.3 1.0
OE1 B:GLU166 3.1 71.9 1.0
CD B:GLU166 3.2 69.6 1.0
CG B:GLU116 3.4 37.3 1.0
OE1 B:GLU112 3.4 40.3 1.0
CD B:GLU116 3.5 41.5 1.0
OE2 B:GLU115 3.6 64.5 1.0
MG B:MG302 4.1 39.5 1.0
CB B:GLU115 4.2 49.4 1.0
CG B:GLU112 4.3 38.4 1.0
O B:ALA96 4.4 33.7 1.0
O B:HOH433 4.4 39.0 1.0
CB B:GLU112 4.5 37.2 1.0
CA B:GLU112 4.6 38.3 1.0
CD B:GLU115 4.6 60.3 1.0
OE1 B:GLU116 4.7 40.6 1.0
O B:GLU112 4.7 33.2 1.0
CG B:GLU166 4.7 72.9 1.0
CB B:GLU116 4.9 37.3 1.0
CG B:GLU115 5.0 56.5 1.0

Magnesium binding site 5 out of 8 in 5qji

Go back to Magnesium Binding Sites List in 5qji
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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:47.5
occ:1.00
 O C:HOH408 1.4 70.2 1.0
O C:HOH404 2.1 45.6 1.0
OE2 C:GLU166 2.3 58.7 1.0
OE2 C:GLU112 2.4 43.3 1.0
MG C:MG303 2.8 39.1 1.0
O C:HOH461 2.8 53.6 1.0
OE2 C:GLU116 2.8 44.5 1.0
CD C:GLU112 3.3 52.9 1.0
O C:ALA96 3.5 35.1 1.0
CD C:GLU166 3.5 59.7 1.0
OE1 C:GLU112 3.6 60.1 1.0
O C:HOH422 3.6 41.4 1.0
O C:HOH432 3.8 29.5 1.0
O C:HOH446 3.9 54.6 1.0
CD C:GLU116 4.0 40.1 1.0
CA C:GLY97 4.1 42.6 1.0
OE1 C:GLU166 4.2 66.1 1.0
CG C:GLU116 4.5 38.1 1.0
C C:ALA96 4.5 37.9 1.0
CG C:GLU166 4.6 57.6 1.0
CG C:GLU112 4.7 47.5 1.0
O C:HOH467 4.7 62.4 1.0
O C:HOH424 4.8 35.2 1.0
N C:GLY97 4.8 37.4 1.0
OE2 C:GLU115 5.0 49.8 1.0
OE1 C:GLU116 5.0 42.5 1.0

Magnesium binding site 6 out of 8 in 5qji

Go back to Magnesium Binding Sites List in 5qji
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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:39.1
occ:1.00
 O C:HOH432 1.7 29.5 1.0
OE2 C:GLU116 1.9 44.5 1.0
O C:HOH408 2.0 70.2 1.0
O C:HOH424 2.0 35.2 1.0
O C:ALA96 2.2 35.1 1.0
O C:HOH422 2.2 41.4 1.0
MG C:MG302 2.8 47.5 1.0
CD C:GLU116 3.0 40.1 1.0
C C:ALA96 3.3 37.9 1.0
OE1 C:GLU116 3.4 42.5 1.0
OE2 C:GLU112 3.8 43.3 1.0
OE2 C:GLU166 3.8 58.7 1.0
N C:GLY97 4.2 37.4 1.0
CA C:GLY97 4.3 42.6 1.0
N C:ALA96 4.3 32.6 1.0
CA C:ALA96 4.3 32.9 1.0
CG C:GLU116 4.3 38.1 1.0
O C:HOH404 4.4 45.6 1.0
NE2 C:GLN82 4.4 46.8 1.0
NH2 C:ARG84 4.4 47.4 1.0
OE1 C:GLN82 4.4 38.0 1.0
CB C:ALA96 4.8 33.2 1.0
CD C:GLN82 4.8 40.0 1.0
CD C:GLU112 4.9 52.9 1.0
O C:HOH461 4.9 53.6 1.0
CD C:GLU166 4.9 59.7 1.0

Magnesium binding site 7 out of 8 in 5qji

Go back to Magnesium Binding Sites List in 5qji
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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:40.9
occ:1.00
 OE2 D:GLU116 2.2 44.9 1.0
O D:HOH409 2.3 30.0 1.0
MG D:MG302 2.3 47.4 1.0
O D:HOH412 2.5 31.0 1.0
O D:ALA96 3.3 46.5 1.0
O D:HOH423 3.3 44.0 1.0
CD D:GLU116 3.3 51.1 1.0
NE2 D:GLN82 3.5 47.0 1.0
OE2 D:GLU166 3.5 0.1 1.0
NH2 D:ARG84 3.7 44.1 1.0
OE1 D:GLU116 3.8 43.0 1.0
OE1 D:GLN82 4.0 49.9 1.0
CD D:GLN82 4.2 50.5 1.0
CD D:GLU166 4.4 0.3 1.0
NH1 D:ARG84 4.5 46.6 1.0
C D:ALA96 4.5 46.6 1.0
CG D:GLU116 4.5 49.0 1.0
CZ D:ARG84 4.5 51.7 1.0
OE2 D:GLU112 4.6 68.3 1.0
CG D:GLU166 4.7 93.5 1.0
CG1 D:VAL168 5.0 81.8 1.0

Magnesium binding site 8 out of 8 in 5qji

Go back to Magnesium Binding Sites List in 5qji
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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:47.4
occ:1.00
 MG D:MG301 2.3 40.9 1.0
OE2 D:GLU166 2.6 0.1 1.0
O D:HOH414 2.8 52.3 1.0
OE2 D:GLU116 2.9 44.9 1.0
O D:HOH412 2.9 31.0 1.0
O D:HOH423 3.2 44.0 1.0
OE2 D:GLU112 3.2 68.3 1.0
O D:ALA96 3.2 46.5 1.0
CD D:GLU112 3.6 65.8 1.0
OE1 D:GLU112 3.8 68.7 1.0
CD D:GLU166 3.8 0.3 1.0
CA D:GLY97 3.9 42.5 1.0
CD D:GLU116 4.1 51.1 1.0
O D:HOH409 4.2 30.0 1.0
C D:ALA96 4.3 46.6 1.0
CG D:GLU112 4.4 64.2 1.0
N D:GLY97 4.6 44.7 1.0
CG D:GLU166 4.6 93.5 1.0
OE1 D:GLU166 4.7 0.0 1.0
O D:HOH405 4.7 76.6 1.0
OE1 D:GLU116 4.8 43.0 1.0
CG D:GLU116 5.0 49.0 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 02:15:45 2024

Last articles

Mg in 4V1O
Mg in 4V1N
Mg in 4V1M
Mg in 4V0R
Mg in 4V0O
Mg in 4V0N
Mg in 4V0M
Mg in 4V0L
Mg in 4V08
Mg in 4V03
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy