Atomistry » Magnesium » PDB 5pnw-5qk4 » 5qj8
Atomistry »
  Magnesium »
    PDB 5pnw-5qk4 »
      5qj8 »

Magnesium in PDB 5qj8: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829

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 Z2856434829:
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 Z2856434829, PDB code: 5qj8 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) 77.81 / 1.76
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.530, 59.990, 79.650, 79.56, 81.09, 75.49
R / Rfree (%) 23.5 / 27.8

Other elements in 5qj8:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829 also contains other interesting chemical elements:

Fluorine (F) 2 atoms
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 Z2856434829 (pdb code 5qj8). 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 Z2856434829, PDB code: 5qj8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qj8

Go back to Magnesium Binding Sites List in 5qj8
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 Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:28.1
occ:1.00
 O A:ALA96 2.0 25.6 1.0
O A:HOH436 2.1 23.2 1.0
O A:HOH451 2.1 24.1 1.0
O A:HOH422 2.1 26.2 1.0
O A:HOH423 2.1 28.5 1.0
OE2 A:GLU116 2.1 26.9 1.0
C A:ALA96 3.1 25.1 1.0
CD A:GLU116 3.1 31.9 1.0
OE1 A:GLU116 3.4 29.5 1.0
MG A:MG302 3.5 65.6 1.0
N A:GLY97 4.0 27.8 1.0
OE2 A:GLU166 4.0 56.1 1.0
CA A:GLY97 4.0 28.9 1.0
OE2 A:GLU112 4.0 38.1 1.0
CA A:ALA96 4.1 23.4 1.0
O A:HOH441 4.1 31.0 1.0
N A:ALA96 4.1 22.6 1.0
NH2 A:ARG84 4.2 29.3 1.0
O A:HOH463 4.3 29.5 1.0
O A:HOH420 4.3 25.8 1.0
NE2 A:GLN82 4.4 30.4 1.0
O A:HOH458 4.4 36.2 1.0
CG A:GLU116 4.4 30.6 1.0
OE1 A:GLN82 4.5 29.5 1.0
CB A:ALA96 4.5 23.2 1.0
CD A:GLN82 4.8 34.0 1.0
CD A:GLU112 4.9 32.2 1.0
O A:HOH470 4.9 54.2 1.0

Magnesium binding site 2 out of 8 in 5qj8

Go back to Magnesium Binding Sites List in 5qj8
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 Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:65.6
occ:1.00
 O A:HOH405 2.0 44.9 1.0
OE2 A:GLU112 2.0 38.1 1.0
O A:HOH436 2.1 23.2 1.0
O A:HOH419 2.5 53.2 1.0
OE2 A:GLU166 2.6 56.1 1.0
OE2 A:GLU116 2.8 26.9 1.0
CD A:GLU112 2.9 32.2 1.0
OE1 A:GLU112 3.0 31.2 1.0
CD A:GLU166 3.3 65.4 1.0
OE1 A:GLU166 3.5 58.0 1.0
MG A:MG301 3.5 28.1 1.0
CD A:GLU116 3.7 31.9 1.0
CG A:GLU116 3.9 30.6 1.0
O A:ALA96 3.9 25.6 1.0
OE2 A:GLU115 4.0 36.1 1.0
O A:HOH423 4.0 28.5 1.0
O A:HOH458 4.1 36.2 1.0
CG A:GLU112 4.3 29.7 1.0
CG A:GLU166 4.5 60.9 1.0
CA A:GLY97 4.6 28.9 1.0
CB A:GLU112 4.8 27.6 1.0
OE1 A:GLU116 4.9 29.5 1.0
O A:HOH403 4.9 42.5 1.0
C A:ALA96 4.9 25.1 1.0

Magnesium binding site 3 out of 8 in 5qj8

Go back to Magnesium Binding Sites List in 5qj8
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 Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:34.5
occ:1.00
 O B:ALA96 2.0 32.9 1.0
O B:HOH422 2.0 40.1 1.0
OE2 B:GLU116 2.1 41.0 1.0
O B:HOH410 2.1 31.6 1.0
O B:HOH440 2.2 27.6 1.0
O B:HOH441 2.4 33.5 1.0
CD B:GLU116 3.1 40.6 1.0
C B:ALA96 3.2 28.1 1.0
OE1 B:GLU116 3.4 32.5 1.0
OE2 B:GLU166 4.0 61.8 1.0
MG B:MG304 4.0 71.6 1.0
N B:GLY97 4.1 31.0 1.0
N B:ALA96 4.1 27.5 1.0
O B:HOH427 4.1 32.5 1.0
CA B:ALA96 4.1 29.3 1.0
OE1 B:GLN82 4.1 40.5 1.0
CA B:GLY97 4.1 31.9 1.0
OE2 B:GLU112 4.2 44.0 1.0
NE2 B:GLN82 4.2 37.6 1.0
NH2 B:ARG84 4.4 29.7 1.0
CG B:GLU116 4.4 36.6 1.0
CB B:ALA96 4.5 31.3 1.0
O B:HOH463 4.6 38.7 1.0
CD B:GLN82 4.6 44.1 1.0
CD B:GLU166 5.0 78.1 1.0

Magnesium binding site 4 out of 8 in 5qj8

Go back to Magnesium Binding Sites List in 5qj8
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 Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:71.6
occ:1.00
 OE2 B:GLU112 1.7 44.0 1.0
O B:HOH458 2.4 46.5 1.0
O B:HOH405 2.6 64.0 1.0
OE2 B:GLU166 2.7 61.8 1.0
OE2 B:GLU116 2.8 41.0 1.0
CD B:GLU112 2.8 38.9 1.0
O B:HOH441 2.9 33.5 1.0
OE1 B:GLU112 3.2 38.2 1.0
CG B:GLU116 3.3 36.6 1.0
OE2 B:GLU115 3.4 55.1 1.0
CD B:GLU116 3.4 40.6 1.0
CD B:GLU166 3.6 78.1 1.0
OE1 B:GLU166 3.7 77.2 1.0
MG B:MG303 4.0 34.5 1.0
CG B:GLU112 4.1 36.4 1.0
O B:ALA96 4.1 32.9 1.0
CB B:GLU115 4.3 40.3 1.0
CB B:GLU112 4.4 36.8 1.0
CA B:GLU112 4.4 33.3 1.0
CD B:GLU115 4.5 51.0 1.0
O B:GLU112 4.5 32.9 1.0
OE1 B:GLU116 4.6 32.5 1.0
O B:HOH422 4.7 40.1 1.0
CB B:GLU116 4.8 34.6 1.0
C B:GLU112 4.9 29.6 1.0
C B:ALA96 5.0 28.1 1.0
CG B:GLU166 5.0 73.2 1.0
CG B:GLU115 5.0 46.6 1.0
N B:GLU116 5.0 38.0 1.0

Magnesium binding site 5 out of 8 in 5qj8

Go back to Magnesium Binding Sites List in 5qj8
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 Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:71.0
occ:1.00
 O C:HOH410 1.8 44.5 1.0
O C:HOH404 2.1 46.9 1.0
OE2 C:GLU166 2.3 62.5 1.0
OE2 C:GLU112 2.5 36.5 1.0
O C:HOH444 2.7 66.1 1.0
O C:HOH435 3.0 59.4 1.0
CD C:GLU166 3.2 65.8 1.0
CD C:GLU112 3.2 43.8 1.0
OE1 C:GLU112 3.2 52.6 1.0
OE2 C:GLU116 3.4 35.6 1.0
OE1 C:GLU166 3.5 58.6 1.0
MG C:MG303 3.7 35.0 1.0
O C:ALA96 4.0 31.5 1.0
O C:HOH403 4.1 39.7 1.0
CA C:GLY97 4.4 35.7 1.0
CD C:GLU116 4.4 33.3 1.0
OE2 C:GLU115 4.4 46.5 1.0
CG C:GLU166 4.5 59.7 1.0
O C:HOH460 4.5 64.6 1.0
O C:HOH442 4.7 30.0 1.0
CG C:GLU116 4.7 32.8 1.0
CG C:GLU112 4.7 39.5 1.0
C C:ALA96 4.9 35.8 1.0
N C:GLY97 5.0 34.5 1.0

Magnesium binding site 6 out of 8 in 5qj8

Go back to Magnesium Binding Sites List in 5qj8
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 Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:35.0
occ:1.00
 OE2 C:GLU116 1.9 35.6 1.0
O C:HOH442 2.0 30.0 1.0
O C:HOH410 2.0 44.5 1.0
O C:HOH416 2.1 31.1 1.0
O C:ALA96 2.1 31.5 1.0
O C:HOH403 2.2 39.7 1.0
CD C:GLU116 3.1 33.3 1.0
C C:ALA96 3.3 35.8 1.0
OE2 C:GLU166 3.3 62.5 1.0
OE1 C:GLU116 3.4 39.3 1.0
MG C:MG302 3.7 71.0 1.0
NH2 C:ARG84 4.2 35.4 1.0
N C:GLY97 4.2 34.5 1.0
CA C:ALA96 4.2 32.2 1.0
CA C:GLY97 4.2 35.7 1.0
N C:ALA96 4.2 30.2 1.0
OE1 C:GLN82 4.3 32.3 1.0
NE2 C:GLN82 4.3 40.6 1.0
CG C:GLU116 4.4 32.8 1.0
OE2 C:GLU112 4.5 36.5 1.0
CD C:GLU166 4.5 65.8 1.0
CB C:ALA96 4.5 31.5 1.0
CD C:GLN82 4.8 36.9 1.0
O C:HOH404 4.9 46.9 1.0
NH1 C:ARG84 5.0 34.3 1.0
CZ C:ARG84 5.0 38.3 1.0

Magnesium binding site 7 out of 8 in 5qj8

Go back to Magnesium Binding Sites List in 5qj8
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 Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:40.7
occ:1.00
 OE2 D:GLU116 2.0 51.8 1.0
O D:HOH411 2.1 31.3 1.0
O D:HOH415 2.1 33.3 1.0
MG D:MG302 2.2 46.8 1.0
O D:HOH427 2.7 45.7 1.0
O D:ALA96 3.1 45.4 1.0
CD D:GLU116 3.2 60.1 1.0
NE2 D:GLN82 3.5 48.9 1.0
OE1 D:GLU116 3.6 52.0 1.0
OE2 D:GLU112 3.8 63.7 1.0
OE2 D:GLU166 3.9 97.8 1.0
NH2 D:ARG84 4.0 45.5 1.0
OE1 D:GLN82 4.1 56.8 1.0
C D:ALA96 4.2 52.9 1.0
CD D:GLN82 4.3 55.0 1.0
CG D:GLU116 4.4 56.0 1.0
CD D:GLU166 4.7 88.0 1.0
N D:ALA96 4.8 50.6 1.0
O D:HOH406 4.8 61.2 1.0
NH1 D:ARG84 4.8 42.9 1.0
CD D:GLU112 4.9 60.7 1.0
CZ D:ARG84 4.9 48.0 1.0
CA D:GLY97 4.9 53.7 1.0
CA D:ALA96 5.0 52.1 1.0
O D:HOH409 5.0 43.9 1.0

Magnesium binding site 8 out of 8 in 5qj8

Go back to Magnesium Binding Sites List in 5qj8
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 Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:46.8
occ:1.00
 OE2 D:GLU112 2.1 63.7 1.0
O D:HOH427 2.2 45.7 1.0
MG D:MG301 2.2 40.7 1.0
O D:HOH415 2.7 33.3 1.0
O D:HOH409 2.8 43.9 1.0
OE2 D:GLU116 2.9 51.8 1.0
OE2 D:GLU166 3.0 97.8 1.0
O D:ALA96 3.1 45.4 1.0
CD D:GLU112 3.3 60.7 1.0
CA D:GLY97 3.6 53.7 1.0
O D:HOH406 3.8 61.2 1.0
CD D:GLU116 4.0 60.1 1.0
C D:ALA96 4.0 52.9 1.0
OE1 D:GLU112 4.1 61.4 1.0
O D:HOH411 4.1 31.3 1.0
CG D:GLU112 4.1 58.9 1.0
CD D:GLU166 4.1 88.0 1.0
N D:GLY97 4.3 49.3 1.0
OE1 D:GLU116 4.7 52.0 1.0
C D:GLY97 4.8 58.6 1.0
N D:LEU98 4.9 56.8 1.0
CG D:GLU166 4.9 79.5 1.0
OE1 D:GLU166 5.0 87.3 1.0
CG D:GLU116 5.0 56.0 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 02:11:14 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy