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

Magnesium in PDB 5qjr: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z220816104

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z220816104

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 Z220816104:
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 Z220816104, PDB code: 5qjr 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) 78.08 / 1.62
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.540, 60.030, 79.990, 79.25, 81.06, 75.33
R / Rfree (%) 24.2 / 27.7

Other elements in 5qjr:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z220816104 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 Z220816104 (pdb code 5qjr). 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 Z220816104, PDB code: 5qjr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjr

Go back to Magnesium Binding Sites List in 5qjr
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 Z220816104


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 Z220816104 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:26.1
occ:1.00
 OE2 A:GLU116 2.0 23.4 1.0
O A:HOH416 2.0 22.7 1.0
O A:HOH438 2.0 22.1 1.0
O A:ALA96 2.1 22.8 1.0
O A:HOH456 2.1 20.8 1.0
O A:HOH422 2.2 25.2 1.0
CD A:GLU116 3.0 26.5 1.0
C A:ALA96 3.3 22.8 1.0
OE1 A:GLU116 3.4 25.7 1.0
MG A:MG302 3.4 60.0 1.0
OE2 A:GLU166 3.9 61.6 1.0
O A:HOH436 4.1 21.8 0.7
CA A:GLY97 4.1 24.9 1.0
N A:GLY97 4.1 22.8 1.0
OE2 A:GLU112 4.1 36.4 1.0
N A:ALA96 4.2 18.7 1.0
CA A:ALA96 4.2 20.8 1.0
NH2 A:ARG84 4.3 26.1 1.0
O A:HOH421 4.3 23.2 1.0
NE2 A:GLN82 4.3 28.6 1.0
CG A:GLU116 4.4 26.1 1.0
O A:HOH468 4.4 26.8 1.0
OE1 A:GLN82 4.5 26.1 1.0
O A:HOH460 4.6 30.2 1.0
CB A:ALA96 4.7 19.2 1.0
CD A:GLN82 4.7 30.8 1.0
O A:HOH473 4.9 52.6 1.0
CD A:GLU112 4.9 31.2 1.0

Magnesium binding site 2 out of 8 in 5qjr

Go back to Magnesium Binding Sites List in 5qjr
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 Z220816104


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 Z220816104 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:60.0
occ:1.00
 O A:HOH406 1.9 45.9 1.0
OE2 A:GLU112 2.0 36.4 1.0
O A:HOH438 2.1 22.1 1.0
OE2 A:GLU166 2.5 61.6 1.0
OE2 A:GLU116 2.7 23.4 1.0
O A:HOH417 2.7 44.8 1.0
CD A:GLU112 2.9 31.2 1.0
OE1 A:GLU112 3.2 32.4 1.0
CD A:GLU166 3.2 67.4 1.0
OE1 A:GLU166 3.4 60.8 1.0
MG A:MG301 3.4 26.1 1.0
CD A:GLU116 3.6 26.5 1.0
CG A:GLU116 3.7 26.1 1.0
OE2 A:GLU115 4.0 34.1 1.0
O A:ALA96 4.1 22.8 1.0
O A:HOH422 4.1 25.2 1.0
CG A:GLU112 4.4 28.9 1.0
O A:HOH460 4.5 30.2 1.0
CG A:GLU166 4.5 63.0 1.0
OE1 A:GLU116 4.7 25.7 1.0
CA A:GLY97 4.7 24.9 1.0
CB A:GLU112 4.8 27.3 1.0
C A:ALA96 4.9 22.8 1.0

Magnesium binding site 3 out of 8 in 5qjr

Go back to Magnesium Binding Sites List in 5qjr
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 Z220816104


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 Z220816104 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:27.3
occ:1.00
 O B:HOH440 2.0 31.3 1.0
O B:ALA96 2.0 28.1 1.0
O B:HOH413 2.0 31.2 1.0
O B:HOH435 2.1 26.3 1.0
OE2 B:GLU116 2.1 37.1 1.0
O B:HOH436 2.1 28.4 1.0
CD B:GLU116 3.1 36.6 1.0
C B:ALA96 3.2 24.9 1.0
OE1 B:GLU116 3.4 31.7 1.0
MG B:MG304 4.0 73.2 1.0
OE2 B:GLU166 4.0 57.8 1.0
N B:GLY97 4.1 27.6 1.0
CA B:ALA96 4.2 25.8 1.0
OE2 B:GLU112 4.2 39.1 1.0
N B:ALA96 4.2 25.4 1.0
CA B:GLY97 4.2 27.9 1.0
O B:HOH437 4.2 28.5 1.0
NH2 B:ARG84 4.3 29.8 1.0
NE2 B:GLN82 4.4 36.6 1.0
OE1 B:GLN82 4.4 37.0 1.0
O B:HOH466 4.4 44.7 1.0
CG B:GLU116 4.5 33.0 1.0
CD B:GLU166 4.6 69.3 1.0
CB B:ALA96 4.6 28.5 1.0
CD B:GLN82 4.8 40.9 1.0
OE1 B:GLU166 4.9 70.2 1.0
O B:HOH410 5.0 48.8 1.0

Magnesium binding site 4 out of 8 in 5qjr

Go back to Magnesium Binding Sites List in 5qjr
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 Z220816104


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 Z220816104 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:73.2
occ:1.00
 OE2 B:GLU112 2.0 39.1 1.0
O B:HOH410 2.4 48.8 1.0
OE2 B:GLU166 2.7 57.8 1.0
OE2 B:GLU116 2.8 37.1 1.0
O B:HOH420 2.9 66.4 1.0
O B:HOH436 3.0 28.4 1.0
CD B:GLU112 3.1 38.2 1.0
OE1 B:GLU166 3.2 70.2 1.0
OE2 B:GLU115 3.3 51.8 1.0
CG B:GLU116 3.3 33.0 1.0
CD B:GLU166 3.4 69.3 1.0
CD B:GLU116 3.4 36.6 1.0
OE1 B:GLU112 3.5 37.0 1.0
MG B:MG303 4.0 27.3 1.0
CB B:GLU115 4.3 34.8 1.0
O B:ALA96 4.3 28.1 1.0
CG B:GLU112 4.4 35.7 1.0
CD B:GLU115 4.4 43.8 1.0
CB B:GLU112 4.6 35.8 1.0
OE1 B:GLU116 4.6 31.7 1.0
O B:GLU112 4.6 29.2 1.0
CA B:GLU112 4.6 33.2 1.0
O B:HOH440 4.6 31.3 1.0
CB B:GLU116 4.8 30.3 1.0
CG B:GLU166 4.9 64.6 1.0

Magnesium binding site 5 out of 8 in 5qjr

Go back to Magnesium Binding Sites List in 5qjr
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 Z220816104


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 Z220816104 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:59.0
occ:1.00
 MG C:MG303 2.3 35.2 1.0
OE2 C:GLU166 2.6 70.5 1.0
OE2 C:GLU116 2.8 32.0 1.0
O C:ALA96 2.9 28.0 1.0
O C:HOH442 3.0 45.8 1.0
OE2 C:GLU112 3.0 35.9 1.0
O C:HOH427 3.1 35.1 1.0
O C:HOH445 3.2 28.5 1.0
O C:HOH409 3.4 52.4 1.0
CA C:GLY97 3.6 33.8 1.0
O C:HOH404 3.7 52.2 1.0
CD C:GLU166 3.7 71.3 1.0
CD C:GLU112 3.8 37.4 1.0
OE1 C:GLU112 3.9 45.5 1.0
C C:ALA96 3.9 31.6 1.0
CD C:GLU116 4.0 31.7 1.0
N C:GLY97 4.2 33.3 1.0
O C:HOH425 4.2 25.1 1.0
OE1 C:GLU166 4.4 74.5 1.0
CG C:GLU166 4.7 65.3 1.0
C C:GLY97 4.8 35.4 1.0
OE1 C:GLU116 4.8 33.8 1.0
CG C:GLU116 4.9 30.1 1.0
CG C:GLU112 5.0 33.4 1.0
N C:LEU98 5.0 39.7 1.0

Magnesium binding site 6 out of 8 in 5qjr

Go back to Magnesium Binding Sites List in 5qjr
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 Z220816104


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 Z220816104 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:35.2
occ:1.00
 O C:HOH445 2.0 28.5 1.0
O C:HOH425 2.0 25.1 1.0
OE2 C:GLU116 2.1 32.0 1.0
O C:ALA96 2.1 28.0 1.0
O C:HOH427 2.2 35.1 1.0
MG C:MG302 2.3 59.0 1.0
CD C:GLU116 3.2 31.7 1.0
C C:ALA96 3.2 31.6 1.0
OE1 C:GLU116 3.5 33.8 1.0
OE2 C:GLU166 3.7 70.5 1.0
N C:GLY97 4.1 33.3 1.0
CA C:GLY97 4.1 33.8 1.0
NH2 C:ARG84 4.1 30.3 1.0
N C:ALA96 4.2 24.9 1.0
CA C:ALA96 4.2 26.2 1.0
OE2 C:GLU112 4.3 35.9 1.0
NE2 C:GLN82 4.3 33.4 1.0
OE1 C:GLN82 4.4 33.3 1.0
O C:HOH460 4.5 42.1 1.0
O C:HOH442 4.5 45.8 1.0
CG C:GLU116 4.5 30.1 1.0
CB C:ALA96 4.6 24.8 1.0
O C:HOH409 4.8 52.4 1.0
CD C:GLN82 4.8 36.8 1.0
CD C:GLU166 4.9 71.3 1.0

Magnesium binding site 7 out of 8 in 5qjr

Go back to Magnesium Binding Sites List in 5qjr
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 Z220816104


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 Z220816104 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:38.8
occ:1.00
 OE2 D:GLU116 1.9 43.9 1.0
O D:HOH404 2.1 32.0 1.0
O D:HOH418 2.1 27.2 1.0
MG D:MG302 2.3 40.6 1.0
O D:HOH423 2.4 36.9 1.0
O D:ALA96 2.8 39.4 1.0
CD D:GLU116 3.0 53.7 1.0
OE1 D:GLU116 3.5 50.3 1.0
OE2 D:GLU166 3.8 78.6 1.0
OE2 D:GLU112 3.8 51.7 1.0
C D:ALA96 3.8 46.0 1.0
NE2 D:GLN82 3.9 42.8 1.0
NH2 D:ARG84 4.1 44.7 1.0
OE1 D:GLN82 4.2 46.5 1.0
O D:HOH402 4.3 49.7 1.0
CG D:GLU116 4.3 50.8 1.0
N D:ALA96 4.5 44.8 1.0
CD D:GLN82 4.5 45.8 1.0
CA D:GLY97 4.5 45.2 1.0
N D:GLY97 4.6 45.2 1.0
CA D:ALA96 4.7 47.2 1.0
O D:HOH401 4.8 37.6 1.0
CD D:GLU112 4.8 54.1 1.0
CD D:GLU166 4.9 78.7 1.0
CG D:GLU112 5.0 53.7 1.0

Magnesium binding site 8 out of 8 in 5qjr

Go back to Magnesium Binding Sites List in 5qjr
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 Z220816104


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 Z220816104 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:40.6
occ:1.00
 O D:HOH423 1.7 36.9 1.0
OE2 D:GLU112 2.0 51.7 1.0
MG D:MG301 2.3 38.8 1.0
O D:HOH401 2.5 37.6 1.0
OE2 D:GLU116 2.9 43.9 1.0
O D:ALA96 2.9 39.4 1.0
OE2 D:GLU166 3.0 78.6 1.0
O D:HOH402 3.1 49.7 1.0
O D:HOH418 3.1 27.2 1.0
CD D:GLU112 3.1 54.1 1.0
CA D:GLY97 3.4 45.2 1.0
C D:ALA96 3.9 46.0 1.0
OE1 D:GLU112 4.0 56.8 1.0
CD D:GLU116 4.0 53.7 1.0
CG D:GLU112 4.0 53.7 1.0
N D:GLY97 4.1 45.2 1.0
O D:HOH404 4.2 32.0 1.0
CD D:GLU166 4.3 78.7 1.0
C D:GLY97 4.7 44.8 1.0
OE1 D:GLU116 4.7 50.3 1.0
CG D:GLU116 4.8 50.8 1.0
N D:LEU98 4.9 43.6 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 Dec 14 21:07:15 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy