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

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

Go back to Magnesium Binding Sites List in 5qjd
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

Go back to Magnesium Binding Sites List in 5qjd
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

Go back to Magnesium Binding Sites List in 5qjd
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

Go back to Magnesium Binding Sites List in 5qjd
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

Go back to Magnesium Binding Sites List in 5qjd
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

Go back to Magnesium Binding Sites List in 5qjd
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy