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Magnesium in PDB 5qjj: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z24758179

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z24758179

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 Z24758179:
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 Z24758179, PDB code: 5qjj 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 / 1.71
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.863, 59.604, 79.855, 79.70, 81.81, 76.08
R / Rfree (%) 21.5 / 24.7

Other elements in 5qjj:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z24758179 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 Z24758179 (pdb code 5qjj). 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 Z24758179, PDB code: 5qjj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjj

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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 Z24758179


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 Z24758179 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:29.4
occ:1.00
 OE2 A:GLU116 2.0 26.2 1.0
O A:HOH421 2.1 22.4 1.0
O A:ALA96 2.1 23.8 1.0
O A:HOH409 2.2 26.9 1.0
O A:HOH447 2.2 24.4 1.0
O A:HOH450 2.2 21.9 1.0
CD A:GLU116 3.1 25.4 1.0
MG A:MG302 3.1 59.6 1.0
C A:ALA96 3.2 20.0 1.0
OE1 A:GLU116 3.4 26.9 1.0
OE2 A:GLU166 4.0 69.5 1.0
N A:GLY97 4.2 23.3 1.0
OE2 A:GLU112 4.2 31.9 1.0
N A:ALA96 4.2 20.3 1.0
CA A:ALA96 4.2 19.6 1.0
NH2 A:ARG84 4.2 23.8 1.0
CA A:GLY97 4.2 24.2 1.0
NE2 A:GLN82 4.2 26.7 1.0
O A:HOH419 4.3 17.3 1.0
OE1 A:GLN82 4.3 25.4 1.0
O A:HOH463 4.4 29.4 1.0
CG A:GLU116 4.4 29.0 1.0
O A:HOH465 4.4 55.6 1.0
O A:HOH455 4.5 33.6 1.0
CD A:GLN82 4.7 32.2 1.0
CB A:ALA96 4.7 16.9 1.0
CD A:GLU112 4.9 30.6 1.0
O A:HOH405 5.0 43.5 1.0

Magnesium binding site 2 out of 8 in 5qjj

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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 Z24758179


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 Z24758179 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:59.6
occ:1.00
 O A:HOH447 2.0 24.4 1.0
O A:HOH405 2.0 43.5 1.0
OE2 A:GLU112 2.2 31.9 1.0
OE2 A:GLU116 2.4 26.2 1.0
OE2 A:GLU166 2.4 69.5 1.0
O A:HOH451 2.7 48.4 1.0
MG A:MG301 3.1 29.4 1.0
CD A:GLU166 3.2 79.0 1.0
CD A:GLU112 3.2 30.6 1.0
OE1 A:GLU166 3.3 77.5 1.0
CD A:GLU116 3.3 25.4 1.0
OE1 A:GLU112 3.4 35.4 1.0
CG A:GLU116 3.7 29.0 1.0
O A:ALA96 3.7 23.8 1.0
O A:HOH409 3.8 26.9 1.0
OE2 A:GLU115 4.3 34.4 1.0
O A:HOH455 4.3 33.6 1.0
O A:HOH465 4.4 55.6 1.0
OE1 A:GLU116 4.4 26.9 1.0
CG A:GLU166 4.5 73.1 1.0
CG A:GLU112 4.6 27.8 1.0
C A:ALA96 4.7 20.0 1.0
CA A:GLY97 4.7 24.2 1.0
O A:HOH450 4.8 21.9 1.0
O A:HOH421 4.8 22.4 1.0
CB A:GLU112 5.0 25.4 1.0

Magnesium binding site 3 out of 8 in 5qjj

Go back to Magnesium Binding Sites List in 5qjj
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 Z24758179


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 Z24758179 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:31.7
occ:1.00
 O B:ALA96 2.1 26.9 1.0
O B:HOH414 2.1 25.7 1.0
OE2 B:GLU116 2.1 34.4 1.0
O B:HOH413 2.1 28.4 1.0
O B:HOH448 2.2 24.5 1.0
O B:HOH443 2.2 30.4 1.0
CD B:GLU116 3.1 33.5 1.0
C B:ALA96 3.3 24.6 1.0
OE1 B:GLU116 3.4 34.0 1.0
MG B:MG303 3.9 73.2 1.0
OE2 B:GLU166 4.0 67.9 1.0
N B:GLY97 4.1 25.9 1.0
O B:HOH420 4.1 30.8 1.0
CA B:GLY97 4.1 27.0 1.0
N B:ALA96 4.2 24.2 1.0
CA B:ALA96 4.2 25.3 1.0
NH2 B:ARG84 4.2 25.6 1.0
OE2 B:GLU112 4.3 39.8 1.0
NE2 B:GLN82 4.3 33.5 1.0
OE1 B:GLN82 4.3 37.5 1.0
CG B:GLU116 4.5 31.9 1.0
O B:HOH464 4.5 33.2 1.0
CB B:ALA96 4.6 24.5 1.0
CD B:GLN82 4.7 38.5 1.0
CD B:GLU166 4.8 78.5 1.0

Magnesium binding site 4 out of 8 in 5qjj

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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 Z24758179


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 Z24758179 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:73.2
occ:1.00
 O B:HOH416 1.9 61.0 1.0
OE2 B:GLU112 2.1 39.8 1.0
OE2 B:GLU166 2.5 67.9 1.0
O B:HOH437 2.7 43.0 1.0
OE2 B:GLU116 2.7 34.4 1.0
O B:HOH443 2.8 30.4 1.0
CD B:GLU112 3.1 33.8 1.0
OE1 B:GLU166 3.2 77.6 1.0
CD B:GLU166 3.2 78.5 1.0
OE1 B:GLU112 3.4 36.6 1.0
CG B:GLU116 3.4 31.9 1.0
CD B:GLU116 3.4 33.5 1.0
OE2 B:GLU115 3.5 51.6 1.0
MG B:MG302 3.9 31.7 1.0
O B:ALA96 4.2 26.9 1.0
CG B:GLU112 4.5 31.2 1.0
CB B:GLU115 4.5 38.6 1.0
O B:HOH413 4.5 28.4 1.0
OE1 B:GLU116 4.6 34.0 1.0
CG B:GLU166 4.7 74.4 1.0
CD B:GLU115 4.7 47.5 1.0
CB B:GLU112 4.9 31.2 1.0
CA B:GLU112 4.9 28.7 1.0
CB B:GLU116 4.9 32.6 1.0
O B:GLU112 5.0 28.9 1.0

Magnesium binding site 5 out of 8 in 5qjj

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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 Z24758179


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 Z24758179 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:46.8
occ:1.00
 MG C:MG303 2.1 31.2 1.0
O C:HOH421 2.2 78.0 1.0
OE2 C:GLU116 2.7 30.1 1.0
O C:ALA96 2.8 25.2 1.0
OE2 C:GLU166 2.9 65.8 1.0
O C:HOH457 2.9 25.6 1.0
O C:HOH415 3.0 30.2 1.0
OE2 C:GLU112 3.1 35.5 1.0
O C:HOH454 3.2 44.6 1.0
CA C:GLY97 3.5 32.6 1.0
C C:ALA96 3.8 26.9 1.0
O C:HOH404 3.9 49.5 1.0
CD C:GLU112 3.9 41.7 1.0
CD C:GLU116 3.9 29.3 1.0
CD C:GLU166 4.0 69.4 1.0
OE1 C:GLU112 4.1 49.6 1.0
N C:GLY97 4.1 27.6 1.0
O C:HOH416 4.1 23.9 1.0
O C:HOH471 4.2 49.3 1.0
O C:HOH441 4.4 62.5 1.0
OE1 C:GLU116 4.7 37.1 1.0
CG C:GLU116 4.8 27.9 1.0
OE1 C:GLU166 4.8 74.8 1.0
C C:GLY97 4.9 31.2 1.0
O C:HOH460 4.9 41.0 1.0
CG C:GLU166 4.9 61.8 1.0
O C:HOH466 5.0 33.5 1.0

Magnesium binding site 6 out of 8 in 5qjj

Go back to Magnesium Binding Sites List in 5qjj
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 Z24758179


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 Z24758179 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:31.2
occ:1.00
 O C:HOH457 2.0 25.6 1.0
OE2 C:GLU116 2.0 30.1 1.0
O C:HOH416 2.1 23.9 1.0
MG C:MG302 2.1 46.8 1.0
O C:HOH415 2.1 30.2 1.0
O C:ALA96 2.2 25.2 1.0
CD C:GLU116 3.1 29.3 1.0
C C:ALA96 3.4 26.9 1.0
OE1 C:GLU116 3.4 37.1 1.0
OE2 C:GLU166 3.7 65.8 1.0
O C:HOH421 4.2 78.0 1.0
O C:HOH420 4.2 34.0 1.0
NE2 C:GLN82 4.2 37.5 1.0
N C:ALA96 4.2 22.9 1.0
N C:GLY97 4.2 27.6 1.0
CA C:ALA96 4.2 23.7 1.0
OE1 C:GLN82 4.2 35.2 1.0
NH2 C:ARG84 4.3 30.2 1.0
CA C:GLY97 4.3 32.6 1.0
OE2 C:GLU112 4.3 35.5 1.0
CG C:GLU116 4.4 27.9 1.0
CB C:ALA96 4.6 22.5 1.0
CD C:GLN82 4.6 43.0 1.0
O C:HOH466 4.7 33.5 1.0
O C:HOH454 4.7 44.6 1.0
O C:HOH460 4.9 41.0 1.0
CD C:GLU166 4.9 69.4 1.0

Magnesium binding site 7 out of 8 in 5qjj

Go back to Magnesium Binding Sites List in 5qjj
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 Z24758179


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 Z24758179 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:35.7
occ:1.00
 O D:HOH418 1.8 27.2 0.9
O D:HOH414 2.0 26.0 1.0
OE2 D:GLU116 2.0 33.2 1.0
O D:HOH411 2.2 29.7 1.0
O D:ALA96 2.2 29.8 1.0
MG D:MG302 2.2 39.6 1.0
O D:HOH435 2.7 60.0 1.0
CD D:GLU116 3.1 39.0 1.0
C D:ALA96 3.4 31.4 1.0
OE1 D:GLU116 3.5 34.4 1.0
OE2 D:GLU166 3.8 86.8 1.0
OE2 D:GLU112 4.1 56.1 1.0
NH2 D:ARG84 4.2 33.2 1.0
N D:GLY97 4.3 31.2 1.0
CA D:GLY97 4.3 33.0 1.0
N D:ALA96 4.3 30.1 1.0
NE2 D:GLN82 4.3 42.0 1.0
CA D:ALA96 4.4 32.1 1.0
OE1 D:GLN82 4.4 37.0 1.0
CG D:GLU116 4.4 35.8 1.0
O D:HOH408 4.5 25.8 0.9
O D:HOH422 4.5 33.0 0.9
O D:HOH431 4.6 34.5 0.9
O D:HOH405 4.6 53.2 1.0
CD D:GLU112 4.7 54.6 1.0
O D:HOH426 4.7 35.0 0.9
CB D:ALA96 4.8 31.3 1.0
CD D:GLN82 4.8 41.9 1.0
CG D:GLU112 4.8 56.9 1.0
CD D:GLU166 4.9 85.7 1.0
O D:HOH403 5.0 47.6 1.0

Magnesium binding site 8 out of 8 in 5qjj

Go back to Magnesium Binding Sites List in 5qjj
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 Z24758179


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 Z24758179 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:39.6
occ:1.00
 MG D:MG301 2.2 35.7 1.0
O D:HOH435 2.3 60.0 1.0
O D:HOH405 2.6 53.2 1.0
OE2 D:GLU112 2.6 56.1 1.0
OE2 D:GLU166 2.6 86.8 1.0
OE2 D:GLU116 2.7 33.2 1.0
O D:HOH418 3.0 27.2 0.9
O D:ALA96 3.0 29.8 1.0
O D:HOH414 3.3 26.0 1.0
CD D:GLU112 3.3 54.6 1.0
O D:HOH426 3.3 35.0 0.9
CA D:GLY97 3.6 33.0 1.0
O D:HOH403 3.7 47.6 1.0
CD D:GLU116 3.9 39.0 1.0
OE1 D:GLU112 3.9 48.9 1.0
CD D:GLU166 3.9 85.7 1.0
C D:ALA96 4.0 31.4 1.0
CG D:GLU112 4.1 56.9 1.0
N D:GLY97 4.2 31.2 1.0
O D:HOH411 4.3 29.7 1.0
CG D:GLU116 4.6 35.8 1.0
OE1 D:GLU166 4.7 77.5 1.0
OE1 D:GLU116 4.7 34.4 1.0
C D:GLY97 4.8 34.8 1.0
O D:HOH422 4.9 33.0 0.9
CG D:GLU166 4.9 79.4 1.0
N D:LEU98 5.0 38.0 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 02:17:12 2024

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