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Magnesium in PDB 5qjl: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z56983806

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z56983806

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 Z56983806:
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 Z56983806, PDB code: 5qjl 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) 78.29 / 1.66
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.890, 59.510, 79.980, 79.68, 82.07, 76.20
R / Rfree (%) 20.8 / 24.1

Other elements in 5qjl:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z56983806 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 Z56983806 (pdb code 5qjl). 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 Z56983806, PDB code: 5qjl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjl

Go back to Magnesium Binding Sites List in 5qjl
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 Z56983806


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 Z56983806 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:27.9
occ:1.00
 OE2 A:GLU116 2.0 26.4 1.0
O A:ALA96 2.1 22.3 1.0
O A:HOH450 2.1 22.6 1.0
O A:HOH458 2.2 21.4 1.0
O A:HOH418 2.2 25.3 1.0
O A:HOH419 2.3 27.1 1.0
CD A:GLU116 3.1 27.4 1.0
MG A:MG302 3.2 63.0 1.0
C A:ALA96 3.2 23.7 1.0
OE1 A:GLU116 3.4 26.4 1.0
OE2 A:GLU112 4.0 32.6 1.0
CA A:GLY97 4.0 22.3 1.0
N A:GLY97 4.1 22.8 1.0
N A:ALA96 4.2 20.2 1.0
CA A:ALA96 4.2 20.2 1.0
O A:HOH436 4.3 27.9 0.8
OE2 A:GLU166 4.3 74.7 0.8
NH2 A:ARG84 4.3 24.3 1.0
NE2 A:GLN82 4.4 28.0 1.0
O A:HOH413 4.4 20.8 1.0
CG A:GLU116 4.4 24.8 1.0
OE1 A:GLN82 4.4 27.8 1.0
O A:HOH471 4.5 27.6 1.0
O A:HOH457 4.5 49.5 1.0
O A:HOH464 4.7 35.0 1.0
CB A:ALA96 4.7 19.0 1.0
CD A:GLU112 4.7 31.5 1.0
CD A:GLN82 4.8 33.3 1.0

Magnesium binding site 2 out of 8 in 5qjl

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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 Z56983806


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 Z56983806 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:63.0
occ:1.00
 O A:HOH414 2.0 42.0 1.0
O A:HOH450 2.0 22.6 1.0
OE2 A:GLU112 2.2 32.6 1.0
OE2 A:GLU116 2.5 26.4 1.0
O A:HOH410 2.5 48.6 1.0
OE2 A:GLU166 2.5 74.7 0.8
CD A:GLU112 3.2 31.5 1.0
MG A:MG301 3.2 27.9 1.0
OE1 A:GLU112 3.3 34.1 1.0
CD A:GLU116 3.4 27.4 1.0
CD A:GLU166 3.4 69.8 0.8
OE1 A:GLU166 3.6 71.1 0.8
CG A:GLU116 3.7 24.8 1.0
O A:HOH419 3.8 27.1 1.0
O A:ALA96 3.9 22.3 1.0
OE2 A:GLU115 4.3 34.2 1.0
O A:HOH464 4.5 35.0 1.0
OE1 A:GLU116 4.5 26.4 1.0
CG A:GLU112 4.6 30.3 1.0
O A:HOH457 4.7 49.5 1.0
CA A:GLY97 4.8 22.3 1.0
CG A:GLU166 4.8 66.5 0.8
O A:HOH458 4.9 21.4 1.0
C A:ALA96 4.9 23.7 1.0
O A:HOH418 5.0 25.3 1.0

Magnesium binding site 3 out of 8 in 5qjl

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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 Z56983806


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 Z56983806 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:31.1
occ:1.00
 OE2 B:GLU116 2.0 34.8 1.0
O B:HOH433 2.0 29.9 1.0
O B:ALA96 2.1 28.2 1.0
O B:HOH412 2.1 29.1 1.0
O B:HOH443 2.2 27.4 1.0
O B:HOH458 2.2 30.2 1.0
CD B:GLU116 3.0 34.8 1.0
C B:ALA96 3.3 23.3 1.0
OE1 B:GLU116 3.4 33.4 1.0
OE2 B:GLU166 3.8 53.7 1.0
MG B:MG303 4.1 99.7 1.0
CA B:GLY97 4.2 26.4 1.0
N B:GLY97 4.2 27.1 1.0
OE2 B:GLU112 4.2 38.9 1.0
N B:ALA96 4.2 26.5 1.0
NH2 B:ARG84 4.3 28.3 1.0
O B:HOH425 4.3 28.7 1.0
NE2 B:GLN82 4.3 34.5 1.0
CA B:ALA96 4.3 28.3 1.0
CG B:GLU116 4.4 34.4 1.0
O B:HOH446 4.4 36.6 0.8
OE1 B:GLN82 4.4 36.0 1.0
CD B:GLU166 4.5 77.7 1.0
O B:HOH469 4.5 35.8 0.8
CD B:GLN82 4.7 43.8 1.0
O B:HOH473 4.8 35.2 1.0
CB B:ALA96 4.8 29.0 1.0

Magnesium binding site 4 out of 8 in 5qjl

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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 Z56983806


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 Z56983806 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:99.7
occ:1.00
 O B:HOH414 1.6 53.3 1.0
O B:HOH426 2.1 54.5 1.0
OE2 B:GLU112 2.3 38.9 1.0
OE2 B:GLU166 2.6 53.7 1.0
O B:HOH458 2.6 30.2 1.0
OE1 B:GLU166 2.9 79.2 1.0
CD B:GLU112 3.1 38.9 1.0
CD B:GLU166 3.1 77.7 1.0
OE1 B:GLU112 3.2 41.5 1.0
OE2 B:GLU116 3.4 34.8 1.0
OE2 B:GLU115 3.5 48.2 1.0
MG B:MG302 4.1 31.1 1.0
O B:HOH469 4.1 35.8 0.8
CD B:GLU116 4.1 34.8 1.0
CG B:GLU116 4.1 34.4 1.0
O B:ALA96 4.6 28.2 1.0
CG B:GLU112 4.6 35.0 1.0
O B:HOH433 4.6 29.9 1.0
CG B:GLU166 4.6 72.2 1.0
CD B:GLU115 4.7 45.5 1.0
CB B:GLU115 4.9 36.9 1.0
NH1 B:ARG111 4.9 36.6 1.0

Magnesium binding site 5 out of 8 in 5qjl

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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 Z56983806


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 Z56983806 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:39.7
occ:1.00
 MG C:MG303 2.1 31.2 1.0
OE2 C:GLU116 2.8 32.0 1.0
OE2 C:GLU166 2.8 58.9 1.0
O C:HOH465 2.9 43.8 1.0
O C:HOH423 2.9 30.8 1.0
O C:HOH452 3.0 24.5 1.0
O C:ALA96 3.1 26.7 1.0
OE2 C:GLU112 3.1 33.2 1.0
O C:HOH441 3.2 45.8 1.0
O C:HOH409 3.6 45.4 1.0
CA C:GLY97 3.7 31.4 1.0
CD C:GLU112 3.7 36.2 1.0
OE1 C:GLU112 3.7 49.3 1.0
CD C:GLU166 3.9 72.6 1.0
O C:HOH473 4.0 51.9 1.0
CD C:GLU116 4.0 28.9 1.0
C C:ALA96 4.0 28.5 1.0
O C:HOH444 4.3 28.8 1.0
N C:GLY97 4.4 27.4 1.0
O C:HOH461 4.5 39.1 1.0
OE1 C:GLU166 4.7 72.4 1.0
OE1 C:GLU116 4.8 32.8 1.0
CG C:GLU116 4.9 27.4 1.0
CG C:GLU166 4.9 64.5 1.0
C C:GLY97 4.9 32.6 1.0
CG C:GLU112 5.0 30.0 1.0

Magnesium binding site 6 out of 8 in 5qjl

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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 Z56983806


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 Z56983806 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:31.2
occ:1.00
 O C:HOH452 1.9 24.5 1.0
OE2 C:GLU116 2.0 32.0 1.0
O C:ALA96 2.1 26.7 1.0
MG C:MG302 2.1 39.7 1.0
O C:HOH444 2.2 28.8 1.0
O C:HOH423 2.2 30.8 1.0
CD C:GLU116 3.1 28.9 1.0
C C:ALA96 3.3 28.5 1.0
OE1 C:GLU116 3.4 32.8 1.0
OE2 C:GLU166 3.7 58.9 1.0
OE2 C:GLU112 4.0 33.2 1.0
CA C:GLY97 4.1 31.4 1.0
N C:GLY97 4.1 27.4 1.0
N C:ALA96 4.2 25.0 1.0
CA C:ALA96 4.2 23.1 1.0
O C:HOH419 4.3 29.5 1.0
NE2 C:GLN82 4.4 34.7 1.0
CG C:GLU116 4.4 27.4 1.0
NH2 C:ARG84 4.4 32.1 1.0
OE1 C:GLN82 4.5 31.8 1.0
O C:HOH461 4.5 39.1 1.0
O C:HOH475 4.6 27.9 0.8
O C:HOH465 4.6 43.8 1.0
CB C:ALA96 4.6 24.0 1.0
O C:HOH409 4.7 45.4 1.0
CD C:GLU112 4.8 36.2 1.0
CD C:GLN82 4.9 42.0 1.0
CD C:GLU166 4.9 72.6 1.0

Magnesium binding site 7 out of 8 in 5qjl

Go back to Magnesium Binding Sites List in 5qjl
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 Z56983806


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 Z56983806 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:28.4
occ:1.00
 O D:HOH424 1.9 26.5 0.8
O D:ALA96 2.0 26.9 1.0
OE2 D:GLU116 2.0 28.5 1.0
O D:HOH420 2.0 27.2 1.0
O D:HOH432 2.0 29.2 1.0
MG D:MG302 2.1 40.9 1.0
CD D:GLU116 3.0 38.8 1.0
C D:ALA96 3.2 28.7 1.0
OE1 D:GLU116 3.4 32.7 1.0
OE2 D:GLU112 3.9 57.0 1.0
CA D:GLY97 4.0 27.6 1.0
N D:GLY97 4.1 27.6 1.0
N D:ALA96 4.1 28.9 1.0
CA D:ALA96 4.1 26.9 1.0
NH2 D:ARG84 4.3 29.1 1.0
O D:HOH411 4.3 25.4 0.8
O D:HOH440 4.4 30.9 0.8
CG D:GLU116 4.4 33.1 1.0
NE2 D:GLN82 4.4 34.3 1.0
OE1 D:GLN82 4.4 32.2 1.0
O D:HOH446 4.5 27.4 0.8
OE2 D:GLU166 4.6 52.9 0.8
CD D:GLU112 4.6 54.2 1.0
CB D:ALA96 4.6 29.3 1.0
CG D:GLU112 4.7 57.3 1.0
O D:HOH406 4.7 45.4 0.8
O D:HOH402 4.8 52.7 1.0
O D:HOH438 4.8 31.0 0.8
CD D:GLN82 4.9 35.8 1.0

Magnesium binding site 8 out of 8 in 5qjl

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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 Z56983806


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 Z56983806 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:40.9
occ:1.00
 MG D:MG301 2.1 28.4 1.0
O D:HOH424 2.7 26.5 0.8
OE2 D:GLU112 2.7 57.0 1.0
OE2 D:GLU116 2.8 28.5 1.0
O D:ALA96 3.0 26.9 1.0
O D:HOH420 3.1 27.2 1.0
O D:HOH438 3.2 31.0 0.8
OE2 D:GLU166 3.3 52.9 0.8
O D:HOH422 3.4 50.9 1.0
CD D:GLU112 3.5 54.2 1.0
CA D:GLY97 3.5 27.6 1.0
O D:HOH402 3.7 52.7 1.0
C D:ALA96 3.9 28.7 1.0
OE1 D:GLU112 4.0 51.3 1.0
CD D:GLU116 4.0 38.8 1.0
O D:HOH406 4.1 45.4 0.8
O D:HOH432 4.2 29.2 1.0
CG D:GLU112 4.2 57.3 1.0
N D:GLY97 4.2 27.6 1.0
CD D:GLU166 4.4 57.9 0.8
O D:HOH440 4.4 30.9 0.8
O C:HOH424 4.6 41.6 0.8
C D:GLY97 4.8 30.7 1.0
OE1 D:GLU116 4.8 32.7 1.0
O D:HOH446 4.8 27.4 0.8
CG D:GLU116 4.9 33.1 1.0
N D:LEU98 4.9 32.2 1.0
OE1 D:GLU166 5.0 63.1 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 02:19:06 2024

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