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Magnesium in PDB 5qk8: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1271660837

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1271660837

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 Z1271660837:
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 Z1271660837, PDB code: 5qk8 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) 78.20 / 1.71
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.270, 59.910, 80.011, 79.55, 81.38, 75.74
R / Rfree (%) 22.5 / 26

Other elements in 5qk8:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1271660837 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 Z1271660837 (pdb code 5qk8). 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 Z1271660837, PDB code: 5qk8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qk8

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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 Z1271660837


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 Z1271660837 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:27.9
occ:1.00
 O A:HOH448 2.0 24.7 1.0
OE2 A:GLU116 2.1 24.3 1.0
O A:ALA96 2.1 21.3 1.0
O A:HOH412 2.1 28.7 1.0
O A:HOH455 2.2 20.8 1.0
O A:HOH427 2.2 25.6 1.0
CD A:GLU116 3.1 23.7 1.0
MG A:MG302 3.2 38.4 1.0
C A:ALA96 3.3 23.0 1.0
OE1 A:GLU116 3.4 25.9 1.0
OE2 A:GLU166 3.6 42.8 1.0
OE2 A:GLU112 4.0 28.8 1.0
CA A:GLY97 4.1 22.0 1.0
N A:GLY97 4.1 21.9 1.0
O A:HOH445 4.2 31.0 1.0
N A:ALA96 4.2 17.8 1.0
CA A:ALA96 4.2 19.8 1.0
NH2 A:ARG84 4.3 25.3 1.0
NE2 A:GLN82 4.3 27.9 1.0
O A:HOH465 4.4 28.4 1.0
O A:HOH406 4.4 21.3 1.0
CG A:GLU116 4.4 24.9 1.0
O A:HOH460 4.4 39.2 1.0
OE1 A:GLN82 4.5 26.4 1.0
CB A:ALA96 4.7 18.5 1.0
O A:HOH469 4.8 47.8 1.0
CD A:GLN82 4.8 31.2 1.0
O A:HOH411 4.9 36.0 1.0
CD A:GLU166 4.9 51.0 1.0
CD A:GLU112 4.9 27.2 1.0

Magnesium binding site 2 out of 8 in 5qk8

Go back to Magnesium Binding Sites List in 5qk8
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 Z1271660837


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 Z1271660837 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:38.4
occ:1.00
 O A:HOH407 2.0 32.2 1.0
OE2 A:GLU112 2.1 28.8 1.0
O A:HOH448 2.1 24.7 1.0
O A:HOH411 2.2 36.0 1.0
OE2 A:GLU166 2.3 42.8 1.0
OE2 A:GLU116 2.4 24.3 1.0
CD A:GLU112 3.0 27.2 1.0
CD A:GLU166 3.2 51.0 1.0
MG A:MG301 3.2 27.9 1.0
CD A:GLU116 3.3 23.7 1.0
OE1 A:GLU112 3.3 24.5 1.0
OE1 A:GLU166 3.5 40.6 1.0
CG A:GLU116 3.6 24.9 1.0
O A:HOH412 3.9 28.7 1.0
O A:ALA96 3.9 21.3 1.0
OE2 A:GLU115 4.1 32.0 1.0
O A:HOH460 4.2 39.2 1.0
OE1 A:GLU116 4.4 25.9 1.0
CG A:GLU112 4.4 25.6 1.0
CG A:GLU166 4.5 50.5 1.0
CA A:GLY97 4.7 22.0 1.0
CB A:GLU112 4.7 24.6 1.0
C A:ALA96 4.8 23.0 1.0
O A:HOH455 5.0 20.8 1.0
O A:HOH427 5.0 25.6 1.0

Magnesium binding site 3 out of 8 in 5qk8

Go back to Magnesium Binding Sites List in 5qk8
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 Z1271660837


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 Z1271660837 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:29.2
occ:1.00
 O B:ALA96 2.0 26.5 1.0
O B:HOH424 2.0 29.4 1.0
O B:HOH421 2.1 30.5 1.0
O B:HOH441 2.1 27.3 1.0
O B:HOH442 2.1 28.8 1.0
OE2 B:GLU116 2.1 32.2 1.0
CD B:GLU116 3.2 32.5 1.0
C B:ALA96 3.2 21.7 1.0
MG B:MG303 3.3 46.9 1.0
OE1 B:GLU116 3.5 30.8 1.0
OE2 B:GLU166 3.7 40.4 1.0
N B:GLY97 4.1 24.6 1.0
CA B:GLY97 4.1 26.2 1.0
OE2 B:GLU112 4.1 36.8 1.0
O B:HOH436 4.2 27.0 1.0
N B:ALA96 4.2 22.6 1.0
CA B:ALA96 4.2 25.1 1.0
NE2 B:GLN82 4.3 30.6 1.0
NH2 B:ARG84 4.3 27.4 1.0
OE1 B:GLN82 4.4 30.8 1.0
CG B:GLU116 4.5 30.4 1.0
O B:HOH471 4.7 38.3 1.0
CB B:ALA96 4.7 25.9 1.0
CD B:GLN82 4.8 36.5 1.0
CD B:GLU166 4.9 54.7 1.0
O B:HOH466 5.0 38.1 0.8

Magnesium binding site 4 out of 8 in 5qk8

Go back to Magnesium Binding Sites List in 5qk8
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 Z1271660837


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 Z1271660837 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:46.9
occ:1.00
 OE2 B:GLU112 1.9 36.8 1.0
O B:HOH405 2.2 44.1 1.0
O B:HOH442 2.2 28.8 1.0
OE2 B:GLU116 2.3 32.2 1.0
O B:HOH428 2.5 38.5 1.0
OE2 B:GLU166 2.5 40.4 1.0
CD B:GLU112 3.0 37.4 1.0
CD B:GLU116 3.2 32.5 1.0
CD B:GLU166 3.3 54.7 1.0
MG B:MG302 3.3 29.2 1.0
OE1 B:GLU112 3.4 34.5 1.0
OE1 B:GLU166 3.5 61.5 1.0
CG B:GLU116 3.5 30.4 1.0
O B:ALA96 3.6 26.5 1.0
O B:HOH424 3.9 29.4 1.0
OE2 B:GLU115 4.1 44.9 1.0
CG B:GLU112 4.3 36.2 1.0
OE1 B:GLU116 4.4 30.8 1.0
CA B:GLY97 4.5 26.2 1.0
C B:ALA96 4.5 21.7 1.0
CG B:GLU166 4.6 53.2 1.0
CB B:GLU112 4.7 34.4 1.0
N B:GLY97 4.8 24.6 1.0
O B:HOH421 4.9 30.5 1.0
O B:HOH441 4.9 27.3 1.0
CA B:GLU112 5.0 31.3 1.0

Magnesium binding site 5 out of 8 in 5qk8

Go back to Magnesium Binding Sites List in 5qk8
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 Z1271660837


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 Z1271660837 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:43.1
occ:1.00
 O C:HOH453 1.8 47.0 1.0
O C:HOH402 1.8 31.9 1.0
MG C:MG303 2.2 32.0 1.0
OE2 C:GLU166 2.4 42.1 1.0
O C:HOH414 2.4 61.2 1.0
OE2 C:GLU116 2.5 29.8 1.0
OE2 C:GLU112 2.7 29.2 1.0
O C:ALA96 3.1 29.1 1.0
O C:HOH412 3.2 35.2 1.0
O C:HOH433 3.4 27.0 1.0
CD C:GLU112 3.5 34.9 1.0
CD C:GLU166 3.6 48.7 1.0
CD C:GLU116 3.7 34.0 1.0
OE1 C:GLU112 3.8 45.3 1.0
CA C:GLY97 3.9 31.8 1.0
C C:ALA96 4.1 31.8 1.0
OE1 C:GLU166 4.3 51.5 1.0
O C:HOH428 4.3 28.6 1.0
N C:GLY97 4.5 31.5 1.0
CG C:GLU116 4.5 31.2 1.0
CG C:GLU166 4.5 45.5 1.0
O C:HOH463 4.6 48.8 1.0
OE1 C:GLU116 4.6 31.1 1.0
O C:HOH443 4.8 52.5 1.0
CG C:GLU112 4.8 33.9 1.0

Magnesium binding site 6 out of 8 in 5qk8

Go back to Magnesium Binding Sites List in 5qk8
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 Z1271660837


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 Z1271660837 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:32.0
occ:1.00
 O C:HOH433 1.9 27.0 1.0
OE2 C:GLU116 2.0 29.8 1.0
O C:HOH428 2.1 28.6 1.0
O C:ALA96 2.1 29.1 1.0
O C:HOH412 2.2 35.2 1.0
MG C:MG302 2.2 43.1 1.0
O C:HOH453 2.6 47.0 1.0
CD C:GLU116 3.1 34.0 1.0
OE2 C:GLU166 3.3 42.1 1.0
C C:ALA96 3.3 31.8 1.0
OE1 C:GLU116 3.4 31.1 1.0
O C:HOH402 3.4 31.9 1.0
OE2 C:GLU112 4.0 29.2 1.0
CA C:GLY97 4.2 31.8 1.0
N C:GLY97 4.2 31.5 1.0
N C:ALA96 4.3 24.7 1.0
CA C:ALA96 4.3 23.9 1.0
CG C:GLU116 4.4 31.2 1.0
NE2 C:GLN82 4.4 38.0 1.0
NH2 C:ARG84 4.5 33.3 1.0
OE1 C:GLN82 4.5 33.5 1.0
CD C:GLU166 4.5 48.7 1.0
O C:HOH414 4.6 61.2 1.0
CB C:ALA96 4.8 24.2 1.0
CD C:GLN82 4.9 43.2 1.0
CD C:GLU112 4.9 34.9 1.0

Magnesium binding site 7 out of 8 in 5qk8

Go back to Magnesium Binding Sites List in 5qk8
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 Z1271660837


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 Z1271660837 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:34.3
occ:1.00
 O D:HOH405 1.9 24.9 1.0
OE2 D:GLU116 1.9 34.7 1.0
O D:HOH403 2.0 26.3 1.0
O D:ALA96 2.1 35.0 1.0
MG D:MG302 2.2 36.8 1.0
CD D:GLU116 2.9 45.3 1.0
O D:HOH423 3.0 45.5 1.0
OE1 D:GLU116 3.3 39.9 1.0
C D:ALA96 3.3 38.9 1.0
OE2 D:GLU166 3.5 67.5 1.0
OE2 D:GLU112 3.7 60.8 1.0
N D:ALA96 4.1 37.8 1.0
CA D:GLY97 4.2 38.5 1.0
N D:GLY97 4.2 38.4 1.0
CA D:ALA96 4.2 39.5 1.0
CG D:GLU116 4.3 41.0 1.0
NE2 D:GLN82 4.3 36.5 1.0
NH2 D:ARG84 4.3 41.5 1.0
OE1 D:GLN82 4.5 39.6 1.0
CD D:GLU112 4.5 54.5 1.0
O D:HOH408 4.5 37.9 1.0
CG D:GLU112 4.6 56.7 1.0
CD D:GLU166 4.6 72.1 1.0
CB D:ALA96 4.8 40.7 1.0
CD D:GLN82 4.8 44.8 1.0
O D:HOH402 4.9 44.4 1.0

Magnesium binding site 8 out of 8 in 5qk8

Go back to Magnesium Binding Sites List in 5qk8
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 Z1271660837


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 Z1271660837 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:36.8
occ:1.00
 O D:HOH423 2.0 45.5 1.0
MG D:MG301 2.2 34.3 1.0
OE2 D:GLU112 2.4 60.8 1.0
O D:HOH408 2.5 37.9 1.0
OE2 D:GLU166 2.5 67.5 1.0
OE2 D:GLU116 2.8 34.7 1.0
O D:HOH405 2.9 24.9 1.0
O D:ALA96 3.0 35.0 1.0
CD D:GLU112 3.3 54.5 1.0
CA D:GLY97 3.6 38.5 1.0
CD D:GLU166 3.8 72.1 1.0
O D:HOH402 3.9 44.4 1.0
OE1 D:GLU112 4.0 50.6 1.0
C D:ALA96 4.0 38.9 1.0
CD D:GLU116 4.0 45.3 1.0
CG D:GLU112 4.1 56.7 1.0
O D:HOH403 4.2 26.3 1.0
N D:GLY97 4.3 38.4 1.0
CG D:GLU166 4.6 65.8 1.0
OE1 D:GLU166 4.7 65.0 1.0
OE1 D:GLU116 4.8 39.9 1.0
C D:GLY97 4.8 43.3 1.0
CG D:GLU116 4.9 41.0 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 02:29:47 2024

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