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Magnesium in PDB 5qk9: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z102895082

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z102895082

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 Z102895082:
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 Z102895082, PDB code: 5qk9 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) 78.61 / 1.56
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.333, 59.839, 80.492, 79.07, 81.63, 75.64
R / Rfree (%) 21.5 / 25.1

Other elements in 5qk9:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z102895082 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 Z102895082 (pdb code 5qk9). 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 Z102895082, PDB code: 5qk9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qk9

Go back to Magnesium Binding Sites List in 5qk9
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 Z102895082


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 Z102895082 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:28.0
occ:1.00
 O A:HOH424 2.1 22.0 1.0
OE2 A:GLU116 2.1 24.0 1.0
O A:ALA96 2.1 24.5 1.0
O A:HOH458 2.1 23.9 1.0
O A:HOH441 2.2 27.7 1.0
O A:HOH466 2.2 22.1 1.0
CD A:GLU116 3.1 25.6 1.0
C A:ALA96 3.3 20.8 1.0
MG A:MG302 3.4 56.6 1.0
OE1 A:GLU116 3.4 23.7 1.0
OE2 A:GLU166 3.8 54.1 1.0
CA A:GLY97 4.1 21.6 1.0
N A:GLY97 4.1 21.6 1.0
OE2 A:GLU112 4.2 32.6 1.0
N A:ALA96 4.2 18.4 1.0
O A:HOH437 4.2 22.7 0.8
CA A:ALA96 4.2 19.9 1.0
NH2 A:ARG84 4.3 23.1 1.0
O A:HOH426 4.3 20.8 1.0
O A:HOH477 4.4 28.3 1.0
O A:HOH476 4.4 52.6 1.0
NE2 A:GLN82 4.4 27.6 1.0
OE1 A:GLN82 4.5 25.5 1.0
CG A:GLU116 4.5 25.5 1.0
O A:HOH475 4.6 32.6 1.0
CB A:ALA96 4.7 18.9 1.0
CD A:GLN82 4.8 32.0 1.0
CD A:GLU112 5.0 32.8 1.0

Magnesium binding site 2 out of 8 in 5qk9

Go back to Magnesium Binding Sites List in 5qk9
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 Z102895082


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 Z102895082 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:56.6
occ:1.00
 O A:HOH458 2.0 23.9 1.0
O A:HOH405 2.0 45.4 1.0
OE2 A:GLU112 2.2 32.6 1.0
O A:HOH459 2.3 50.7 1.0
OE2 A:GLU166 2.5 54.1 1.0
OE2 A:GLU116 2.7 24.0 1.0
CD A:GLU112 3.1 32.8 1.0
OE1 A:GLU112 3.2 32.3 1.0
CD A:GLU166 3.2 70.2 1.0
MG A:MG301 3.4 28.0 1.0
OE1 A:GLU166 3.5 62.0 1.0
CD A:GLU116 3.6 25.6 1.0
CG A:GLU116 3.9 25.5 1.0
O A:ALA96 3.9 24.5 1.0
O A:HOH441 4.0 27.7 1.0
O A:HOH476 4.2 52.6 1.0
OE2 A:GLU115 4.2 36.5 1.0
O A:HOH475 4.4 32.6 1.0
CG A:GLU166 4.5 66.6 1.0
CG A:GLU112 4.5 28.9 1.0
CA A:GLY97 4.6 21.6 1.0
OE1 A:GLU116 4.7 23.7 1.0
C A:ALA96 4.9 20.8 1.0
CB A:GLU112 4.9 27.5 1.0
O A:HOH466 5.0 22.1 1.0

Magnesium binding site 3 out of 8 in 5qk9

Go back to Magnesium Binding Sites List in 5qk9
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 Z102895082


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 Z102895082 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:28.5
occ:1.00
 O B:ALA96 2.0 26.2 1.0
OE2 B:GLU116 2.1 31.9 1.0
O B:HOH404 2.1 28.9 1.0
O B:HOH414 2.1 28.5 1.0
O B:HOH443 2.2 28.3 1.0
O B:HOH454 2.2 26.0 1.0
CD B:GLU116 3.1 31.9 1.0
C B:ALA96 3.2 22.8 1.0
MG B:MG304 3.4 61.2 1.0
OE1 B:GLU116 3.4 28.4 1.0
OE2 B:GLU166 3.8 58.4 1.0
N B:GLY97 4.1 25.4 1.0
CA B:GLY97 4.2 27.1 1.0
NE2 B:GLN82 4.2 35.3 1.0
N B:ALA96 4.2 24.1 1.0
CA B:ALA96 4.2 23.1 1.0
OE2 B:GLU112 4.2 37.0 1.0
NH2 B:ARG84 4.3 28.2 1.0
O B:HOH423 4.3 26.1 1.0
OE1 B:GLN82 4.4 36.0 1.0
CG B:GLU116 4.5 30.2 1.0
O B:HOH470 4.5 34.5 1.0
O B:HOH467 4.5 39.2 0.9
CD B:GLU166 4.7 69.9 1.0
CD B:GLN82 4.7 41.8 1.0
CB B:ALA96 4.7 27.0 1.0

Magnesium binding site 4 out of 8 in 5qk9

Go back to Magnesium Binding Sites List in 5qk9
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 Z102895082


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 Z102895082 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:61.2
occ:1.00
 OE2 B:GLU112 1.8 37.0 1.0
O B:HOH408 2.0 50.5 1.0
O B:HOH443 2.4 28.3 1.0
OE2 B:GLU116 2.4 31.9 1.0
O B:HOH441 2.5 48.3 1.0
OE2 B:GLU166 2.6 58.4 1.0
CD B:GLU112 2.9 36.0 1.0
CD B:GLU116 3.2 31.9 1.0
OE1 B:GLU112 3.3 34.6 1.0
MG B:MG303 3.4 28.5 1.0
CD B:GLU166 3.4 69.9 1.0
CG B:GLU116 3.4 30.2 1.0
OE1 B:GLU166 3.4 76.6 1.0
O B:ALA96 3.7 26.2 1.0
OE2 B:GLU115 4.0 45.5 1.0
CG B:GLU112 4.2 33.0 1.0
O B:HOH404 4.3 28.9 1.0
OE1 B:GLU116 4.3 28.4 1.0
CB B:GLU112 4.5 33.9 1.0
C B:ALA96 4.6 22.8 1.0
CA B:GLY97 4.6 27.1 1.0
O B:HOH467 4.7 39.2 0.9
CA B:GLU112 4.8 29.8 1.0
CG B:GLU166 4.9 63.5 1.0
N B:GLY97 4.9 25.4 1.0
CB B:GLU116 4.9 29.0 1.0
O B:GLU112 4.9 29.3 1.0
CB B:GLU115 5.0 39.9 1.0
O B:HOH414 5.0 28.5 1.0

Magnesium binding site 5 out of 8 in 5qk9

Go back to Magnesium Binding Sites List in 5qk9
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 Z102895082


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 Z102895082 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:45.2
occ:1.00
 MG C:MG303 2.1 33.4 1.0
O C:HOH451 2.8 85.5 1.0
OE2 C:GLU116 2.8 30.9 1.0
O C:ALA96 2.9 25.8 1.0
O C:HOH419 3.0 33.2 1.0
OE2 C:GLU166 3.0 64.4 1.0
O C:HOH458 3.1 26.1 1.0
OE2 C:GLU112 3.2 34.6 1.0
O C:HOH463 3.2 44.4 1.0
O C:HOH403 3.3 45.7 1.0
CA C:GLY97 3.6 30.5 1.0
CD C:GLU112 3.8 36.2 1.0
O C:HOH426 3.8 59.5 1.0
OE1 C:GLU112 3.9 42.0 1.0
C C:ALA96 3.9 28.6 1.0
CD C:GLU166 3.9 71.8 1.0
CD C:GLU116 4.0 28.4 1.0
O C:HOH438 4.2 28.6 1.0
O C:HOH446 4.2 39.1 0.9
N C:GLY97 4.3 26.8 1.0
OE1 C:GLU166 4.4 78.3 1.0
OE1 C:GLU116 4.8 35.2 1.0
O C:HOH468 4.9 31.8 0.9
C C:GLY97 4.9 28.8 1.0
CG C:GLU166 4.9 65.0 1.0
CG C:GLU116 4.9 27.7 1.0

Magnesium binding site 6 out of 8 in 5qk9

Go back to Magnesium Binding Sites List in 5qk9
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 Z102895082


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 Z102895082 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:33.4
occ:1.00
 OE2 C:GLU116 2.0 30.9 1.0
MG C:MG302 2.1 45.2 1.0
O C:HOH438 2.1 28.6 1.0
O C:HOH419 2.1 33.2 1.0
O C:HOH458 2.2 26.1 1.0
O C:ALA96 2.2 25.8 1.0
CD C:GLU116 3.1 28.4 1.0
C C:ALA96 3.4 28.6 1.0
OE1 C:GLU116 3.4 35.2 1.0
OE2 C:GLU166 3.7 64.4 1.0
OE2 C:GLU112 4.2 34.6 1.0
N C:ALA96 4.2 22.9 1.0
O C:HOH407 4.2 25.3 0.9
O C:HOH446 4.2 39.1 0.9
CA C:ALA96 4.3 22.3 1.0
CA C:GLY97 4.3 30.5 1.0
N C:GLY97 4.3 26.8 1.0
NE2 C:GLN82 4.3 32.4 1.0
NH2 C:ARG84 4.3 30.8 1.0
O C:HOH403 4.4 45.7 1.0
OE1 C:GLN82 4.4 31.2 1.0
CG C:GLU116 4.4 27.7 1.0
O C:HOH468 4.5 31.8 0.9
CB C:ALA96 4.7 23.2 1.0
O C:HOH463 4.7 44.4 1.0
CD C:GLN82 4.8 40.0 1.0
CD C:GLU166 4.9 71.8 1.0
O C:HOH451 4.9 85.5 1.0
CD C:GLU112 5.0 36.2 1.0

Magnesium binding site 7 out of 8 in 5qk9

Go back to Magnesium Binding Sites List in 5qk9
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 Z102895082


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 Z102895082 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:30.0
occ:1.00
 O D:HOH428 1.9 29.1 0.9
O D:HOH427 2.0 26.4 1.0
O D:HOH405 2.0 29.8 1.0
OE2 D:GLU116 2.1 31.2 1.0
O D:ALA96 2.1 28.4 1.0
MG D:MG302 2.2 39.0 1.0
CD D:GLU116 3.1 35.5 1.0
C D:ALA96 3.3 29.5 1.0
OE1 D:GLU116 3.4 33.6 1.0
OE2 D:GLU112 4.0 47.4 1.0
N D:ALA96 4.1 28.6 1.0
N D:GLY97 4.2 32.0 1.0
CA D:GLY97 4.2 35.5 1.0
CA D:ALA96 4.2 28.0 1.0
O D:HOH402 4.2 46.1 1.0
NH2 D:ARG84 4.2 28.1 1.0
O D:HOH431 4.2 30.3 0.9
O D:HOH409 4.3 28.0 0.9
NE2 D:GLN82 4.4 33.1 1.0
CG D:GLU116 4.4 33.8 1.0
OE1 D:GLN82 4.5 33.4 1.0
CB D:ALA96 4.5 28.9 1.0
O D:HOH440 4.6 31.0 0.9
O D:HOH434 4.7 42.7 1.0
OE2 D:GLU166 4.7 86.2 1.0
CD D:GLU112 4.8 45.9 1.0
CD D:GLN82 4.9 36.1 1.0
CG D:GLU112 4.9 50.9 1.0
O D:HOH429 5.0 66.6 1.0

Magnesium binding site 8 out of 8 in 5qk9

Go back to Magnesium Binding Sites List in 5qk9
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 Z102895082


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 Z102895082 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:39.0
occ:1.00
 MG D:MG301 2.2 30.0 1.0
O D:HOH428 2.8 29.1 0.9
OE2 D:GLU112 2.9 47.4 1.0
OE2 D:GLU116 2.9 31.2 1.0
O D:HOH429 2.9 66.6 1.0
O D:ALA96 3.0 28.4 1.0
O D:HOH402 3.0 46.1 1.0
O D:HOH427 3.1 26.4 1.0
O D:HOH434 3.2 42.7 1.0
OE2 D:GLU166 3.5 86.2 1.0
CA D:GLY97 3.5 35.5 1.0
CD D:GLU112 3.8 45.9 1.0
C D:ALA96 3.9 29.5 1.0
CD D:GLU116 4.1 35.5 1.0
O D:HOH431 4.1 30.3 0.9
O D:HOH405 4.2 29.8 1.0
N D:GLY97 4.2 32.0 1.0
OE1 D:GLU112 4.4 52.0 1.0
CG D:GLU112 4.6 50.9 1.0
CD D:GLU166 4.6 78.9 1.0
C D:GLY97 4.8 36.6 1.0
OE1 D:GLU116 4.9 33.6 1.0
N D:LEU98 4.9 36.5 1.0
CG D:GLU116 4.9 33.8 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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