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Magnesium in PDB 5qjc: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z755044716

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z755044716

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 Z755044716:
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 Z755044716, PDB code: 5qjc 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) 78.45 / 1.47
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.261, 59.768, 80.262, 79.25, 81.78, 75.66
R / Rfree (%) 22.1 / 25.4

Other elements in 5qjc:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z755044716 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 Z755044716 (pdb code 5qjc). 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 Z755044716, PDB code: 5qjc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjc

Go back to Magnesium Binding Sites List in 5qjc
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 Z755044716


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 Z755044716 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:30.8
occ:1.00
 O A:HOH411 2.1 24.4 1.0
O A:ALA96 2.1 24.6 1.0
O A:HOH462 2.1 25.4 1.0
OE2 A:GLU116 2.1 27.6 1.0
O A:HOH465 2.2 22.6 1.0
O A:HOH447 2.2 29.4 1.0
CD A:GLU116 3.2 28.1 1.0
C A:ALA96 3.2 22.9 1.0
OE1 A:GLU116 3.5 30.0 1.0
MG A:MG302 3.6 71.3 1.0
OE2 A:GLU112 4.0 35.0 1.0
OE2 A:GLU166 4.1 72.5 1.0
N A:GLY97 4.1 22.9 1.0
CA A:GLY97 4.1 23.5 1.0
O A:HOH442 4.2 22.1 0.6
N A:ALA96 4.2 20.5 1.0
CA A:ALA96 4.2 21.1 1.0
O A:HOH426 4.3 21.9 1.0
NH2 A:ARG84 4.3 25.4 1.0
O A:HOH483 4.4 54.9 1.0
O A:HOH478 4.4 32.6 1.0
OE1 A:GLN82 4.5 22.4 0.6
NE2 A:GLN82 4.5 22.7 0.6
CG A:GLU116 4.5 26.8 1.0
CB A:ALA96 4.7 20.2 1.0
O A:HOH471 4.7 32.8 1.0
CD A:GLU112 4.7 29.1 1.0
CD A:GLN82 4.9 22.4 0.6

Magnesium binding site 2 out of 8 in 5qjc

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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 Z755044716


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 Z755044716 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:71.3
occ:1.00
 O A:HOH420 2.0 39.7 1.0
O A:HOH462 2.1 25.4 1.0
OE2 A:GLU112 2.4 35.0 1.0
OE2 A:GLU166 2.7 72.5 1.0
OE2 A:GLU116 3.1 27.6 1.0
OE1 A:GLU112 3.1 34.6 1.0
CD A:GLU166 3.1 83.1 1.0
CD A:GLU112 3.2 29.1 1.0
OE1 A:GLU166 3.3 73.9 1.0
MG A:MG301 3.6 30.8 1.0
O A:HOH404 3.8 55.8 1.0
O A:HOH447 4.0 29.4 1.0
CD A:GLU116 4.0 28.1 1.0
O A:ALA96 4.2 24.6 1.0
CG A:GLU116 4.2 26.8 1.0
OE2 A:GLU115 4.3 37.3 1.0
O A:HOH483 4.3 54.9 1.0
CG A:GLU166 4.3 73.8 1.0
O A:HOH471 4.4 32.8 1.0
CG A:GLU112 4.6 28.5 1.0
O A:HOH401 4.8 49.6 1.0
CA A:GLY97 4.9 23.5 1.0

Magnesium binding site 3 out of 8 in 5qjc

Go back to Magnesium Binding Sites List in 5qjc
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 Z755044716


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 Z755044716 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:32.8
occ:1.00
 O B:ALA96 1.9 26.6 1.0
OE2 B:GLU116 2.1 34.9 1.0
O B:HOH423 2.1 31.6 1.0
O B:HOH431 2.1 32.8 1.0
O B:HOH440 2.2 27.8 1.0
O B:HOH442 2.2 33.0 1.0
CD B:GLU116 3.1 35.4 1.0
C B:ALA96 3.2 21.8 1.0
OE1 B:GLU116 3.5 31.6 1.0
OE2 B:GLU166 3.9 57.7 1.0
N B:GLY97 4.1 27.7 1.0
CA B:GLY97 4.1 27.2 1.0
OE2 B:GLU112 4.1 39.1 1.0
N B:ALA96 4.2 24.7 1.0
CA B:ALA96 4.2 25.7 1.0
O B:HOH416 4.2 27.6 1.0
NH2 B:ARG84 4.3 28.8 1.0
OE1 B:GLN82 4.4 34.1 1.0
NE2 B:GLN82 4.4 38.3 1.0
O B:HOH468 4.5 41.6 1.0
CG B:GLU116 4.5 35.2 1.0
O B:HOH464 4.5 39.4 1.0
O B:HOH401 4.5 51.8 1.0
CB B:ALA96 4.7 27.6 1.0
CD B:GLN82 4.8 43.7 1.0
MG B:MG304 4.8 63.4 1.0
CD B:GLU166 4.9 72.4 1.0
CD B:GLU112 4.9 37.4 1.0

Magnesium binding site 4 out of 8 in 5qjc

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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 Z755044716


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 Z755044716 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:63.4
occ:1.00
 O B:HOH471 2.1 65.7 1.0
O B:HOH401 2.8 51.8 1.0
O B:HOH442 2.8 33.0 1.0
OE1 B:GLU112 3.0 40.0 1.0
OE2 B:GLU112 3.3 39.1 1.0
OE1 B:GLU166 3.4 67.2 1.0
O B:HOH464 3.4 39.4 1.0
CD B:GLU112 3.6 37.4 1.0
OE2 B:GLU166 3.6 57.7 1.0
CD B:GLU166 3.8 72.4 1.0
OE2 B:GLU115 4.0 48.5 1.0
NH1 B:ARG111 4.6 37.3 1.0
OE2 B:GLU116 4.7 34.9 1.0
MG B:MG303 4.8 32.8 1.0
CA B:GLY97 4.9 27.2 1.0

Magnesium binding site 5 out of 8 in 5qjc

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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 Z755044716


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 Z755044716 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:45.9
occ:1.00
 MG C:MG303 2.2 36.2 1.0
O C:HOH403 2.7 56.5 1.0
OE2 C:GLU116 3.0 40.1 1.0
O C:ALA96 3.0 31.0 1.0
O C:HOH453 3.1 45.7 1.0
O C:HOH458 3.1 29.3 1.0
O C:HOH426 3.1 35.4 1.0
OE2 C:GLU112 3.2 39.4 1.0
OE2 C:GLU166 3.2 90.4 1.0
O C:HOH466 3.4 66.2 1.0
O C:HOH444 3.6 56.6 1.0
CA C:GLY97 3.7 32.4 1.0
CD C:GLU112 3.8 42.2 1.0
OE1 C:GLU112 3.9 54.4 1.0
C C:ALA96 4.0 33.0 1.0
O C:HOH435 4.1 29.9 1.0
CD C:GLU166 4.1 87.0 1.0
CD C:GLU116 4.2 38.8 1.0
OE1 C:GLU166 4.4 86.1 1.0
N C:GLY97 4.4 31.2 1.0
C C:GLY97 5.0 35.0 1.0

Magnesium binding site 6 out of 8 in 5qjc

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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 Z755044716


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 Z755044716 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:36.2
occ:1.00
 O C:HOH435 1.9 29.9 1.0
O C:HOH458 2.0 29.3 1.0
OE2 C:GLU116 2.1 40.1 1.0
MG C:MG302 2.2 45.9 1.0
O C:ALA96 2.2 31.0 1.0
O C:HOH426 2.3 35.4 1.0
CD C:GLU116 3.2 38.8 1.0
C C:ALA96 3.3 33.0 1.0
OE1 C:GLU116 3.6 43.7 1.0
O C:HOH403 3.8 56.5 1.0
OE2 C:GLU112 4.1 39.4 1.0
OE2 C:GLU166 4.1 90.4 1.0
N C:ALA96 4.2 24.9 1.0
O C:HOH416 4.2 24.5 0.7
CA C:ALA96 4.2 24.7 1.0
N C:GLY97 4.3 31.2 1.0
CA C:GLY97 4.3 32.4 1.0
NH2 C:ARG84 4.3 32.3 1.0
NE2 C:GLN82 4.3 31.5 1.0
OE1 C:GLN82 4.4 32.0 1.0
CG C:GLU116 4.6 32.2 1.0
O C:HOH453 4.6 45.7 1.0
O C:HOH469 4.7 33.5 0.7
CB C:ALA96 4.7 26.5 1.0
CD C:GLN82 4.8 39.0 1.0
CD C:GLU112 5.0 42.2 1.0

Magnesium binding site 7 out of 8 in 5qjc

Go back to Magnesium Binding Sites List in 5qjc
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 Z755044716


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 Z755044716 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:32.8
occ:1.00
 O D:HOH426 1.9 28.5 0.7
O D:HOH418 2.0 27.9 1.0
OE2 D:GLU116 2.1 36.3 1.0
O D:HOH408 2.1 29.9 1.0
MG D:MG302 2.2 41.5 1.0
O D:ALA96 2.2 28.1 1.0
O D:HOH447 2.7 60.5 1.0
CD D:GLU116 3.1 39.2 1.0
C D:ALA96 3.4 28.2 1.0
OE1 D:GLU116 3.5 36.4 1.0
OE2 D:GLU112 3.8 56.2 1.0
N D:ALA96 4.2 28.9 1.0
O D:HOH436 4.2 27.5 0.7
CA D:GLY97 4.2 32.2 1.0
NH2 D:ARG84 4.2 30.2 1.0
N D:GLY97 4.2 31.1 1.0
CA D:ALA96 4.3 27.1 1.0
NE2 D:GLN82 4.3 36.0 1.0
O D:HOH407 4.4 25.1 0.7
OE1 D:GLN82 4.4 32.9 1.0
CG D:GLU116 4.5 34.1 1.0
CB D:ALA96 4.6 28.2 1.0
CD D:GLU112 4.6 54.0 1.0
O D:HOH443 4.6 30.9 0.7
O D:HOH403 4.7 58.3 1.0
CG D:GLU112 4.7 58.5 1.0
CD D:GLN82 4.8 41.9 1.0

Magnesium binding site 8 out of 8 in 5qjc

Go back to Magnesium Binding Sites List in 5qjc
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 Z755044716


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 Z755044716 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:41.5
occ:1.00
 O D:HOH447 1.9 60.5 1.0
MG D:MG301 2.2 32.8 1.0
OE2 D:GLU112 2.5 56.2 1.0
O D:HOH426 2.8 28.5 0.7
OE2 D:GLU116 2.9 36.3 1.0
O D:HOH417 3.0 67.4 1.0
O D:ALA96 3.0 28.1 1.0
O D:HOH418 3.1 27.9 1.0
O D:HOH403 3.5 58.3 1.0
CD D:GLU112 3.5 54.0 1.0
CA D:GLY97 3.6 32.2 1.0
C D:ALA96 4.0 28.2 1.0
CD D:GLU116 4.1 39.2 1.0
O D:HOH436 4.2 27.5 0.7
O D:HOH408 4.2 29.9 1.0
OE1 D:GLU112 4.3 62.1 1.0
N D:GLY97 4.4 31.1 1.0
CG D:GLU112 4.4 58.5 1.0
OE2 D:GLU166 4.8 72.7 1.0
OE1 D:GLU116 4.9 36.4 1.0
CG D:GLU116 4.9 34.1 1.0
C D:GLY97 4.9 35.4 1.0
CD D:GLU166 5.0 72.9 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 02:15:05 2024

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