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Magnesium in PDB 5qjg: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z44567722

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z44567722

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 Z44567722:
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 Z44567722, PDB code: 5qjg 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) 78.46 / 1.57
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.852, 59.531, 80.121, 79.71, 82.19, 76.21
R / Rfree (%) 20.6 / 23.3

Other elements in 5qjg:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z44567722 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 Z44567722 (pdb code 5qjg). 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 Z44567722, PDB code: 5qjg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjg

Go back to Magnesium Binding Sites List in 5qjg
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 Z44567722


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 Z44567722 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:23.0
occ:1.00
 OE2 A:GLU116 2.0 23.4 1.0
O A:ALA96 2.0 20.7 1.0
O A:HOH442 2.1 21.8 1.0
O A:HOH422 2.1 24.2 1.0
O A:HOH458 2.1 22.8 1.0
O A:HOH414 2.2 21.3 1.0
MG A:MG302 3.0 53.1 1.0
CD A:GLU116 3.1 24.8 1.0
C A:ALA96 3.2 20.8 1.0
OE1 A:GLU116 3.4 23.5 1.0
OE2 A:GLU112 4.0 34.2 1.0
N A:GLY97 4.1 21.9 1.0
CA A:GLY97 4.1 20.8 1.0
N A:ALA96 4.1 18.6 1.0
CA A:ALA96 4.2 17.9 1.0
O A:HOH451 4.2 25.4 0.7
O A:HOH418 4.3 20.3 1.0
NE2 A:GLN82 4.4 21.3 0.7
O A:HOH477 4.4 29.6 1.0
NH2 A:ARG84 4.4 22.8 1.0
CG A:GLU116 4.4 25.0 1.0
OE1 A:GLN82 4.6 22.6 0.7
O A:HOH466 4.7 39.5 1.0
CB A:ALA96 4.7 18.6 1.0
O A:HOH476 4.7 49.1 1.0
CD A:GLU112 4.8 32.8 1.0
CD A:GLN82 4.9 22.1 0.7

Magnesium binding site 2 out of 8 in 5qjg

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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 Z44567722


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 Z44567722 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:53.1
occ:1.00
 O A:HOH442 1.9 21.8 1.0
OE2 A:GLU112 2.1 34.2 1.0
O A:HOH410 2.2 41.9 1.0
OE2 A:GLU116 2.2 23.4 1.0
MG A:MG301 3.0 23.0 1.0
CD A:GLU112 3.2 32.8 1.0
CD A:GLU116 3.2 24.8 1.0
O A:HOH431 3.2 51.6 1.0
CG A:GLU116 3.5 25.0 1.0
OE1 A:GLU112 3.6 33.8 1.0
O A:ALA96 3.7 20.7 1.0
O A:HOH422 3.7 24.2 1.0
OE2 A:GLU166 3.9 69.0 0.7
OE1 A:GLU116 4.3 23.5 1.0
OE1 A:GLU166 4.3 64.8 0.7
CD A:GLU166 4.4 65.8 0.7
OE2 A:GLU115 4.5 37.3 1.0
CG A:GLU112 4.5 28.2 1.0
O A:HOH466 4.6 39.5 1.0
C A:ALA96 4.7 20.8 1.0
O A:HOH458 4.7 22.8 1.0
O A:HOH414 4.7 21.3 1.0
CA A:GLY97 4.7 20.8 1.0
CB A:GLU112 4.8 26.6 1.0

Magnesium binding site 3 out of 8 in 5qjg

Go back to Magnesium Binding Sites List in 5qjg
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 Z44567722


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 Z44567722 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:27.3
occ:1.00
 O B:ALA96 2.0 27.4 1.0
OE2 B:GLU116 2.0 30.8 1.0
O B:HOH431 2.0 26.6 1.0
O B:HOH416 2.1 26.8 1.0
O B:HOH420 2.1 28.5 1.0
O B:HOH453 2.2 29.8 1.0
CD B:GLU116 3.0 33.6 1.0
C B:ALA96 3.2 24.7 1.0
OE1 B:GLU116 3.4 31.4 1.0
N B:GLY97 4.1 25.3 1.0
CA B:GLY97 4.1 26.4 1.0
N B:ALA96 4.2 25.0 1.0
OE2 B:GLU112 4.2 39.0 1.0
CA B:ALA96 4.2 23.1 1.0
O B:HOH428 4.2 25.4 1.0
NH2 B:ARG84 4.3 27.1 1.0
NE2 B:GLN82 4.3 32.3 1.0
OE2 B:GLU166 4.3 63.3 0.7
CG B:GLU116 4.4 32.0 1.0
O B:HOH434 4.4 30.3 0.7
OE1 B:GLN82 4.4 33.6 1.0
O B:HOH472 4.5 30.6 0.7
O B:HOH479 4.6 42.0 1.0
O B:HOH408 4.6 50.0 1.0
CB B:ALA96 4.7 25.7 1.0
CD B:GLN82 4.7 38.1 1.0
MG B:MG303 4.8 72.5 1.0
CD B:GLU112 5.0 38.7 1.0

Magnesium binding site 4 out of 8 in 5qjg

Go back to Magnesium Binding Sites List in 5qjg
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 Z44567722


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 Z44567722 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:72.5
occ:1.00
 O B:HOH443 1.9 53.7 1.0
O B:HOH408 2.1 50.0 1.0
O B:HOH453 2.9 29.8 1.0
OE2 B:GLU112 3.2 39.0 1.0
OE1 B:GLU166 3.3 68.2 0.7
OE1 B:GLU112 3.4 39.1 1.0
OE2 B:GLU115 3.7 42.5 1.0
CD B:GLU112 3.8 38.7 1.0
O B:HOH472 3.9 30.6 0.7
CD B:GLU166 4.1 66.5 0.7
OE2 B:GLU166 4.1 63.3 0.7
OE2 B:GLU116 4.3 30.8 1.0
MG B:MG302 4.8 27.3 1.0
NH1 B:ARG111 5.0 36.4 1.0
O B:HOH420 5.0 28.5 1.0
CD B:GLU115 5.0 45.0 1.0

Magnesium binding site 5 out of 8 in 5qjg

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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 Z44567722


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 Z44567722 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:35.6
occ:1.00
 MG C:MG303 2.1 27.1 1.0
O C:HOH404 2.7 45.0 1.0
OE2 C:GLU116 2.8 26.9 1.0
O C:HOH443 2.9 26.1 1.0
O C:HOH417 2.9 31.4 1.0
O C:ALA96 3.1 24.6 1.0
O C:HOH426 3.1 64.5 1.0
O C:HOH466 3.1 45.0 1.0
OE2 C:GLU112 3.2 36.7 1.0
OE2 C:GLU166 3.7 63.8 0.7
CA C:GLY97 3.7 26.3 1.0
O C:HOH472 3.8 32.5 0.7
CD C:GLU112 3.8 39.9 1.0
OE1 C:GLU112 3.9 45.0 1.0
CD C:GLU116 4.0 27.9 1.0
C C:ALA96 4.1 26.7 1.0
O C:HOH433 4.3 25.7 1.0
N C:GLY97 4.4 24.5 1.0
OE1 C:GLU116 4.9 30.7 1.0
CD C:GLU166 4.9 58.5 0.7
CG C:GLU116 4.9 26.4 1.0
O C:HOH487 5.0 59.0 1.0
O C:HOH479 5.0 28.2 0.7

Magnesium binding site 6 out of 8 in 5qjg

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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 Z44567722


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 Z44567722 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:27.1
occ:1.00
 O C:HOH443 2.0 26.1 1.0
OE2 C:GLU116 2.0 26.9 1.0
O C:ALA96 2.1 24.6 1.0
MG C:MG302 2.1 35.6 1.0
O C:HOH433 2.1 25.7 1.0
O C:HOH417 2.2 31.4 1.0
CD C:GLU116 3.1 27.9 1.0
C C:ALA96 3.3 26.7 1.0
OE1 C:GLU116 3.4 30.7 1.0
O C:HOH472 3.8 32.5 0.7
O C:HOH404 3.8 45.0 1.0
OE2 C:GLU112 4.0 36.7 1.0
CA C:GLY97 4.1 26.3 1.0
N C:ALA96 4.1 22.1 1.0
N C:GLY97 4.1 24.5 1.0
CA C:ALA96 4.2 22.2 1.0
O C:HOH414 4.3 18.7 0.7
NH2 C:ARG84 4.3 28.9 1.0
NE2 C:GLN82 4.4 30.9 1.0
CG C:GLU116 4.4 26.4 1.0
O C:HOH479 4.4 28.2 0.7
OE1 C:GLN82 4.4 28.9 1.0
O C:HOH466 4.6 45.0 1.0
CB C:ALA96 4.6 22.6 1.0
CD C:GLN82 4.8 33.9 1.0
CD C:GLU112 4.9 39.9 1.0

Magnesium binding site 7 out of 8 in 5qjg

Go back to Magnesium Binding Sites List in 5qjg
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 Z44567722


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 Z44567722 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:25.6
occ:1.00
 O D:HOH449 2.0 25.0 0.7
O D:HOH421 2.1 25.0 1.0
OE2 D:GLU116 2.1 26.6 1.0
O D:ALA96 2.1 24.6 1.0
MG D:MG302 2.1 35.0 1.0
O D:HOH448 2.1 26.2 1.0
CD D:GLU116 3.1 32.2 1.0
C D:ALA96 3.3 24.2 1.0
OE1 D:GLU116 3.4 28.5 1.0
CA D:GLY97 4.1 26.6 1.0
N D:ALA96 4.1 24.0 1.0
OE2 D:GLU112 4.1 37.3 1.0
N D:GLY97 4.2 24.7 1.0
CA D:ALA96 4.2 23.3 1.0
O D:HOH456 4.2 26.4 0.7
O D:HOH419 4.3 18.5 0.7
NH2 D:ARG84 4.4 26.5 1.0
NE2 D:GLN82 4.4 28.0 1.0
O D:HOH463 4.4 26.1 0.7
OE1 D:GLN82 4.4 28.4 1.0
CG D:GLU116 4.5 26.2 1.0
CB D:ALA96 4.6 25.1 1.0
O D:HOH447 4.7 34.1 0.7
CD D:GLN82 4.9 29.4 1.0
O D:HOH417 5.0 57.1 1.0

Magnesium binding site 8 out of 8 in 5qjg

Go back to Magnesium Binding Sites List in 5qjg
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 Z44567722


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 Z44567722 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:35.0
occ:1.00
 MG D:MG301 2.1 25.6 1.0
O D:HOH449 2.8 25.0 0.7
OE2 D:GLU116 2.9 26.6 1.0
O D:HOH447 3.0 34.1 0.7
O D:ALA96 3.0 24.6 1.0
O D:HOH448 3.1 26.2 1.0
OE2 D:GLU112 3.3 37.3 1.0
O D:HOH432 3.5 52.3 1.0
CA D:GLY97 3.5 26.6 1.0
O D:HOH417 3.9 57.1 1.0
CD D:GLU112 4.0 38.6 1.0
C D:ALA96 4.0 24.2 1.0
OE1 D:GLU112 4.1 35.2 1.0
O D:HOH456 4.1 26.4 0.7
CD D:GLU116 4.1 32.2 1.0
O D:HOH421 4.2 25.0 1.0
N D:GLY97 4.3 24.7 1.0
O D:HOH463 4.7 26.1 0.7
C D:GLY97 4.8 25.3 1.0
OE1 D:GLU116 4.9 28.5 1.0
N D:LEU98 4.9 31.2 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 02:15:18 2024

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