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Magnesium in PDB 5qjp: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1578665941

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1578665941

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 Z1578665941:
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 Z1578665941, PDB code: 5qjp 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) 77.92 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.132, 59.626, 79.620, 79.86, 81.64, 76.07
R / Rfree (%) 22.3 / 25.5

Other elements in 5qjp:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1578665941 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 Z1578665941 (pdb code 5qjp). 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 Z1578665941, PDB code: 5qjp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qjp

Go back to Magnesium Binding Sites List in 5qjp
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 Z1578665941


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 Z1578665941 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:31.3
occ:1.00
 OE2 A:GLU116 2.0 29.8 1.0
O A:ALA96 2.1 26.8 1.0
O A:HOH436 2.1 27.5 1.0
O A:HOH415 2.1 27.8 1.0
O A:HOH419 2.1 30.3 1.0
O A:HOH454 2.2 25.8 1.0
CD A:GLU116 3.0 31.2 1.0
MG A:MG302 3.2 37.8 1.0
C A:ALA96 3.3 28.2 1.0
OE1 A:GLU116 3.3 28.9 1.0
OE2 A:GLU166 3.7 42.8 1.0
OE2 A:GLU112 4.0 32.2 1.0
N A:GLY97 4.1 27.7 1.0
N A:ALA96 4.1 23.2 1.0
CA A:GLY97 4.2 26.4 1.0
O A:HOH461 4.2 28.6 0.8
CA A:ALA96 4.2 24.7 1.0
O A:HOH416 4.3 25.0 1.0
NH2 A:ARG84 4.3 29.6 1.0
NE2 A:GLN82 4.3 35.0 1.0
CG A:GLU116 4.4 26.8 1.0
O A:HOH472 4.4 34.9 1.0
OE1 A:GLN82 4.4 33.5 1.0
O A:HOH464 4.7 52.4 1.0
CB A:ALA96 4.7 25.0 1.0
O A:HOH479 4.7 48.5 1.0
CD A:GLN82 4.8 38.4 1.0
O A:HOH412 4.8 47.8 1.0
CD A:GLU112 4.8 33.5 1.0
O A:HOH413 4.9 34.2 1.0
CD A:GLU166 4.9 54.5 1.0

Magnesium binding site 2 out of 8 in 5qjp

Go back to Magnesium Binding Sites List in 5qjp
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 Z1578665941


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 Z1578665941 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:37.8
occ:1.00
 O A:HOH413 1.9 34.2 1.0
OE2 A:GLU112 2.1 32.2 1.0
O A:HOH436 2.1 27.5 1.0
OE2 A:GLU166 2.2 42.8 1.0
O A:HOH412 2.3 47.8 1.0
OE2 A:GLU116 2.3 29.8 1.0
CD A:GLU112 3.1 33.5 1.0
CD A:GLU166 3.1 54.5 1.0
CD A:GLU116 3.2 31.2 1.0
MG A:MG301 3.2 31.3 1.0
OE1 A:GLU112 3.4 33.5 1.0
OE1 A:GLU166 3.4 46.6 1.0
CG A:GLU116 3.4 26.8 1.0
O A:HOH419 3.7 30.3 1.0
O A:ALA96 3.9 26.8 1.0
OE2 A:GLU115 4.1 35.8 1.0
O A:HOH405 4.3 58.5 1.0
OE1 A:GLU116 4.3 28.9 1.0
CG A:GLU112 4.4 28.0 1.0
CG A:GLU166 4.4 53.8 1.0
O A:HOH464 4.5 52.4 1.0
CB A:GLU112 4.7 27.4 1.0
CA A:GLY97 4.8 26.4 1.0
C A:ALA96 4.8 28.2 1.0
O A:HOH415 4.9 27.8 1.0
O A:HOH454 5.0 25.8 1.0
CB A:GLU116 5.0 26.4 1.0

Magnesium binding site 3 out of 8 in 5qjp

Go back to Magnesium Binding Sites List in 5qjp
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 Z1578665941


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 Z1578665941 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:34.1
occ:1.00
 O B:ALA96 1.9 33.9 1.0
O B:HOH427 2.0 34.0 1.0
OE2 B:GLU116 2.1 38.0 1.0
O B:HOH435 2.1 33.4 1.0
O B:HOH409 2.1 36.3 1.0
O B:HOH406 2.2 33.7 1.0
C B:ALA96 3.1 25.1 1.0
CD B:GLU116 3.1 37.4 1.0
MG B:MG303 3.3 54.5 1.0
OE1 B:GLU116 3.4 34.2 1.0
OE2 B:GLU166 3.5 51.0 1.0
N B:GLY97 4.0 31.2 1.0
CA B:GLY97 4.0 31.6 1.0
OE2 B:GLU112 4.1 43.1 1.0
CA B:ALA96 4.1 28.5 1.0
N B:ALA96 4.2 30.1 1.0
O B:HOH436 4.2 32.0 1.0
NE2 B:GLN82 4.3 43.7 1.0
NH2 B:ARG84 4.3 34.7 1.0
CG B:GLU116 4.4 37.1 1.0
OE1 B:GLN82 4.5 39.2 1.0
O B:HOH466 4.6 44.1 1.0
CB B:ALA96 4.6 33.0 1.0
CD B:GLU166 4.7 60.2 1.0
CD B:GLN82 4.8 47.6 1.0
CD B:GLU112 4.9 41.6 1.0

Magnesium binding site 4 out of 8 in 5qjp

Go back to Magnesium Binding Sites List in 5qjp
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 Z1578665941


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 Z1578665941 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:54.5
occ:1.00
 OE2 B:GLU112 1.9 43.1 1.0
O B:HOH401 2.1 49.4 1.0
OE2 B:GLU166 2.2 51.0 1.0
O B:HOH435 2.2 33.4 1.0
OE2 B:GLU116 2.4 38.0 1.0
O B:HOH433 2.6 51.0 1.0
CD B:GLU112 3.0 41.6 1.0
CD B:GLU166 3.2 60.2 1.0
CD B:GLU116 3.2 37.4 1.0
OE1 B:GLU112 3.3 44.6 1.0
MG B:MG302 3.3 34.1 1.0
CG B:GLU116 3.4 37.1 1.0
OE1 B:GLU166 3.5 63.8 1.0
O B:ALA96 3.8 33.9 1.0
OE2 B:GLU115 4.0 45.3 1.0
O B:HOH409 4.0 36.3 1.0
CG B:GLU112 4.3 39.7 1.0
OE1 B:GLU116 4.4 34.2 1.0
CG B:GLU166 4.5 57.3 1.0
C B:ALA96 4.6 25.1 1.0
CA B:GLY97 4.7 31.6 1.0
CB B:GLU112 4.7 38.2 1.0
CB B:GLU116 4.9 34.6 1.0
O B:HOH406 4.9 33.7 1.0
O B:HOH427 4.9 34.0 1.0
CA B:GLU112 5.0 36.2 1.0

Magnesium binding site 5 out of 8 in 5qjp

Go back to Magnesium Binding Sites List in 5qjp
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 Z1578665941


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 Z1578665941 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:44.0
occ:1.00
 O C:HOH464 1.9 64.8 1.0
O C:HOH402 2.0 32.8 1.0
MG C:MG303 2.2 34.1 1.0
OE2 C:GLU166 2.6 43.5 1.0
OE2 C:GLU116 2.7 33.8 1.0
O C:HOH443 2.8 51.3 1.0
OE2 C:GLU112 2.9 34.3 1.0
O C:ALA96 3.0 29.1 1.0
O C:HOH414 3.1 33.4 1.0
O C:HOH429 3.1 28.7 1.0
CD C:GLU112 3.5 40.1 1.0
OE1 C:GLU112 3.6 44.5 1.0
O C:HOH445 3.6 53.4 1.0
CA C:GLY97 3.7 33.5 1.0
CD C:GLU166 3.8 49.5 1.0
CD C:GLU116 3.9 37.6 1.0
C C:ALA96 4.0 33.1 1.0
O C:HOH466 4.1 54.5 1.0
O C:HOH418 4.2 29.5 1.0
N C:GLY97 4.4 33.4 1.0
OE1 C:GLU166 4.7 49.6 1.0
CG C:GLU166 4.7 49.4 1.0
OE1 C:GLU116 4.7 35.6 1.0
CG C:GLU116 4.7 33.3 1.0
CG C:GLU112 4.8 36.3 1.0
C C:GLY97 5.0 33.6 1.0

Magnesium binding site 6 out of 8 in 5qjp

Go back to Magnesium Binding Sites List in 5qjp
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 Z1578665941


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 Z1578665941 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:34.1
occ:1.00
 O C:HOH429 1.9 28.7 1.0
OE2 C:GLU116 2.0 33.8 1.0
O C:HOH418 2.1 29.5 1.0
O C:ALA96 2.1 29.1 1.0
O C:HOH414 2.2 33.4 1.0
MG C:MG302 2.2 44.0 1.0
O C:HOH464 2.9 64.8 1.0
CD C:GLU116 3.0 37.6 1.0
O C:HOH402 3.3 32.8 1.0
C C:ALA96 3.3 33.1 1.0
OE1 C:GLU116 3.4 35.6 1.0
OE2 C:GLU166 3.6 43.5 1.0
OE2 C:GLU112 3.9 34.3 1.0
CA C:GLY97 4.2 33.5 1.0
N C:ALA96 4.2 28.0 1.0
N C:GLY97 4.2 33.4 1.0
CA C:ALA96 4.2 27.7 1.0
NE2 C:GLN82 4.3 34.8 1.0
CG C:GLU116 4.4 33.3 1.0
NH2 C:ARG84 4.4 39.8 1.0
O C:HOH460 4.5 43.1 1.0
OE1 C:GLN82 4.6 33.9 1.0
CD C:GLU166 4.7 49.5 1.0
CD C:GLU112 4.8 40.1 1.0
CB C:ALA96 4.8 29.0 1.0
CD C:GLN82 4.8 41.8 1.0
O C:HOH443 4.8 51.3 1.0

Magnesium binding site 7 out of 8 in 5qjp

Go back to Magnesium Binding Sites List in 5qjp
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 Z1578665941


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 Z1578665941 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:33.4
occ:1.00
 O D:HOH417 2.0 32.6 1.0
O D:HOH402 2.0 30.2 1.0
OE2 D:GLU116 2.1 36.3 1.0
MG D:MG302 2.1 42.0 1.0
O D:ALA96 2.2 33.4 1.0
O D:HOH433 2.8 57.4 1.0
CD D:GLU116 3.1 46.1 1.0
C D:ALA96 3.3 31.6 1.0
OE1 D:GLU116 3.4 37.6 1.0
OE2 D:GLU166 3.4 64.2 1.0
OE2 D:GLU112 3.7 52.3 1.0
CA D:GLY97 4.2 34.2 1.0
N D:ALA96 4.2 33.6 1.0
N D:GLY97 4.2 31.9 1.0
NH2 D:ARG84 4.3 39.0 1.0
CA D:ALA96 4.3 34.8 1.0
NE2 D:GLN82 4.4 38.4 1.0
CD D:GLU112 4.4 46.0 1.0
CG D:GLU116 4.4 41.5 1.0
O D:HOH410 4.4 30.7 0.8
OE1 D:GLN82 4.4 41.4 1.0
CD D:GLU166 4.5 68.1 1.0
CG D:GLU112 4.6 55.2 1.0
O D:HOH418 4.6 51.1 1.0
CB D:ALA96 4.7 35.3 1.0
O D:HOH404 4.8 48.0 1.0
CD D:GLN82 4.8 42.2 1.0
O D:HOH401 4.9 44.2 1.0

Magnesium binding site 8 out of 8 in 5qjp

Go back to Magnesium Binding Sites List in 5qjp
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 Z1578665941


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 Z1578665941 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:42.0
occ:1.00
 O D:HOH433 2.0 57.4 1.0
MG D:MG301 2.1 33.4 1.0
OE2 D:GLU112 2.5 52.3 1.0
OE2 D:GLU166 2.6 64.2 1.0
O D:HOH418 2.7 51.1 1.0
OE2 D:GLU116 2.8 36.3 1.0
O D:HOH404 2.8 48.0 1.0
O D:ALA96 3.0 33.4 1.0
O D:HOH417 3.0 32.6 1.0
CD D:GLU112 3.3 46.0 1.0
CA D:GLY97 3.5 34.2 1.0
OE1 D:GLU112 3.8 50.8 1.0
CD D:GLU166 3.8 68.1 1.0
C D:ALA96 3.9 31.6 1.0
O D:HOH401 3.9 44.2 1.0
CD D:GLU116 4.0 46.1 1.0
CG D:GLU112 4.1 55.2 1.0
O D:HOH402 4.1 30.2 1.0
N D:GLY97 4.2 31.9 1.0
OE1 D:GLU166 4.6 67.0 1.0
OE1 D:GLU116 4.8 37.6 1.0
C D:GLY97 4.8 36.5 1.0
CG D:GLU166 4.8 61.0 1.0
CG D:GLU116 4.9 41.5 1.0
N D:LEU98 4.9 41.3 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 02:19:21 2024

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