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Magnesium in PDB 5qtn: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432:
2.7.7.96; 3.6.1.13; 3.6.1.58;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432, PDB code: 5qtn was solved by Y.Dubianok, T.Krojer, H.Kovacs, F.Moriaud, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.91 / 1.83
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.083, 59.814, 79.586, 79.55, 81.29, 75.78
R / Rfree (%) 23.8 / 27.5

Other elements in 5qtn:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432 also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432 (pdb code 5qtn). 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 -- Crystal Structure of NUDT5 in Complex with Ss-4432, PDB code: 5qtn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qtn

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Magnesium binding site 1 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432


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 -- Crystal Structure of NUDT5 in Complex with Ss-4432 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:35.1
occ:1.00
 OE2 A:GLU116 2.0 29.4 1.0
O A:HOH435 2.0 30.5 1.0
O A:HOH452 2.0 26.3 1.0
O A:ALA96 2.1 26.3 1.0
O A:HOH419 2.1 26.4 1.0
O A:HOH415 2.2 27.0 1.0
CD A:GLU116 3.0 30.6 1.0
MG A:MG302 3.2 57.1 1.0
C A:ALA96 3.3 24.8 1.0
OE1 A:GLU116 3.4 32.3 1.0
OE2 A:GLU166 3.8 62.2 1.0
O A:HOH448 4.1 26.4 0.7
OE2 A:GLU112 4.1 37.0 1.0
N A:GLY97 4.1 26.7 1.0
CA A:GLY97 4.2 28.2 1.0
N A:ALA96 4.2 23.2 1.0
NH2 A:ARG84 4.2 28.1 1.0
CA A:ALA96 4.2 24.0 1.0
CG A:GLU116 4.3 30.6 1.0
NE2 A:GLN82 4.3 31.2 1.0
O A:HOH420 4.4 23.3 1.0
OE1 A:GLN82 4.4 25.7 1.0
O A:HOH467 4.5 34.1 1.0
O A:HOH459 4.5 36.9 1.0
CB A:ALA96 4.6 21.8 1.0
CD A:GLN82 4.7 34.5 1.0
CD A:GLU112 4.8 33.2 1.0

Magnesium binding site 2 out of 8 in 5qtn

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Magnesium binding site 2 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432


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 -- Crystal Structure of NUDT5 in Complex with Ss-4432 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:57.1
occ:1.00
 O A:HOH435 1.9 30.5 1.0
OE2 A:GLU112 2.1 37.0 1.0
O A:HOH403 2.1 39.7 1.0
O A:HOH432 2.3 54.4 1.0
OE2 A:GLU166 2.4 62.2 1.0
OE2 A:GLU116 2.5 29.4 1.0
CD A:GLU112 3.0 33.2 1.0
MG A:MG301 3.2 35.1 1.0
OE1 A:GLU112 3.2 34.4 1.0
CD A:GLU166 3.3 68.1 1.0
CD A:GLU116 3.4 30.6 1.0
OE1 A:GLU166 3.6 65.2 1.0
CG A:GLU116 3.7 30.6 1.0
O A:ALA96 3.8 26.3 1.0
O A:HOH415 3.9 27.0 1.0
OE2 A:GLU115 4.1 36.3 1.0
O A:HOH459 4.2 36.9 1.0
CG A:GLU112 4.4 30.7 1.0
OE1 A:GLU116 4.5 32.3 1.0
CG A:GLU166 4.6 65.7 1.0
CA A:GLY97 4.6 28.2 1.0
O A:HOH452 4.7 26.3 1.0
C A:ALA96 4.8 24.8 1.0
CB A:GLU112 4.9 30.4 1.0
O A:HOH419 4.9 26.4 1.0

Magnesium binding site 3 out of 8 in 5qtn

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Magnesium binding site 3 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432


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 -- Crystal Structure of NUDT5 in Complex with Ss-4432 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:30.1
occ:1.00
 O B:ALA96 1.9 30.4 1.0
O B:HOH437 1.9 27.5 1.0
OE2 B:GLU116 2.0 36.7 1.0
O B:HOH413 2.1 34.5 1.0
O B:HOH451 2.2 26.1 1.0
O B:HOH438 2.2 40.6 1.0
CD B:GLU116 2.9 38.1 1.0
C B:ALA96 3.1 27.5 1.0
OE1 B:GLU116 3.2 37.7 1.0
O B:HOH419 4.0 35.1 1.0
N B:ALA96 4.0 26.2 1.0
CA B:ALA96 4.0 29.3 1.0
N B:GLY97 4.0 29.3 1.0
OE2 B:GLU112 4.0 45.2 1.0
MG B:MG303 4.1 73.0 1.0
OE2 B:GLU166 4.1 56.2 1.0
CA B:GLY97 4.2 32.0 1.0
NE2 B:GLN82 4.3 47.1 1.0
NH2 B:ARG84 4.3 35.3 1.0
OE1 B:GLN82 4.3 44.2 1.0
CG B:GLU116 4.3 36.1 1.0
CB B:ALA96 4.4 29.5 1.0
O B:HOH461 4.6 39.5 1.0
CD B:GLN82 4.7 49.3 1.0
CD B:GLU166 4.8 68.2 1.0
CD B:GLU112 4.9 44.4 1.0

Magnesium binding site 4 out of 8 in 5qtn

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Magnesium binding site 4 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432


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 -- Crystal Structure of NUDT5 in Complex with Ss-4432 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:73.0
occ:1.00
 OE2 B:GLU112 2.1 45.2 1.0
O B:HOH415 2.4 41.1 1.0
O B:HOH445 2.5 65.2 1.0
OE2 B:GLU116 2.8 36.7 1.0
OE2 B:GLU166 2.8 56.2 1.0
OE1 B:GLU166 3.1 71.8 1.0
O B:HOH438 3.1 40.6 1.0
CD B:GLU112 3.1 44.4 1.0
OE2 B:GLU115 3.3 55.4 1.0
CD B:GLU166 3.3 68.2 1.0
CG B:GLU116 3.3 36.1 1.0
OE1 B:GLU112 3.5 42.5 1.0
CD B:GLU116 3.5 38.1 1.0
MG B:MG302 4.1 30.1 1.0
CB B:GLU115 4.1 44.0 1.0
CD B:GLU115 4.4 51.9 1.0
O B:ALA96 4.4 30.4 1.0
CG B:GLU112 4.5 39.9 1.0
O B:HOH437 4.5 27.5 1.0
OE1 B:GLU116 4.7 37.7 1.0
O B:GLU112 4.7 30.8 1.0
CA B:GLU112 4.7 38.0 1.0
CB B:GLU116 4.8 35.5 1.0
CB B:GLU112 4.8 42.2 1.0
CG B:GLU166 4.8 68.1 1.0
CG B:GLU115 4.9 48.0 1.0
N B:GLU116 5.0 35.6 1.0

Magnesium binding site 5 out of 8 in 5qtn

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Magnesium binding site 5 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432


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 -- Crystal Structure of NUDT5 in Complex with Ss-4432 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:79.8
occ:1.00
 O C:HOH427 1.8 43.0 1.0
O C:HOH420 2.1 45.0 1.0
OE2 C:GLU112 2.3 40.8 1.0
OE2 C:GLU166 2.6 71.9 1.0
O C:HOH448 2.7 62.2 1.0
CD C:GLU112 3.1 44.1 1.0
OE1 C:GLU112 3.1 53.3 1.0
OE2 C:GLU116 3.2 32.6 1.0
CD C:GLU166 3.3 71.3 1.0
OE1 C:GLU166 3.5 70.2 1.0
MG C:MG303 3.6 30.3 1.0
O C:ALA96 3.9 30.9 1.0
O C:HOH440 4.1 53.0 1.0
O C:HOH429 4.1 36.9 1.0
CD C:GLU116 4.2 32.6 1.0
OE2 C:GLU115 4.4 48.8 1.0
CG C:GLU116 4.4 32.2 1.0
CA C:GLY97 4.4 34.1 1.0
CG C:GLU112 4.5 37.8 1.0
CG C:GLU166 4.6 66.5 1.0
O C:HOH464 4.7 50.4 1.0
C C:ALA96 4.8 29.3 1.0
O C:HOH443 4.9 25.5 1.0

Magnesium binding site 6 out of 8 in 5qtn

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Magnesium binding site 6 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432


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 -- Crystal Structure of NUDT5 in Complex with Ss-4432 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:30.3
occ:1.00
 OE2 C:GLU116 2.0 32.6 1.0
O C:HOH429 2.0 36.9 1.0
O C:HOH443 2.0 25.5 1.0
O C:ALA96 2.1 30.9 1.0
O C:HOH427 2.1 43.0 1.0
O C:HOH423 2.1 23.3 1.0
CD C:GLU116 3.0 32.6 1.0
C C:ALA96 3.2 29.3 1.0
OE1 C:GLU116 3.4 39.1 1.0
OE2 C:GLU166 3.5 71.9 1.0
MG C:MG302 3.6 79.8 1.0
N C:GLY97 4.1 31.2 1.0
N C:ALA96 4.1 27.5 1.0
CA C:ALA96 4.2 26.3 1.0
NE2 C:GLN82 4.2 31.9 1.0
CA C:GLY97 4.3 34.1 1.0
NH2 C:ARG84 4.3 30.8 1.0
OE2 C:GLU112 4.3 40.8 1.0
OE1 C:GLN82 4.3 33.2 1.0
CG C:GLU116 4.3 32.2 1.0
CB C:ALA96 4.6 24.4 1.0
CD C:GLN82 4.7 38.3 1.0
CD C:GLU166 4.8 71.3 1.0
O C:HOH420 4.9 45.0 1.0

Magnesium binding site 7 out of 8 in 5qtn

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Magnesium binding site 7 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432


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 -- Crystal Structure of NUDT5 in Complex with Ss-4432 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:43.8
occ:1.00
 OE2 D:GLU116 2.0 49.1 1.0
O D:HOH407 2.2 28.5 1.0
MG D:MG302 2.3 49.0 1.0
O D:HOH404 2.4 34.2 1.0
O D:HOH425 2.8 50.7 1.0
O D:ALA96 3.1 54.0 1.0
CD D:GLU116 3.2 52.6 1.0
OE2 D:GLU166 3.4 93.1 1.0
NE2 D:GLN82 3.6 57.6 1.0
OE1 D:GLU116 3.7 42.9 1.0
NH2 D:ARG84 4.1 49.9 1.0
C D:ALA96 4.2 57.3 1.0
CG D:GLU116 4.4 49.6 1.0
OE1 D:GLN82 4.4 61.1 1.0
CD D:GLU166 4.4 91.1 1.0
CD D:GLN82 4.4 56.5 1.0
OE2 D:GLU112 4.5 64.5 1.0
NH1 D:ARG84 4.5 45.1 1.0
O D:HOH408 4.7 44.5 1.0
CZ D:ARG84 4.8 46.1 1.0
N D:ALA96 4.9 51.6 1.0
CG D:GLU166 4.9 83.7 1.0

Magnesium binding site 8 out of 8 in 5qtn

Go back to Magnesium Binding Sites List in 5qtn
Magnesium binding site 8 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432


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 -- Crystal Structure of NUDT5 in Complex with Ss-4432 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:49.0
occ:1.00
 MG D:MG301 2.3 43.8 1.0
OE2 D:GLU112 2.4 64.5 1.0
O D:HOH425 2.6 50.7 1.0
OE2 D:GLU116 2.7 49.1 1.0
OE2 D:GLU166 2.8 93.1 1.0
O D:HOH407 2.9 28.5 1.0
O D:HOH402 2.9 49.0 1.0
O D:ALA96 2.9 54.0 1.0
CD D:GLU112 3.4 66.1 1.0
O D:HOH408 3.6 44.5 1.0
CA D:GLY97 3.6 54.1 1.0
CD D:GLU116 3.8 52.6 1.0
C D:ALA96 3.9 57.3 1.0
CG D:GLU112 3.9 63.3 1.0
CD D:GLU166 4.1 91.1 1.0
O D:HOH404 4.1 34.2 1.0
N D:GLY97 4.2 52.1 1.0
OE1 D:GLU112 4.5 73.0 1.0
OE1 D:GLU116 4.6 42.9 1.0
CG D:GLU116 4.7 49.6 1.0
OE1 D:GLU166 4.8 88.0 1.0
C D:GLY97 4.9 53.2 1.0

Reference:

Y.Dubianok, T.Krojer, H.Kovacs, F.Moriaud, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft. Pandda Analysis Group Deposition To Be Published.
Page generated: Mon Sep 30 02:33:43 2024

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