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Magnesium in PDB 5qtm: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639:
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 Fs-2639, PDB code: 5qtm 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) 47.50 / 1.79
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.270, 59.808, 80.068, 79.33, 81.48, 75.66
R / Rfree (%) 21.4 / 24.7

Other elements in 5qtm:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639 also contains other interesting chemical elements:

Fluorine (F) 4 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 Fs-2639 (pdb code 5qtm). 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 Fs-2639, PDB code: 5qtm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qtm

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Magnesium binding site 1 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639


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 Fs-2639 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:26.1
occ:1.00
 O A:HOH439 2.0 23.6 1.0
OE2 A:GLU116 2.0 23.5 1.0
O A:ALA96 2.1 20.4 1.0
O A:HOH460 2.1 20.4 1.0
O A:HOH433 2.1 27.4 1.0
O A:HOH427 2.1 23.1 1.0
CD A:GLU116 3.1 24.0 1.0
C A:ALA96 3.2 19.7 1.0
MG A:MG302 3.4 49.6 1.0
OE1 A:GLU116 3.5 24.9 1.0
OE2 A:GLU166 3.8 56.7 1.0
N A:GLY97 4.1 21.1 1.0
CA A:GLY97 4.1 21.5 1.0
OE2 A:GLU112 4.1 28.9 1.0
N A:ALA96 4.2 18.1 1.0
CA A:ALA96 4.2 18.2 1.0
O A:HOH459 4.2 20.9 0.8
NH2 A:ARG84 4.3 22.2 1.0
O A:HOH422 4.3 20.4 1.0
CG A:GLU116 4.4 24.4 1.0
O A:HOH472 4.4 24.7 1.0
NE2 A:GLN82 4.4 22.7 1.0
OE1 A:GLN82 4.5 23.0 1.0
O A:HOH469 4.6 36.0 1.0
CB A:ALA96 4.7 16.3 1.0
CD A:GLN82 4.8 27.9 1.0
CD A:GLU112 4.8 27.0 1.0

Magnesium binding site 2 out of 8 in 5qtm

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Magnesium binding site 2 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639


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 Fs-2639 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:49.6
occ:1.00
 O A:HOH404 1.9 32.6 1.0
OE2 A:GLU112 2.1 28.9 1.0
O A:HOH439 2.2 23.6 1.0
OE2 A:GLU166 2.4 56.7 1.0
O A:HOH417 2.4 49.7 1.0
OE2 A:GLU116 2.7 23.5 1.0
CD A:GLU112 3.1 27.0 1.0
CD A:GLU166 3.1 65.2 1.0
OE1 A:GLU112 3.3 29.5 1.0
MG A:MG301 3.4 26.1 1.0
OE1 A:GLU166 3.4 60.8 1.0
CD A:GLU116 3.5 24.0 1.0
CG A:GLU116 3.7 24.4 1.0
OE2 A:GLU115 4.0 32.9 1.0
O A:HOH433 4.0 27.4 1.0
O A:ALA96 4.0 20.4 1.0
CG A:GLU166 4.4 60.9 1.0
CG A:GLU112 4.5 25.0 1.0
O A:HOH469 4.6 36.0 1.0
OE1 A:GLU116 4.7 24.9 1.0
CA A:GLY97 4.8 21.5 1.0
CB A:GLU112 4.9 23.3 1.0
C A:ALA96 5.0 19.7 1.0

Magnesium binding site 3 out of 8 in 5qtm

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Magnesium binding site 3 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639


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 Fs-2639 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:29.1
occ:1.00
 O B:ALA96 2.0 25.4 1.0
OE2 B:GLU116 2.1 31.9 1.0
O B:HOH418 2.1 24.7 1.0
O B:HOH461 2.1 22.3 1.0
O B:HOH406 2.2 26.0 1.0
O B:HOH449 2.2 29.5 1.0
CD B:GLU116 3.1 31.6 1.0
C B:ALA96 3.2 22.6 1.0
OE1 B:GLU116 3.4 29.1 1.0
OE2 B:GLU166 4.0 31.2 0.5
N B:GLY97 4.0 25.2 1.0
O B:HOH423 4.1 29.5 1.0
CA B:GLY97 4.1 25.2 1.0
CA B:ALA96 4.2 23.1 1.0
NE2 B:GLN82 4.2 35.0 1.0
N B:ALA96 4.2 24.1 1.0
NH2 B:ARG84 4.3 25.9 1.0
OE2 B:GLU112 4.3 37.2 1.0
CD B:GLU166 4.4 42.4 0.5
OE1 B:GLN82 4.4 33.4 1.0
CG B:GLU116 4.5 30.1 1.0
O B:HOH474 4.5 39.0 1.0
O B:HOH472 4.6 31.2 0.9
CB B:ALA96 4.6 24.7 1.0
OE1 B:GLU166 4.6 41.0 0.5
MG B:MG303 4.7 72.2 1.0
CD B:GLN82 4.7 38.5 1.0

Magnesium binding site 4 out of 8 in 5qtm

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Magnesium binding site 4 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639


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 Fs-2639 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:72.2
occ:1.00
 O B:HOH440 1.6 48.9 1.0
OE1 B:GLU166 2.4 41.0 0.5
O B:HOH449 2.8 29.5 1.0
CD B:GLU166 3.2 42.4 0.5
OE2 B:GLU166 3.2 31.2 0.5
OE2 B:GLU112 3.3 37.2 1.0
OE1 B:GLU112 3.4 31.5 1.0
CD B:GLU112 3.8 34.8 1.0
OE2 B:GLU115 3.8 45.2 1.0
OE2 B:GLU116 4.3 31.9 1.0
CG B:GLU166 4.6 44.1 0.5
MG B:MG302 4.7 29.1 1.0
O B:HOH406 4.9 26.0 1.0

Magnesium binding site 5 out of 8 in 5qtm

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Magnesium binding site 5 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639


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 Fs-2639 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:64.7
occ:1.00
 O C:HOH445 2.0 36.0 1.0
O C:HOH408 2.2 40.3 1.0
OE2 C:GLU112 2.2 33.7 1.0
O C:HOH454 2.2 51.2 1.0
OE2 C:GLU166 2.4 61.7 1.0
OE2 C:GLU116 2.5 31.9 1.0
MG C:MG303 3.1 35.3 1.0
CD C:GLU112 3.2 36.7 1.0
CD C:GLU166 3.2 64.2 1.0
OE1 C:GLU166 3.4 61.9 1.0
CD C:GLU116 3.4 31.0 1.0
OE1 C:GLU112 3.5 42.0 1.0
O C:ALA96 3.6 26.4 1.0
O C:HOH410 3.7 36.6 1.0
CG C:GLU116 3.8 28.0 1.0
O C:HOH463 3.8 51.0 1.0
OE2 C:GLU115 4.3 40.2 1.0
OE1 C:GLU116 4.5 37.3 1.0
CG C:GLU112 4.5 32.7 1.0
CG C:GLU166 4.5 58.3 1.0
O C:HOH457 4.6 42.6 0.9
CA C:GLY97 4.6 27.9 1.0
C C:ALA96 4.6 26.6 1.0
O C:HOH429 4.7 24.7 1.0
O C:HOH432 4.9 23.8 1.0

Magnesium binding site 6 out of 8 in 5qtm

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Magnesium binding site 6 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639


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 Fs-2639 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:35.3
occ:1.00
 OE2 C:GLU116 2.0 31.9 1.0
O C:HOH445 2.1 36.0 1.0
O C:HOH432 2.1 23.8 1.0
O C:HOH429 2.1 24.7 1.0
O C:ALA96 2.1 26.4 1.0
O C:HOH410 2.2 36.6 1.0
MG C:MG302 3.1 64.7 1.0
CD C:GLU116 3.1 31.0 1.0
C C:ALA96 3.3 26.6 1.0
OE1 C:GLU116 3.4 37.3 1.0
OE2 C:GLU166 3.4 61.7 1.0
N C:GLY97 4.2 27.0 1.0
N C:ALA96 4.2 22.5 1.0
O C:HOH414 4.2 27.3 0.9
OE2 C:GLU112 4.3 33.7 1.0
CA C:GLY97 4.3 27.9 1.0
CA C:ALA96 4.3 23.4 1.0
NH2 C:ARG84 4.3 28.9 1.0
O2 C:EDO306 4.3 44.3 0.9
NE2 C:GLN82 4.4 31.1 1.0
OE1 C:GLN82 4.4 30.5 1.0
CG C:GLU116 4.4 28.0 1.0
CB C:ALA96 4.7 21.7 1.0
CD C:GLU166 4.7 64.2 1.0
O C:HOH465 4.7 35.1 0.9
CD C:GLN82 4.8 33.7 1.0
O C:HOH457 4.9 42.6 0.9
CD C:GLU112 5.0 36.7 1.0

Magnesium binding site 7 out of 8 in 5qtm

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Magnesium binding site 7 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639


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 Fs-2639 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:32.5
occ:1.00
 O D:HOH623 1.8 23.8 0.8
O D:HOH614 1.9 27.9 1.0
OE2 D:GLU116 1.9 29.4 1.0
O D:HOH604 2.1 27.0 1.0
O D:ALA96 2.2 33.3 1.0
MG D:MG504 2.3 42.7 1.0
O D:HOH640 2.6 38.8 1.0
CD D:GLU116 3.0 37.6 1.0
OE1 D:GLU116 3.3 32.8 1.0
C D:ALA96 3.3 34.8 1.0
OE2 D:GLU166 3.8 87.1 1.0
OE2 D:GLU112 4.2 53.5 1.0
N D:ALA96 4.2 31.6 1.0
N D:GLY97 4.2 36.2 1.0
NE2 D:GLN82 4.2 37.7 1.0
NH2 D:ARG84 4.2 34.9 1.0
CA D:ALA96 4.3 31.3 1.0
CA D:GLY97 4.3 36.8 1.0
CG D:GLU116 4.3 36.6 1.0
OE1 D:GLN82 4.4 36.4 1.0
O D:HOH608 4.4 29.7 0.8
O D:HOH636 4.6 33.7 0.8
O D:HOH624 4.7 49.8 1.0
CB D:ALA96 4.7 30.1 1.0
CD D:GLN82 4.8 39.5 1.0
O D:HOH642 4.8 36.8 0.8
CD D:GLU112 4.8 52.9 1.0
CG D:GLU112 4.8 56.1 1.0
O D:HOH603 4.9 47.9 1.0
CD D:GLU166 5.0 81.6 1.0

Magnesium binding site 8 out of 8 in 5qtm

Go back to Magnesium Binding Sites List in 5qtm
Magnesium binding site 8 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639


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 Fs-2639 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg504

b:42.7
occ:1.00
 O D:HOH640 1.7 38.8 1.0
MG D:MG503 2.3 32.5 1.0
OE2 D:GLU112 2.4 53.5 1.0
O D:HOH624 2.6 49.8 1.0
OE2 D:GLU116 2.7 29.4 1.0
OE2 D:GLU166 2.9 87.1 1.0
O D:ALA96 2.9 33.3 1.0
O D:HOH623 3.1 23.8 0.8
CD D:GLU112 3.2 52.9 1.0
O D:HOH614 3.2 27.9 1.0
O D:HOH610 3.3 50.9 1.0
O D:HOH603 3.5 47.9 1.0
CA D:GLY97 3.5 36.8 1.0
CD D:GLU116 3.8 37.6 1.0
C D:ALA96 3.9 34.8 1.0
CG D:GLU112 3.9 56.1 1.0
OE1 D:GLU112 4.0 59.2 1.0
CD D:GLU166 4.1 81.6 1.0
N D:GLY97 4.2 36.2 1.0
O D:HOH604 4.3 27.0 1.0
CG D:GLU116 4.6 36.6 1.0
OE1 D:GLU116 4.7 32.8 1.0
OE1 D:GLU166 4.8 80.5 1.0
C D:GLY97 4.8 37.2 1.0
CG D:GLU166 5.0 73.5 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 02:33:24 2024

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