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Magnesium in PDB 5qtr: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-3764

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-3764, PDB code: 5qtr 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) 35.06 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.992, 59.760, 80.343, 79.35, 81.73, 75.91
R / Rfree (%) 19.8 / 22.4

Other elements in 5qtr:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-3764 also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-3764 (pdb code 5qtr). 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-3764, PDB code: 5qtr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qtr

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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-3764


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-3764 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:22.6
occ:1.00
 OE2 A:GLU116 2.0 21.9 1.0
O A:HOH468 2.1 20.8 1.0
O A:ALA96 2.1 21.3 1.0
O A:HOH456 2.1 23.3 1.0
O A:HOH496 2.1 21.0 1.0
O A:HOH424 2.1 19.9 1.0
CD A:GLU116 3.1 21.2 1.0
MG A:MG302 3.1 48.5 1.0
C A:ALA96 3.3 20.0 1.0
OE1 A:GLU116 3.4 23.1 1.0
OE2 A:GLU166 3.8 50.8 1.0
OE2 A:GLU112 4.1 30.1 1.0
CA A:GLY97 4.1 19.4 1.0
N A:GLY97 4.1 19.0 1.0
N A:ALA96 4.2 18.5 1.0
O A:HOH491 4.2 24.6 0.8
CA A:ALA96 4.2 17.2 1.0
NH2 A:ARG84 4.3 23.6 1.0
O A:HOH440 4.3 19.7 1.0
O A:HOH509 4.4 27.4 1.0
NE2 A:GLN82 4.4 21.6 0.8
CG A:GLU116 4.4 22.8 1.0
OE1 A:GLN82 4.5 22.2 0.8
O A:HOH498 4.6 36.7 1.0
O A:HOH517 4.6 49.1 1.0
CB A:ALA96 4.7 17.7 1.0
O A:HOH414 4.9 36.1 1.0
CD A:GLU112 4.9 29.7 1.0
CD A:GLN82 4.9 23.1 0.8
CD A:GLU166 4.9 67.1 1.0

Magnesium binding site 2 out of 8 in 5qtr

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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-3764


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-3764 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:48.5
occ:1.00
 O A:HOH468 1.8 20.8 1.0
O A:HOH414 1.9 36.1 1.0
OE2 A:GLU112 2.1 30.1 1.0
O A:HOH483 2.2 46.3 1.0
OE2 A:GLU116 2.5 21.9 1.0
OE2 A:GLU166 2.5 50.8 1.0
CD A:GLU112 3.1 29.7 1.0
MG A:MG301 3.1 22.6 1.0
CD A:GLU166 3.2 67.1 1.0
OE1 A:GLU112 3.4 31.6 1.0
CD A:GLU116 3.4 21.2 1.0
OE1 A:GLU166 3.4 59.8 1.0
O A:ALA96 3.7 21.3 1.0
CG A:GLU116 3.7 22.8 1.0
O A:HOH456 3.8 23.3 1.0
O A:HOH498 4.3 36.7 1.0
CG A:GLU166 4.4 58.7 1.0
CG A:GLU112 4.4 27.2 1.0
OE2 A:GLU115 4.4 33.8 1.0
OE1 A:GLU116 4.5 23.1 1.0
CA A:GLY97 4.6 19.4 1.0
O A:HOH517 4.6 49.1 1.0
O A:HOH496 4.7 21.0 1.0
C A:ALA96 4.7 20.0 1.0
CB A:GLU112 4.8 24.3 1.0
O A:HOH424 4.9 19.9 1.0

Magnesium binding site 3 out of 8 in 5qtr

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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-3764


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-3764 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:26.1
occ:1.00
 O B:ALA96 2.0 23.2 1.0
O B:HOH615 2.0 27.2 1.0
O B:HOH643 2.0 27.4 1.0
OE2 B:GLU116 2.1 30.3 1.0
O B:HOH656 2.1 25.1 1.0
O B:HOH655 2.1 26.4 1.0
CD B:GLU116 3.0 29.8 1.0
C B:ALA96 3.2 20.9 1.0
OE1 B:GLU116 3.4 27.6 1.0
OE2 B:GLU166 4.0 56.4 1.0
N B:GLY97 4.1 23.4 1.0
CA B:GLY97 4.1 22.8 1.0
OE2 B:GLU112 4.1 33.3 1.0
NH2 B:ARG84 4.2 26.5 1.0
N B:ALA96 4.2 23.1 1.0
CA B:ALA96 4.2 21.0 1.0
O B:HOH633 4.3 25.6 1.0
O B:HOH689 4.3 32.5 0.8
OE1 B:GLN82 4.4 30.6 1.0
NE2 B:GLN82 4.4 31.7 1.0
CG B:GLU116 4.4 30.5 1.0
O B:HOH688 4.5 36.4 0.8
O B:HOH693 4.5 38.5 1.0
CD B:GLU166 4.7 65.4 1.0
CB B:ALA96 4.7 23.4 1.0
CD B:GLN82 4.7 35.8 1.0
O B:HOH610 4.9 52.2 1.0
CD B:GLU112 4.9 33.5 1.0
O B:HOH631 5.0 52.2 1.0

Magnesium binding site 4 out of 8 in 5qtr

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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-3764


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-3764 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:71.8
occ:1.00
 O B:HOH631 1.9 52.2 1.0
OE2 B:GLU115 3.0 44.1 1.0
OE1 B:GLU112 3.1 32.4 1.0
NH1 B:ARG111 3.3 37.0 1.0
O B:HOH610 3.6 52.2 1.0
OE1 B:GLU166 3.7 67.4 1.0
CD B:GLU112 3.9 33.5 1.0
CD B:GLU115 3.9 42.5 1.0
OE2 B:GLU112 4.0 33.3 1.0
OE1 B:GLU115 4.2 45.2 1.0
CZ B:ARG111 4.5 35.0 1.0
O B:HOH689 4.6 32.5 0.8
CD B:GLU166 4.8 65.4 1.0
O B:HOH655 4.8 26.4 1.0
NH2 B:ARG111 4.9 35.6 1.0

Magnesium binding site 5 out of 8 in 5qtr

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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-3764


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-3764 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:38.4
occ:1.00
 O C:HOH402 2.1 34.7 0.8
MG C:MG303 2.2 29.9 1.0
OE2 C:GLU116 2.9 27.7 1.0
O C:HOH454 3.0 29.1 1.0
O C:ALA96 3.0 25.8 1.0
O C:HOH471 3.1 26.4 1.0
O C:HOH438 3.2 45.1 0.8
OE2 C:GLU112 3.2 34.6 1.0
O C:HOH469 3.2 38.4 0.8
OE2 C:GLU166 3.3 64.8 1.0
CA C:GLY97 3.7 28.2 1.0
CD C:GLU112 3.8 37.1 1.0
OE1 C:GLU112 3.8 38.6 1.0
O C:HOH415 3.9 51.4 1.0
O C:HOH417 4.0 45.0 1.0
CD C:GLU166 4.0 75.1 1.0
C C:ALA96 4.0 27.8 1.0
O1 C:EDO306 4.0 40.2 0.8
CD C:GLU116 4.1 28.7 1.0
C1 C:EDO306 4.3 37.9 0.8
O C:HOH445 4.3 26.6 1.0
N C:GLY97 4.3 25.4 1.0
OE1 C:GLU166 4.4 72.8 1.0
OE1 C:GLU116 4.9 31.7 1.0
CG C:GLU166 4.9 65.6 1.0
CG C:GLU116 5.0 25.5 1.0
C C:GLY97 5.0 29.2 1.0

Magnesium binding site 6 out of 8 in 5qtr

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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-3764


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-3764 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:29.9
occ:1.00
 O C:HOH471 2.1 26.4 1.0
O C:ALA96 2.1 25.8 1.0
OE2 C:GLU116 2.1 27.7 1.0
O C:HOH445 2.1 26.6 1.0
MG C:MG302 2.2 38.4 1.0
O C:HOH454 2.2 29.1 1.0
CD C:GLU116 3.1 28.7 1.0
O C:HOH402 3.2 34.7 0.8
C C:ALA96 3.3 27.8 1.0
OE1 C:GLU116 3.5 31.7 1.0
OE2 C:GLU166 4.1 64.8 1.0
O1 C:EDO306 4.1 40.2 0.8
N C:GLY97 4.1 25.4 1.0
N C:ALA96 4.1 22.5 1.0
OE2 C:GLU112 4.1 34.6 1.0
CA C:GLY97 4.2 28.2 1.0
CA C:ALA96 4.2 23.2 1.0
O C:HOH418 4.3 18.9 0.8
C1 C:EDO306 4.3 37.9 0.8
NH2 C:ARG84 4.3 26.3 1.0
O C:HOH485 4.4 30.3 0.8
OE1 C:GLN82 4.4 30.9 1.0
CG C:GLU116 4.5 25.5 1.0
NE2 C:GLN82 4.5 32.1 1.0
O C:HOH469 4.7 38.4 0.8
CB C:ALA96 4.7 22.8 1.0
CD C:GLU112 4.9 37.1 1.0
CD C:GLN82 4.9 37.6 1.0

Magnesium binding site 7 out of 8 in 5qtr

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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-3764


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-3764 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:25.4
occ:1.00
 O D:HOH463 2.0 23.6 0.8
OE2 D:GLU116 2.0 25.9 1.0
MG D:MG302 2.0 34.0 1.0
O D:HOH444 2.1 24.9 1.0
O D:HOH422 2.1 23.9 1.0
O D:ALA96 2.1 24.8 1.0
CD D:GLU116 3.0 32.6 1.0
C D:ALA96 3.3 23.0 1.0
OE1 D:GLU116 3.3 27.8 1.0
OE2 D:GLU166 3.6 72.9 1.0
OE2 D:GLU112 4.0 33.7 1.0
N D:ALA96 4.1 22.4 1.0
CA D:GLY97 4.2 26.9 1.0
N D:GLY97 4.2 24.7 1.0
CA D:ALA96 4.2 22.4 1.0
O D:HOH473 4.3 25.9 0.8
O D:HOH419 4.4 19.9 0.8
NH2 D:ARG84 4.4 26.2 1.0
CG D:GLU116 4.4 28.5 1.0
NE2 D:GLN82 4.4 27.6 1.0
OE1 D:GLN82 4.5 28.0 1.0
O D:HOH484 4.5 22.7 0.8
CB D:ALA96 4.6 24.3 1.0
O D:HOH459 4.6 33.0 0.8
CD D:GLU166 4.8 74.9 1.0
O D:HOH409 4.9 44.1 1.0
CD D:GLN82 4.9 29.1 1.0
CD D:GLU112 5.0 38.4 1.0

Magnesium binding site 8 out of 8 in 5qtr

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Magnesium binding site 8 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-3764


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-3764 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:34.0
occ:1.00
 MG D:MG301 2.0 25.4 1.0
O D:HOH463 2.8 23.6 0.8
OE2 D:GLU116 2.8 25.9 1.0
OE2 D:GLU166 2.9 72.9 1.0
O D:HOH459 2.9 33.0 0.8
O D:HOH444 2.9 24.9 1.0
O D:ALA96 3.0 24.8 1.0
OE2 D:GLU112 3.2 33.7 1.0
O D:HOH433 3.4 47.0 1.0
CA D:GLY97 3.6 26.9 1.0
O D:HOH409 3.9 44.1 1.0
C D:ALA96 3.9 23.0 1.0
CD D:GLU112 3.9 38.4 1.0
CD D:GLU166 4.0 74.9 1.0
CD D:GLU116 4.0 32.6 1.0
O D:HOH473 4.1 25.9 0.8
O D:HOH422 4.1 23.9 1.0
OE1 D:GLU112 4.1 36.3 1.0
N D:GLY97 4.2 24.7 1.0
O D:HOH484 4.7 22.7 0.8
OE1 D:GLU166 4.8 79.2 1.0
OE1 D:GLU116 4.8 27.8 1.0
C D:GLY97 4.8 27.6 1.0
CG D:GLU166 4.8 64.1 1.0
CG D:GLU116 4.9 28.5 1.0
N D:LEU98 5.0 30.1 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 02:33:44 2024

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