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Magnesium in PDB 5qtq: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-1169

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-1169

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-1169:
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-1169, PDB code: 5qtq 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) 47.30 / 1.82
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.998, 59.703, 80.195, 79.38, 81.67, 75.86
R / Rfree (%) 21.1 / 25

Other elements in 5qtq:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-1169 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-1169 (pdb code 5qtq). 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-1169, PDB code: 5qtq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qtq

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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-1169


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-1169 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:29.2
occ:1.00
 OE2 A:GLU116 1.9 23.8 1.0
O A:HOH455 2.0 21.1 1.0
O A:HOH437 2.1 29.9 1.0
O A:ALA96 2.1 19.8 1.0
O A:HOH410 2.2 23.3 1.0
O A:HOH465 2.2 20.0 1.0
CD A:GLU116 3.0 22.7 1.0
MG A:MG302 3.0 57.9 1.0
C A:ALA96 3.3 20.4 1.0
OE1 A:GLU116 3.4 23.2 1.0
OE2 A:GLU166 3.6 44.5 0.5
CA A:GLY97 4.1 21.0 1.0
OE2 A:GLU112 4.1 26.3 1.0
N A:GLY97 4.1 20.1 1.0
O A:HOH477 4.2 25.2 1.0
N A:ALA96 4.2 19.9 1.0
CA A:ALA96 4.2 18.4 1.0
O A:HOH454 4.3 23.0 0.8
CG A:GLU116 4.3 22.7 1.0
NH2 A:ARG84 4.3 21.8 1.0
NE2 A:GLN82 4.4 23.3 1.0
O A:HOH472 4.4 34.2 1.0
O A:HOH427 4.4 20.0 1.0
O A:HOH480 4.4 47.7 1.0
OE1 A:GLN82 4.5 26.3 1.0
CB A:ALA96 4.7 15.2 1.0
CD A:GLN82 4.8 31.2 1.0
CD A:GLU166 4.8 50.8 0.5
CD A:GLU112 4.8 25.6 1.0
O A:HOH407 4.8 35.5 1.0

Magnesium binding site 2 out of 8 in 5qtq

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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-1169


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-1169 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:57.9
occ:1.00
 O A:HOH407 2.0 35.5 1.0
O A:HOH455 2.0 21.1 1.0
OE2 A:GLU112 2.1 26.3 1.0
OE2 A:GLU116 2.4 23.8 1.0
OE2 A:GLU166 2.6 44.5 0.5
MG A:MG301 3.0 29.2 1.0
CD A:GLU112 3.1 25.6 1.0
CD A:GLU166 3.3 50.8 0.5
CD A:GLU116 3.4 22.7 1.0
OE1 A:GLU112 3.5 26.1 1.0
CG A:GLU116 3.7 22.7 1.0
O A:ALA96 3.7 19.8 1.0
OE1 A:GLU166 3.8 49.1 0.5
O A:HOH437 3.8 29.9 1.0
O A:HOH480 4.1 47.7 1.0
O A:HOH472 4.2 34.2 1.0
O A:HOH468 4.2 49.2 1.0
OE2 A:GLU115 4.4 35.6 1.0
CG A:GLU112 4.4 24.6 1.0
CG A:GLU166 4.4 51.2 0.5
OE1 A:GLU116 4.5 23.2 1.0
CA A:GLY97 4.6 21.0 1.0
C A:ALA96 4.7 20.4 1.0
O A:HOH465 4.8 20.0 1.0
CB A:GLU112 4.8 22.8 1.0
O A:HOH410 4.8 23.3 1.0

Magnesium binding site 3 out of 8 in 5qtq

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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-1169


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-1169 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:28.1
occ:1.00
 O B:ALA96 2.0 23.7 1.0
O B:HOH407 2.1 25.7 1.0
O B:HOH405 2.1 25.1 1.0
OE2 B:GLU116 2.1 31.2 1.0
O B:HOH447 2.1 23.5 1.0
O B:HOH444 2.2 28.2 1.0
CD B:GLU116 3.1 31.4 1.0
C B:ALA96 3.2 22.2 1.0
OE1 B:GLU116 3.4 30.9 1.0
OE2 B:GLU166 3.7 64.5 1.0
N B:GLY97 4.1 22.1 1.0
O B:HOH427 4.1 31.0 1.0
CA B:GLY97 4.1 24.4 1.0
O B:HOH465 4.2 40.7 0.9
CA B:ALA96 4.2 22.5 1.0
N B:ALA96 4.2 22.0 1.0
NH2 B:ARG84 4.2 27.6 1.0
OE2 B:GLU112 4.2 36.5 1.0
NE2 B:GLN82 4.3 34.8 1.0
OE1 B:GLN82 4.3 34.8 1.0
CG B:GLU116 4.4 30.4 1.0
O B:HOH460 4.5 29.4 0.9
O B:HOH472 4.5 38.8 1.0
CB B:ALA96 4.6 22.3 1.0
CD B:GLN82 4.7 36.3 1.0
CD B:GLU166 4.8 68.8 1.0
MG B:MG304 4.9 64.8 1.0
O B:HOH409 5.0 43.9 1.0

Magnesium binding site 4 out of 8 in 5qtq

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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-1169


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-1169 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:64.8
occ:1.00
 O B:HOH422 1.7 44.8 1.0
OE2 B:GLU166 2.5 64.5 1.0
O B:HOH409 2.8 43.9 1.0
CD B:GLU166 3.0 68.8 1.0
O B:HOH444 3.0 28.2 1.0
OE1 B:GLU166 3.5 65.2 1.0
O B:HOH465 3.7 40.7 0.9
CG B:GLU166 3.7 66.7 1.0
OE2 B:GLU112 3.9 36.5 1.0
OE1 B:GLU112 4.1 34.5 1.0
OE2 B:GLU115 4.2 46.3 1.0
CD B:GLU112 4.4 32.9 1.0
OE2 B:GLU116 4.7 31.2 1.0
MG B:MG303 4.9 28.1 1.0

Magnesium binding site 5 out of 8 in 5qtq

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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-1169


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-1169 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:42.9
occ:1.00
 MG C:MG303 2.1 31.2 1.0
OE2 C:GLU166 2.6 78.2 1.0
OE2 C:GLU116 2.7 29.7 1.0
O C:HOH443 2.8 51.9 1.0
O C:ALA96 2.8 26.4 1.0
O C:HOH413 3.0 32.8 1.0
OE2 C:GLU112 3.1 33.6 1.0
O C:HOH460 3.1 24.5 1.0
O C:HOH458 3.3 42.1 1.0
CA C:GLY97 3.6 30.2 1.0
O C:HOH405 3.6 53.7 1.0
CD C:GLU166 3.7 80.8 1.0
CD C:GLU112 3.7 37.8 1.0
OE1 C:GLU112 3.7 42.1 1.0
C C:ALA96 3.8 25.0 1.0
CD C:GLU116 3.9 30.3 1.0
OE1 C:GLU166 4.1 79.4 1.0
N C:GLY97 4.2 29.0 1.0
O C:HOH433 4.2 21.6 1.0
O C:HOH459 4.5 38.0 1.0
CG C:GLU116 4.7 25.9 1.0
OE1 C:GLU116 4.8 35.8 1.0
CG C:GLU166 4.9 71.1 1.0
O C:HOH473 4.9 53.6 1.0
C C:GLY97 4.9 31.1 1.0
CG C:GLU112 5.0 31.9 1.0

Magnesium binding site 6 out of 8 in 5qtq

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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-1169


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-1169 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:31.2
occ:1.00
 OE2 C:GLU116 2.0 29.7 1.0
O C:HOH460 2.0 24.5 1.0
MG C:MG302 2.1 42.9 1.0
O C:HOH413 2.1 32.8 1.0
O C:HOH433 2.1 21.6 1.0
O C:ALA96 2.2 26.4 1.0
CD C:GLU116 3.1 30.3 1.0
C C:ALA96 3.3 25.0 1.0
OE1 C:GLU116 3.5 35.8 1.0
OE2 C:GLU166 3.9 78.2 1.0
N C:GLY97 4.2 29.0 1.0
OE2 C:GLU112 4.2 33.6 1.0
N C:ALA96 4.2 22.6 1.0
CA C:ALA96 4.2 23.1 1.0
NH2 C:ARG84 4.3 27.7 1.0
CA C:GLY97 4.3 30.2 1.0
NE2 C:GLN82 4.3 31.0 1.0
OE1 C:GLN82 4.4 27.9 1.0
O C:HOH414 4.4 23.6 0.9
CG C:GLU116 4.4 25.9 1.0
O C:HOH459 4.4 38.0 1.0
O C:HOH465 4.5 31.4 0.9
CD C:GLU166 4.6 80.8 1.0
CB C:ALA96 4.6 21.4 1.0
CD C:GLN82 4.8 36.6 1.0
O C:HOH405 4.8 53.7 1.0
O C:HOH458 4.8 42.1 1.0
OE1 C:GLU166 4.9 79.4 1.0
O C:HOH443 4.9 51.9 1.0
CD C:GLU112 5.0 37.8 1.0

Magnesium binding site 7 out of 8 in 5qtq

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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-1169


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-1169 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:27.8
occ:1.00
 OE2 D:GLU116 2.0 27.8 1.0
O D:HOH633 2.0 22.5 0.9
O D:HOH632 2.0 24.9 1.0
O D:HOH602 2.1 30.3 1.0
O D:ALA96 2.1 30.3 1.0
MG D:MG503 2.2 39.7 1.0
CD D:GLU116 3.0 32.6 1.0
C D:ALA96 3.3 30.8 1.0
OE1 D:GLU116 3.3 30.1 1.0
OE2 D:GLU112 3.8 46.9 1.0
N D:GLY97 4.2 32.2 1.0
N D:ALA96 4.2 25.9 1.0
CA D:GLY97 4.2 32.8 1.0
CA D:ALA96 4.2 28.4 1.0
CG D:GLU116 4.3 32.5 1.0
NE2 D:GLN82 4.4 32.2 1.0
NH2 D:ARG84 4.4 29.1 1.0
OE2 D:GLU166 4.4 66.8 1.0
O D:HOH604 4.5 44.4 1.0
CD D:GLU112 4.5 45.0 1.0
OE1 D:GLN82 4.5 33.7 1.0
O D:HOH611 4.5 50.1 1.0
CB D:ALA96 4.6 27.8 1.0
O D:HOH607 4.6 24.0 0.9
CG D:GLU112 4.7 50.2 1.0
O D:HOH646 4.7 27.0 0.9
O D:HOH639 4.7 33.1 0.9
O D:HOH635 4.8 35.4 1.0
CD D:GLN82 4.9 34.9 1.0

Magnesium binding site 8 out of 8 in 5qtq

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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-1169


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-1169 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:39.7
occ:1.00
 MG D:MG502 2.2 27.8 1.0
O D:HOH611 2.5 50.1 1.0
OE2 D:GLU112 2.5 46.9 1.0
OE2 D:GLU116 2.7 27.8 1.0
O D:ALA96 3.0 30.3 1.0
OE2 D:GLU166 3.0 66.8 1.0
O D:HOH633 3.0 22.5 0.9
O D:HOH635 3.2 35.4 1.0
O D:HOH632 3.2 24.9 1.0
O D:HOH604 3.3 44.4 1.0
CD D:GLU112 3.4 45.0 1.0
CA D:GLY97 3.5 32.8 1.0
CD D:GLU116 3.9 32.6 1.0
CD D:GLU166 3.9 73.8 1.0
C D:ALA96 4.0 30.8 1.0
OE1 D:GLU112 4.0 47.9 1.0
O D:HOH602 4.2 30.3 1.0
CG D:GLU112 4.2 50.2 1.0
N D:GLY97 4.2 32.2 1.0
OE1 D:GLU166 4.5 72.0 1.0
OE1 D:GLU116 4.7 30.1 1.0
CG D:GLU116 4.7 32.5 1.0
C D:GLY97 4.8 31.1 1.0
O D:HOH639 4.8 33.1 0.9
CG D:GLU166 5.0 65.6 1.0
N D:LEU98 5.0 31.6 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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