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Magnesium in PDB 5qts: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S:
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 8J-537S, PDB code: 5qts 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) 50.11 / 1.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.315, 59.910, 80.078, 79.34, 81.27, 75.59
R / Rfree (%) 21.7 / 25.1

Other elements in 5qts:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S also contains other interesting chemical elements:

Fluorine (F) 12 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 8J-537S (pdb code 5qts). 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 8J-537S, PDB code: 5qts:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qts

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Magnesium binding site 1 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:26.0
occ:1.00
 OE2 A:GLU116 2.0 25.1 1.0
O A:HOH465 2.1 22.9 1.0
O A:ALA96 2.1 24.8 1.0
O A:HOH455 2.1 24.6 1.0
O A:HOH417 2.2 21.8 1.0
O A:HOH406 2.2 24.6 1.0
CD A:GLU116 3.0 23.9 1.0
C A:ALA96 3.3 21.3 1.0
MG A:MG302 3.3 57.5 1.0
OE1 A:GLU116 3.4 27.1 1.0
OE2 A:GLU166 3.9 49.3 1.0
N A:GLY97 4.1 23.4 1.0
CA A:GLY97 4.1 23.5 1.0
OE2 A:GLU112 4.1 30.5 1.0
NH2 A:ARG84 4.2 19.8 1.0
N A:ALA96 4.2 19.2 1.0
CA A:ALA96 4.2 20.3 1.0
NE2 A:GLN82 4.3 27.5 1.0
O A:HOH421 4.3 17.6 1.0
O A:HOH459 4.3 17.7 0.7
CG A:GLU116 4.4 25.3 1.0
O A:HOH473 4.4 26.6 1.0
OE1 A:GLN82 4.5 22.2 1.0
O A:HOH475 4.5 53.5 1.0
O A:HOH468 4.6 27.9 1.0
CB A:ALA96 4.7 17.1 1.0
CD A:GLN82 4.7 31.3 1.0
CD A:GLU112 4.9 27.6 1.0

Magnesium binding site 2 out of 8 in 5qts

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Magnesium binding site 2 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:57.5
occ:1.00
 O A:HOH455 2.0 24.6 1.0
O A:HOH405 2.0 41.8 1.0
OE2 A:GLU112 2.2 30.5 1.0
OE2 A:GLU166 2.3 49.3 1.0
O A:HOH426 2.4 49.2 1.0
OE2 A:GLU116 2.6 25.1 1.0
CD A:GLU166 3.0 64.8 1.0
CD A:GLU112 3.1 27.6 1.0
OE1 A:GLU166 3.2 66.3 1.0
MG A:MG301 3.3 26.0 1.0
OE1 A:GLU112 3.3 31.4 1.0
CD A:GLU116 3.6 23.9 1.0
CG A:GLU116 3.8 25.3 1.0
O A:HOH406 3.9 24.6 1.0
O A:ALA96 3.9 24.8 1.0
OE2 A:GLU115 4.2 34.6 1.0
O A:HOH468 4.3 27.9 1.0
CG A:GLU166 4.3 58.5 1.0
O A:HOH475 4.4 53.5 1.0
CG A:GLU112 4.5 25.4 1.0
CA A:GLY97 4.6 23.5 1.0
OE1 A:GLU116 4.7 27.1 1.0
O A:HOH465 4.8 22.9 1.0
C A:ALA96 4.9 21.3 1.0
CB A:GLU112 5.0 24.0 1.0

Magnesium binding site 3 out of 8 in 5qts

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Magnesium binding site 3 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:26.2
occ:1.00
 O B:ALA96 2.0 24.2 1.0
OE2 B:GLU116 2.0 38.3 1.0
O B:HOH404 2.1 24.0 1.0
O B:HOH431 2.1 23.9 1.0
O B:HOH421 2.2 28.7 1.0
O B:HOH451 2.2 28.4 1.0
CD B:GLU116 3.1 34.7 1.0
C B:ALA96 3.2 23.1 1.0
MG B:MG303 3.4 80.1 1.0
OE1 B:GLU116 3.4 31.3 1.0
N B:GLY97 4.1 25.5 1.0
OE2 B:GLU166 4.1 57.9 1.0
N B:ALA96 4.1 23.4 1.0
CA B:GLY97 4.1 28.4 1.0
O B:HOH418 4.2 33.0 1.0
CA B:ALA96 4.2 23.8 1.0
NE2 B:GLN82 4.2 37.0 1.0
OE2 B:GLU112 4.2 38.9 1.0
NH2 B:ARG84 4.2 27.1 1.0
OE1 B:GLN82 4.4 35.6 1.0
CG B:GLU116 4.4 31.6 1.0
O B:HOH468 4.6 38.9 1.0
CB B:ALA96 4.7 24.6 1.0
O B:HOH463 4.7 21.0 0.7
CD B:GLN82 4.7 39.2 1.0
CD B:GLU166 5.0 71.1 1.0

Magnesium binding site 4 out of 8 in 5qts

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Magnesium binding site 4 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:80.1
occ:1.00
 OE2 B:GLU112 2.1 38.9 1.0
O B:HOH451 2.4 28.4 1.0
O B:HOH416 2.5 51.3 1.0
OE2 B:GLU166 2.5 57.9 1.0
OE2 B:GLU116 2.5 38.3 1.0
O B:HOH439 2.6 44.3 1.0
CD B:GLU112 3.1 34.6 1.0
CD B:GLU166 3.3 71.1 1.0
OE1 B:GLU112 3.4 30.4 1.0
CD B:GLU116 3.4 34.7 1.0
MG B:MG302 3.4 26.2 1.0
CG B:GLU116 3.5 31.6 1.0
OE1 B:GLU166 3.6 76.1 1.0
O B:ALA96 3.9 24.2 1.0
OE2 B:GLU115 4.2 46.8 1.0
O B:HOH404 4.2 24.0 1.0
CG B:GLU112 4.5 33.7 1.0
OE1 B:GLU116 4.5 31.3 1.0
CA B:GLY97 4.7 28.4 1.0
CG B:GLU166 4.7 66.1 1.0
C B:ALA96 4.8 23.1 1.0
CB B:GLU112 4.8 33.3 1.0
CA B:GLU112 5.0 29.9 1.0
CB B:GLU115 5.0 34.9 1.0

Magnesium binding site 5 out of 8 in 5qts

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Magnesium binding site 5 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:65.2
occ:1.00
 O C:HOH442 1.9 34.6 1.0
O C:HOH408 2.1 48.6 1.0
OE2 C:GLU112 2.3 30.4 1.0
OE2 C:GLU166 2.4 58.2 0.7
OE2 C:GLU116 2.6 29.5 1.0
O C:HOH462 2.8 59.6 1.0
MG C:MG303 3.0 30.3 1.0
O C:HOH457 3.2 54.7 1.0
CD C:GLU112 3.2 36.8 1.0
CD C:GLU166 3.3 59.3 0.7
OE1 C:GLU112 3.5 42.7 1.0
CD C:GLU116 3.5 29.0 1.0
O C:ALA96 3.6 25.3 1.0
OE1 C:GLU166 3.6 60.3 0.7
O C:HOH412 3.8 34.3 1.0
CG C:GLU116 3.9 27.9 1.0
CA C:GLY97 4.4 32.3 1.0
O C:HOH450 4.4 29.4 1.0
OE2 C:GLU115 4.5 43.3 1.0
C C:ALA96 4.5 27.8 1.0
CG C:GLU166 4.5 58.3 0.7
CG C:GLU112 4.6 33.2 1.0
OE1 C:GLU116 4.6 34.9 1.0
O C:HOH424 4.8 23.3 1.0
N C:GLY97 4.8 29.4 1.0

Magnesium binding site 6 out of 8 in 5qts

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Magnesium binding site 6 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:30.3
occ:1.00
 OE2 C:GLU116 1.9 29.5 1.0
O C:HOH450 2.0 29.4 1.0
O C:HOH424 2.0 23.3 1.0
O C:HOH442 2.0 34.6 1.0
O C:HOH412 2.1 34.3 1.0
O C:ALA96 2.1 25.3 1.0
CD C:GLU116 3.0 29.0 1.0
MG C:MG302 3.0 65.2 1.0
C C:ALA96 3.3 27.8 1.0
OE2 C:GLU166 3.3 58.2 0.7
OE1 C:GLU116 3.4 34.9 1.0
N C:GLY97 4.2 29.4 1.0
O C:HOH423 4.2 23.7 0.7
CA C:GLY97 4.3 32.3 1.0
CA C:ALA96 4.3 25.5 1.0
N C:ALA96 4.3 24.2 1.0
NH2 C:ARG84 4.3 25.3 1.0
NE2 C:GLN82 4.3 36.6 1.0
CG C:GLU116 4.3 27.9 1.0
OE2 C:GLU112 4.4 30.4 1.0
OE1 C:GLN82 4.4 31.5 1.0
O C:HOH467 4.5 32.5 0.7
CD C:GLU166 4.6 59.3 0.7
CB C:ALA96 4.6 26.4 1.0
CD C:GLN82 4.8 37.8 1.0
O C:HOH408 4.8 48.6 1.0
O C:HOH464 5.0 38.2 1.0

Magnesium binding site 7 out of 8 in 5qts

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Magnesium binding site 7 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:39.4
occ:1.00
 OE2 D:GLU116 2.0 38.3 1.0
O D:HOH607 2.2 29.0 1.0
O D:HOH605 2.3 30.3 1.0
MG D:MG503 2.4 37.4 1.0
O D:HOH630 2.7 40.7 1.0
CD D:GLU116 3.2 46.9 1.0
O D:ALA96 3.2 45.8 1.0
OE2 D:GLU166 3.2 74.1 0.7
NE2 D:GLN82 3.5 44.3 1.0
OE1 D:GLU116 3.7 39.9 1.0
CD D:GLU166 4.1 72.5 0.7
NH2 D:ARG84 4.1 40.2 1.0
OE1 D:GLN82 4.1 39.9 1.0
CD D:GLN82 4.3 45.9 1.0
CG D:GLU166 4.3 68.6 0.7
C D:ALA96 4.4 43.0 1.0
OE2 D:GLU112 4.4 59.6 1.0
CG D:GLU116 4.4 43.2 1.0
O D:HOH620 4.5 32.4 0.7
O D:HOH603 4.5 46.7 1.0
NH1 D:ARG84 4.8 35.5 1.0
CZ D:ARG84 4.9 40.0 1.0

Magnesium binding site 8 out of 8 in 5qts

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Magnesium binding site 8 out of 8 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:37.4
occ:1.00
 O D:HOH630 2.1 40.7 1.0
MG D:MG502 2.4 39.4 1.0
OE2 D:GLU112 2.5 59.6 1.0
O D:HOH609 2.6 44.4 1.0
OE2 D:GLU166 2.7 74.1 0.7
OE2 D:GLU116 2.8 38.3 1.0
O D:HOH607 2.9 29.0 1.0
O D:ALA96 3.1 45.8 1.0
CD D:GLU112 3.3 56.6 1.0
O D:HOH603 3.5 46.7 1.0
CA D:GLY97 3.5 44.8 1.0
CD D:GLU166 3.8 72.5 0.7
CD D:GLU116 4.0 46.9 1.0
C D:ALA96 4.0 43.0 1.0
OE1 D:GLU112 4.0 55.2 1.0
CG D:GLU112 4.1 56.3 1.0
N D:GLY97 4.2 41.5 1.0
O D:HOH605 4.2 30.3 1.0
OE1 D:GLU166 4.5 71.5 0.7
CG D:GLU116 4.8 43.2 1.0
C D:GLY97 4.8 40.7 1.0
OE1 D:GLU116 4.8 39.9 1.0
CG D:GLU166 4.8 68.6 0.7
O D:HOH620 4.9 32.4 0.7
N D:LEU98 5.0 41.2 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 02:33:46 2024

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