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Magnesium in PDB 6gru: Crystal Structure of Human NUDT5

Enzymatic activity of Crystal Structure of Human NUDT5

All present enzymatic activity of Crystal Structure of Human NUDT5:
2.7.7.96; 3.6.1.13; 3.6.1.58;

Protein crystallography data

The structure of Crystal Structure of Human NUDT5, PDB code: 6gru was solved by Y.Dubianok, P.Collins, T.Krojer, M.Fairhead, E.Maclean, L.Diaz Saez, C.Strain-Damerell, J.Elkins, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, K.Huber, F.Von Delft, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.03 / 1.93
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.600, 60.140, 80.010, 79.92, 81.52, 75.49
R / Rfree (%) 23.1 / 27

Other elements in 6gru:

The structure of Crystal Structure of Human NUDT5 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human NUDT5 (pdb code 6gru). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Human NUDT5, PDB code: 6gru:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6gru

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Magnesium binding site 1 out of 8 in the Crystal Structure of Human NUDT5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human NUDT5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:31.5
occ:1.00
 O A:ALA96 1.9 29.9 1.0
O A:HOH436 2.0 26.9 1.0
OE2 A:GLU116 2.1 32.3 1.0
O A:HOH405 2.1 26.9 1.0
O A:HOH414 2.1 30.7 1.0
O A:HOH419 2.1 25.2 1.0
CD A:GLU116 3.0 31.9 1.0
C A:ALA96 3.1 28.6 1.0
OE1 A:GLU116 3.3 32.7 1.0
MG A:MG302 3.3 35.4 1.0
O A:HOH464 3.5 28.2 1.0
OE2 A:GLU166 3.7 43.2 1.0
N A:GLY97 4.0 27.4 1.0
OE2 A:GLU112 4.0 36.6 1.0
CA A:GLY97 4.0 28.6 1.0
CA A:ALA96 4.1 27.6 1.0
N A:ALA96 4.1 26.6 1.0
O A:HOH411 4.2 24.8 1.0
NH2 A:ARG84 4.2 35.1 1.0
NE2 A:GLN82 4.4 29.5 1.0
O A:HOH463 4.4 39.0 1.0
CG A:GLU116 4.4 34.0 1.0
OE1 A:GLN82 4.4 31.2 1.0
CB A:ALA96 4.6 25.9 1.0
O A:HOH454 4.6 46.3 1.0
O A:HOH421 4.7 40.8 1.0
CD A:GLN82 4.8 33.7 1.0
CD A:GLU166 4.8 46.7 1.0
CD A:GLU112 5.0 35.2 1.0

Magnesium binding site 2 out of 8 in 6gru

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Magnesium binding site 2 out of 8 in the Crystal Structure of Human NUDT5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human NUDT5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:35.4
occ:1.00
 O A:HOH417 1.9 35.6 1.0
O A:HOH421 1.9 40.8 1.0
OE2 A:GLU112 1.9 36.6 1.0
O A:HOH405 2.0 26.9 1.0
OE2 A:GLU166 2.0 43.2 1.0
OE2 A:GLU116 2.3 32.3 1.0
CD A:GLU112 3.0 35.2 1.0
CD A:GLU166 3.0 46.7 1.0
CD A:GLU116 3.3 31.9 1.0
O A:HOH464 3.3 28.2 1.0
MG A:MG301 3.3 31.5 1.0
OE1 A:GLU112 3.4 33.5 1.0
OE1 A:GLU166 3.4 46.6 1.0
CG A:GLU116 3.5 34.0 1.0
O A:HOH419 3.7 25.2 1.0
O A:ALA96 3.9 29.9 1.0
OE2 A:GLU115 4.1 35.8 1.0
CG A:GLU112 4.4 31.6 1.0
CG A:GLU166 4.4 51.1 1.0
OE1 A:GLU116 4.5 32.7 1.0
CB A:GLU112 4.7 32.9 1.0
CA A:GLY97 4.7 28.6 1.0
C A:ALA96 4.8 28.6 1.0
O A:HOH436 4.9 26.9 1.0

Magnesium binding site 3 out of 8 in 6gru

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Magnesium binding site 3 out of 8 in the Crystal Structure of Human NUDT5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human NUDT5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:35.8
occ:1.00
 O B:HOH427 2.0 31.9 1.0
O B:ALA96 2.0 32.3 1.0
OE2 B:GLU116 2.0 39.6 1.0
O B:HOH415 2.1 34.1 1.0
O B:HOH441 2.2 28.5 1.0
O B:HOH454 2.5 38.7 1.0
CD B:GLU116 3.0 43.6 1.0
MG B:MG303 3.1 49.7 1.0
C B:ALA96 3.2 32.3 1.0
OE1 B:GLU116 3.3 40.3 1.0
OE2 B:GLU166 3.5 53.8 1.0
OE2 B:GLU112 4.1 35.1 1.0
N B:GLY97 4.1 28.6 1.0
CA B:GLY97 4.1 32.1 1.0
O B:HOH406 4.2 35.5 1.0
N B:ALA96 4.2 28.9 1.0
CA B:ALA96 4.2 32.6 1.0
NH2 B:ARG84 4.3 40.7 1.0
OE1 B:GLN82 4.3 40.0 1.0
NE2 B:GLN82 4.3 37.7 1.0
CG B:GLU116 4.4 37.2 1.0
O B:HOH460 4.5 46.2 1.0
CD B:GLU166 4.6 59.5 1.0
CB B:ALA96 4.7 35.0 1.0
CD B:GLN82 4.7 40.7 1.0
O B:HOH429 4.8 39.5 1.0
O B:HOH416 4.9 50.6 1.0

Magnesium binding site 4 out of 8 in 6gru

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Magnesium binding site 4 out of 8 in the Crystal Structure of Human NUDT5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human NUDT5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:49.7
occ:1.00
 OE2 B:GLU112 1.8 35.1 1.0
O B:HOH429 2.1 39.5 1.0
O B:HOH416 2.1 50.6 1.0
OE2 B:GLU166 2.2 53.8 1.0
OE2 B:GLU116 2.4 39.6 1.0
O B:HOH454 2.4 38.7 1.0
CD B:GLU112 2.8 37.8 1.0
MG B:MG302 3.1 35.8 1.0
OE1 B:GLU112 3.2 41.7 1.0
CD B:GLU166 3.3 59.5 1.0
CD B:GLU116 3.4 43.6 1.0
O B:ALA96 3.6 32.3 1.0
OE1 B:GLU166 3.7 62.9 1.0
CG B:GLU116 3.7 37.2 1.0
O B:HOH427 3.8 31.9 1.0
CG B:GLU112 4.2 36.4 1.0
OE2 B:GLU115 4.3 54.3 1.0
CA B:GLY97 4.4 32.1 1.0
OE1 B:GLU116 4.5 40.3 1.0
C B:ALA96 4.5 32.3 1.0
CG B:GLU166 4.6 61.5 1.0
CB B:GLU112 4.6 38.2 1.0
N B:GLY97 4.8 28.6 1.0
O B:HOH441 4.8 28.5 1.0
O B:HOH415 4.9 34.1 1.0

Magnesium binding site 5 out of 8 in 6gru

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Magnesium binding site 5 out of 8 in the Crystal Structure of Human NUDT5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human NUDT5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:43.8
occ:1.00
 O C:HOH454 2.0 37.5 1.0
O C:HOH401 2.1 40.5 1.0
OE2 C:GLU166 2.3 43.3 1.0
MG C:MG303 2.3 32.0 1.0
OE2 C:GLU112 2.5 43.8 1.0
O C:HOH414 2.5 53.5 1.0
OE2 C:GLU116 2.5 32.9 1.0
O C:HOH425 3.1 35.9 1.0
O C:ALA96 3.2 34.0 1.0
CD C:GLU112 3.3 47.8 1.0
CD C:GLU166 3.5 43.4 1.0
OE1 C:GLU112 3.6 58.8 1.0
O C:HOH423 3.7 35.7 1.0
CD C:GLU116 3.7 30.6 1.0
CA C:GLY97 3.9 43.4 1.0
OE1 C:GLU166 4.2 45.0 1.0
C C:ALA96 4.2 37.4 1.0
O C:HOH412 4.4 31.0 1.0
CG C:GLU116 4.4 29.7 1.0
N C:GLY97 4.5 37.3 1.0
CG C:GLU166 4.5 49.8 1.0
O C:HOH436 4.5 56.5 1.0
OE1 C:GLU116 4.6 36.1 1.0
CG C:GLU112 4.7 46.0 1.0

Magnesium binding site 6 out of 8 in 6gru

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Magnesium binding site 6 out of 8 in the Crystal Structure of Human NUDT5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human NUDT5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:32.0
occ:1.00
 O C:HOH425 1.9 35.9 1.0
OE2 C:GLU116 2.0 32.9 1.0
O C:HOH423 2.0 35.7 1.0
O C:ALA96 2.1 34.0 1.0
O C:HOH412 2.1 31.0 1.0
MG C:MG302 2.3 43.8 1.0
CD C:GLU116 3.0 30.6 1.0
O C:HOH454 3.1 37.5 1.0
C C:ALA96 3.3 37.4 1.0
OE2 C:GLU166 3.3 43.3 1.0
OE1 C:GLU116 3.4 36.1 1.0
O C:HOH401 3.8 40.5 1.0
OE2 C:GLU112 3.9 43.8 1.0
CA C:GLY97 4.1 43.4 1.0
N C:GLY97 4.1 37.3 1.0
N C:ALA96 4.3 32.5 1.0
CA C:ALA96 4.3 32.9 1.0
CG C:GLU116 4.3 29.7 1.0
NE2 C:GLN82 4.4 34.7 1.0
OE1 C:GLN82 4.4 43.2 1.0
NH2 C:ARG84 4.4 43.3 1.0
CD C:GLU166 4.5 43.4 1.0
O C:HOH414 4.6 53.5 1.0
CD C:GLN82 4.8 47.9 1.0
CB C:ALA96 4.9 31.9 1.0
CD C:GLU112 4.9 47.8 1.0

Magnesium binding site 7 out of 8 in 6gru

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Magnesium binding site 7 out of 8 in the Crystal Structure of Human NUDT5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Human NUDT5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:46.4
occ:1.00
 OE2 D:GLU116 2.0 66.6 1.0
O D:HOH403 2.2 33.4 1.0
O D:HOH402 2.2 32.8 1.0
MG D:MG302 2.4 48.6 1.0
O D:ALA96 2.8 58.1 1.0
O D:HOH424 3.0 47.8 1.0
CD D:GLU116 3.0 72.0 1.0
OE2 D:GLU166 3.1 50.5 1.0
OE1 D:GLU116 3.4 71.7 1.0
NE2 D:GLN82 3.8 59.1 1.0
OE2 D:GLU112 3.9 70.8 1.0
OE1 D:GLN82 4.0 54.7 1.0
CD D:GLU166 4.0 63.5 1.0
C D:ALA96 4.0 61.4 1.0
CG D:GLU116 4.3 65.5 1.0
CD D:GLN82 4.3 66.5 1.0
CG D:GLU166 4.4 60.0 1.0
NH2 D:ARG84 4.4 58.9 1.0
CD D:GLU112 4.8 64.9 1.0
N D:ALA96 4.8 58.7 1.0
O D:HOH407 4.8 41.2 1.0
CA D:GLY97 4.8 68.3 1.0
N D:GLY97 4.9 61.1 1.0
CA D:ALA96 5.0 60.9 1.0
NH1 D:ARG84 5.0 61.5 1.0
CG D:GLU112 5.0 68.4 1.0

Magnesium binding site 8 out of 8 in 6gru

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Magnesium binding site 8 out of 8 in the Crystal Structure of Human NUDT5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Human NUDT5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:48.6
occ:1.00
 O D:HOH424 2.1 47.8 1.0
OE2 D:GLU166 2.3 50.5 1.0
OE2 D:GLU112 2.3 70.8 1.0
MG D:MG301 2.4 46.4 1.0
O D:HOH408 2.8 46.4 1.0
OE2 D:GLU116 2.9 66.6 1.0
O D:HOH403 3.2 33.4 1.0
O D:ALA96 3.2 58.1 1.0
CD D:GLU112 3.4 64.9 1.0
CD D:GLU166 3.5 63.5 1.0
CA D:GLY97 3.8 68.3 1.0
O D:HOH407 3.9 41.2 1.0
OE1 D:GLU112 4.1 67.8 1.0
CD D:GLU116 4.1 72.0 1.0
C D:ALA96 4.2 61.4 1.0
CG D:GLU166 4.2 60.0 1.0
CG D:GLU112 4.2 68.4 1.0
O D:HOH402 4.4 32.8 1.0
OE1 D:GLU166 4.4 52.4 1.0
N D:GLY97 4.5 61.1 1.0
CG D:GLU116 4.9 65.5 1.0
OE1 D:GLU116 4.9 71.7 1.0

Reference:

Y.Dubianok, J.Elkins, C.Bountra, C.H.Arrowsmith, A.Edwards, K.Huber, F.Von Delft, Structural Genomics Consortium (Sgc). Crystal Structure of Human NUDT5 To Be Published.
Page generated: Tue Oct 1 01:23:31 2024

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