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Magnesium in PDB 5qkb: Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis

Enzymatic activity of Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis

All present enzymatic activity of Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis:
2.7.7.96; 3.6.1.13; 3.6.1.58;

Protein crystallography data

The structure of Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis, PDB code: 5qkb was solved by Y.Dubianok, P.Collins, T.Krojer, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, K.Huber, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.54 / 1.58
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.074, 59.679, 80.321, 79.44, 81.82, 75.93
R / Rfree (%) 21.9 / 25

Other elements in 5qkb:

The structure of Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis (pdb code 5qkb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis, PDB code: 5qkb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qkb

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Magnesium binding site 1 out of 8 in the Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:23.1
occ:1.00
 OE2 A:GLU116 2.0 24.1 1.0
O A:ALA96 2.1 21.0 1.0
O A:HOH415 2.1 20.5 1.0
O A:HOH433 2.1 20.3 1.0
O A:HOH449 2.2 19.5 1.0
O A:HOH422 2.2 24.2 1.0
CD A:GLU116 3.1 24.6 1.0
MG A:MG302 3.2 50.2 1.0
C A:ALA96 3.3 20.6 1.0
OE1 A:GLU116 3.4 23.7 1.0
OE2 A:GLU166 3.7 53.8 1.0
OE2 A:GLU112 4.1 29.7 1.0
CA A:GLY97 4.1 18.9 1.0
N A:GLY97 4.1 19.4 1.0
N A:ALA96 4.1 16.5 1.0
CA A:ALA96 4.2 17.6 1.0
NH2 A:ARG84 4.3 21.0 1.0
O A:HOH461 4.3 27.6 1.0
O A:HOH416 4.3 19.9 1.0
NE2 A:GLN82 4.4 25.0 1.0
CG A:GLU116 4.4 25.1 1.0
OE1 A:GLN82 4.4 24.8 1.0
O A:HOH454 4.6 34.4 1.0
CB A:ALA96 4.7 17.0 1.0
O A:HOH464 4.7 48.5 1.0
CD A:GLN82 4.8 31.1 1.0
CD A:GLU112 4.9 31.8 1.0
CD A:GLU166 4.9 69.1 1.0
O A:HOH408 4.9 36.2 1.0

Magnesium binding site 2 out of 8 in 5qkb

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Magnesium binding site 2 out of 8 in the Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:50.2
occ:1.00
 O A:HOH408 1.9 36.2 1.0
O A:HOH433 2.0 20.3 1.0
OE2 A:GLU112 2.1 29.7 1.0
OE2 A:GLU166 2.3 53.8 1.0
O A:HOH411 2.4 43.2 1.0
OE2 A:GLU116 2.5 24.1 1.0
CD A:GLU112 3.1 31.8 1.0
CD A:GLU166 3.1 69.1 1.0
MG A:MG301 3.2 23.1 1.0
OE1 A:GLU112 3.4 32.5 1.0
CD A:GLU116 3.4 24.6 1.0
OE1 A:GLU166 3.4 60.3 1.0
CG A:GLU116 3.7 25.1 1.0
O A:ALA96 3.8 21.0 1.0
O A:HOH422 3.8 24.2 1.0
OE2 A:GLU115 4.2 35.1 1.0
CG A:GLU166 4.3 64.6 1.0
O A:HOH454 4.4 34.4 1.0
CG A:GLU112 4.5 26.5 1.0
OE1 A:GLU116 4.5 23.7 1.0
CA A:GLY97 4.7 18.9 1.0
C A:ALA96 4.8 20.6 1.0
CB A:GLU112 4.8 24.9 1.0
O A:HOH449 4.9 19.5 1.0
O A:HOH464 4.9 48.5 1.0
O A:HOH415 4.9 20.5 1.0

Magnesium binding site 3 out of 8 in 5qkb

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Magnesium binding site 3 out of 8 in the Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:26.6
occ:1.00
 O B:ALA96 2.0 24.9 1.0
O B:HOH427 2.0 23.8 1.0
O B:HOH408 2.1 27.2 1.0
OE2 B:GLU116 2.1 30.1 1.0
O B:HOH420 2.1 26.3 1.0
O B:HOH436 2.1 27.9 1.0
CD B:GLU116 3.1 32.0 1.0
C B:ALA96 3.2 23.6 1.0
OE1 B:GLU116 3.3 29.5 1.0
MG B:MG303 3.5 68.4 1.0
OE2 B:GLU166 3.5 56.2 1.0
N B:GLY97 4.1 24.6 1.0
CA B:GLY97 4.1 24.2 1.0
N B:ALA96 4.2 22.1 1.0
OE2 B:GLU112 4.2 36.6 1.0
NH2 B:ARG84 4.2 25.6 1.0
CA B:ALA96 4.2 22.6 1.0
O B:HOH417 4.3 24.6 1.0
NE2 B:GLN82 4.3 34.7 1.0
CG B:GLU116 4.4 31.3 1.0
OE1 B:GLN82 4.5 31.9 1.0
O B:HOH460 4.6 40.9 1.0
CB B:ALA96 4.7 24.9 1.0
CD B:GLU166 4.7 72.8 1.0
CD B:GLN82 4.8 39.0 1.0
CD B:GLU112 5.0 36.9 1.0

Magnesium binding site 4 out of 8 in 5qkb

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Magnesium binding site 4 out of 8 in the Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:68.4
occ:1.00
 O B:HOH404 1.8 52.6 1.0
OE2 B:GLU112 2.0 36.6 1.0
O B:HOH436 2.4 27.9 1.0
OE2 B:GLU166 2.4 56.2 1.0
OE2 B:GLU116 2.5 30.1 1.0
O B:HOH439 2.8 50.9 1.0
CD B:GLU112 3.0 36.9 1.0
CD B:GLU166 3.2 72.8 1.0
OE1 B:GLU166 3.3 79.1 1.0
OE1 B:GLU112 3.3 34.6 1.0
CD B:GLU116 3.4 32.0 1.0
MG B:MG302 3.5 26.6 1.0
CG B:GLU116 3.5 31.3 1.0
OE2 B:GLU115 3.9 42.3 1.0
O B:ALA96 4.0 24.9 1.0
O B:HOH420 4.2 26.3 1.0
CG B:GLU112 4.3 33.7 1.0
OE1 B:GLU116 4.5 29.5 1.0
CG B:GLU166 4.6 67.7 1.0
CB B:GLU112 4.8 33.1 1.0
CA B:GLY97 4.8 24.2 1.0
CB B:GLU115 4.9 35.7 1.0
C B:ALA96 4.9 23.6 1.0
CA B:GLU112 5.0 27.9 1.0
CB B:GLU116 5.0 29.2 1.0

Magnesium binding site 5 out of 8 in 5qkb

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Magnesium binding site 5 out of 8 in the Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:39.1
occ:1.00
 MG C:MG303 2.2 28.0 1.0
O C:HOH402 2.5 41.7 1.0
O C:HOH453 2.7 89.0 1.0
OE2 C:GLU116 2.8 27.7 1.0
O C:ALA96 3.0 23.4 1.0
O C:HOH413 3.0 31.9 1.0
OE2 C:GLU166 3.0 57.8 1.0
O C:HOH443 3.1 26.8 1.0
OE2 C:GLU112 3.1 32.9 1.0
O C:HOH403 3.1 51.5 1.0
CA C:GLY97 3.6 28.8 1.0
CD C:GLU112 3.7 35.1 1.0
OE1 C:GLU112 3.8 44.2 1.0
CD C:GLU166 3.9 69.2 1.0
C C:ALA96 4.0 27.2 1.0
CD C:GLU116 4.1 27.7 1.0
O C:HOH425 4.3 23.8 1.0
N C:GLY97 4.3 26.9 1.0
OE1 C:GLU166 4.5 74.4 1.0
O C:HOH442 4.5 63.8 1.0
O C:HOH462 4.7 49.8 1.0
OE1 C:GLU116 4.8 30.5 1.0
CG C:GLU166 4.9 58.7 1.0
C C:GLY97 4.9 29.3 1.0
CG C:GLU116 5.0 25.9 1.0
CG C:GLU112 5.0 30.9 1.0

Magnesium binding site 6 out of 8 in 5qkb

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Magnesium binding site 6 out of 8 in the Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:28.0
occ:1.00
 OE2 C:GLU116 2.0 27.7 1.0
O C:HOH443 2.0 26.8 1.0
O C:HOH425 2.1 23.8 1.0
O C:ALA96 2.1 23.4 1.0
MG C:MG302 2.2 39.1 1.0
O C:HOH413 2.2 31.9 1.0
CD C:GLU116 3.1 27.7 1.0
C C:ALA96 3.3 27.2 1.0
OE1 C:GLU116 3.4 30.5 1.0
O C:HOH402 3.6 41.7 1.0
OE2 C:GLU166 3.6 57.8 1.0
OE2 C:GLU112 4.1 32.9 1.0
N C:ALA96 4.1 22.7 1.0
CA C:GLY97 4.2 28.8 1.0
N C:GLY97 4.2 26.9 1.0
CA C:ALA96 4.2 22.7 1.0
O C:HOH453 4.3 89.0 1.0
NE2 C:GLN82 4.4 32.1 1.0
NH2 C:ARG84 4.4 28.1 1.0
OE1 C:GLN82 4.5 29.9 1.0
CG C:GLU116 4.5 25.9 1.0
CB C:ALA96 4.6 23.8 1.0
CD C:GLN82 4.8 37.6 1.0
CD C:GLU166 4.9 69.2 1.0
CD C:GLU112 4.9 35.1 1.0

Magnesium binding site 7 out of 8 in 5qkb

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Magnesium binding site 7 out of 8 in the Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:26.9
occ:1.00
 O D:HOH416 2.0 24.9 1.0
OE2 D:GLU116 2.0 26.2 1.0
O D:HOH407 2.0 24.4 1.0
MG D:MG302 2.1 35.4 1.0
O D:ALA96 2.1 25.6 1.0
O D:HOH421 2.9 65.1 1.0
CD D:GLU116 3.1 34.1 1.0
C D:ALA96 3.3 25.7 1.0
OE1 D:GLU116 3.4 28.5 1.0
OE2 D:GLU112 3.7 54.0 1.0
OE2 D:GLU166 3.8 78.7 1.0
CA D:GLY97 4.1 27.3 1.0
N D:ALA96 4.1 24.6 1.0
N D:GLY97 4.1 25.5 1.0
CA D:ALA96 4.2 24.9 1.0
NH2 D:ARG84 4.3 27.7 1.0
CG D:GLU116 4.4 30.0 1.0
NE2 D:GLN82 4.4 29.3 1.0
CD D:GLU112 4.5 45.4 1.0
OE1 D:GLN82 4.5 30.9 1.0
CG D:GLU112 4.6 52.7 1.0
CB D:ALA96 4.6 26.7 1.0
O D:HOH410 4.8 64.7 1.0
CD D:GLN82 4.9 32.8 1.0
CD D:GLU166 5.0 83.3 1.0

Magnesium binding site 8 out of 8 in 5qkb

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Magnesium binding site 8 out of 8 in the Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ground-State Model of NUDT5 and Corresponding Apo Datasets For Pandda Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:35.4
occ:1.00
 O D:HOH421 1.9 65.1 1.0
MG D:MG301 2.1 26.9 1.0
OE2 D:GLU112 2.5 54.0 1.0
OE2 D:GLU166 2.7 78.7 1.0
OE2 D:GLU116 2.8 26.2 1.0
O D:HOH410 2.9 64.7 1.0
O D:HOH416 3.0 24.9 1.0
O D:ALA96 3.1 25.6 1.0
CD D:GLU112 3.4 45.4 1.0
CA D:GLY97 3.6 27.3 1.0
CD D:GLU166 3.9 83.3 1.0
C D:ALA96 4.0 25.7 1.0
CD D:GLU116 4.0 34.1 1.0
O D:HOH406 4.0 47.8 1.0
OE1 D:GLU112 4.1 52.6 1.0
O D:HOH407 4.2 24.4 1.0
CG D:GLU112 4.3 52.7 1.0
N D:GLY97 4.3 25.5 1.0
OE1 D:GLU166 4.7 88.7 1.0
CG D:GLU166 4.8 73.3 1.0
OE1 D:GLU116 4.8 28.5 1.0
C D:GLY97 4.8 27.9 1.0
CG D:GLU116 4.9 30.0 1.0
N D:LEU98 5.0 31.5 1.0

Reference:

Y.Dubianok, P.Collins, T.Krojer, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, K.Huber, F.Von Delft. Pandda Analysis Group Deposition of Ground-State Model To Be Published.
Page generated: Mon Sep 30 02:29:47 2024

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