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Magnesium in PDB 8z2r: Crystal Structure of Trehalose Synthase Mutant N253T From Deinococcus Radiodurans

Enzymatic activity of Crystal Structure of Trehalose Synthase Mutant N253T From Deinococcus Radiodurans

All present enzymatic activity of Crystal Structure of Trehalose Synthase Mutant N253T From Deinococcus Radiodurans:
5.4.99.16;

Protein crystallography data

The structure of Crystal Structure of Trehalose Synthase Mutant N253T From Deinococcus Radiodurans, PDB code: 8z2r was solved by L.C.Ye, S.C.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.79 / 2.53
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.599, 195.382, 131.317, 90, 92.82, 90
R / Rfree (%) 21.7 / 29

Other elements in 8z2r:

The structure of Crystal Structure of Trehalose Synthase Mutant N253T From Deinococcus Radiodurans also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Trehalose Synthase Mutant N253T From Deinococcus Radiodurans (pdb code 8z2r). 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 Trehalose Synthase Mutant N253T From Deinococcus Radiodurans, PDB code: 8z2r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8z2r

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Magnesium binding site 1 out of 8 in the Crystal Structure of Trehalose Synthase Mutant N253T From Deinococcus Radiodurans


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 Trehalose Synthase Mutant N253T From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:51.8
occ:1.00
 OD1 A:ASN26 2.1 35.0 1.0
O A:LYS30 2.3 27.8 1.0
OD2 A:ASP32 2.4 33.5 1.0
OD1 A:ASP28 2.5 33.7 1.0
OD1 A:ASP24 2.7 26.1 1.0
CG A:ASP28 3.2 32.2 1.0
CG A:ASN26 3.2 32.8 1.0
OD2 A:ASP28 3.4 35.4 1.0
C A:LYS30 3.5 22.5 1.0
CG A:ASP32 3.5 27.8 1.0
CG A:ASP24 3.6 28.8 1.0
CB A:ASP32 3.9 20.2 1.0
ND2 A:ASN26 3.9 32.8 1.0
N A:LYS30 4.0 20.9 1.0
N A:ASN26 4.0 26.5 1.0
CA A:LYS30 4.1 23.4 1.0
N A:GLY25 4.2 25.0 1.0
O A:ASP77 4.2 30.7 1.0
OD2 A:ASP24 4.2 23.1 1.0
CB A:LYS30 4.3 25.7 1.0
C A:GLY31 4.3 22.6 1.0
CB A:ASN26 4.3 25.9 1.0
O A:GLY31 4.4 28.1 1.0
CB A:ASP24 4.4 26.4 1.0
CA A:ASP24 4.5 24.4 1.0
N A:GLY31 4.5 21.5 1.0
N A:ASP28 4.5 25.2 1.0
CB A:ASP28 4.5 25.6 1.0
N A:ASP32 4.6 25.1 1.0
OD1 A:ASP32 4.6 29.9 1.0
CA A:ASN26 4.6 30.2 1.0
CA A:GLY31 4.7 24.4 1.0
C A:ASP24 4.8 26.0 1.0
C A:ASN26 4.8 27.1 1.0
CA A:ASP32 4.9 25.8 1.0
N A:GLY27 4.9 27.1 1.0
N A:GLY29 5.0 27.8 1.0
CA A:ASP28 5.0 21.2 1.0
C A:GLY25 5.0 31.9 1.0

Magnesium binding site 2 out of 8 in 8z2r

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Magnesium binding site 2 out of 8 in the Crystal Structure of Trehalose Synthase Mutant N253T From Deinococcus Radiodurans


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 Trehalose Synthase Mutant N253T From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:23.4
occ:1.00
 O B:LYS30 2.0 23.2 1.0
OD1 B:ASP24 2.1 20.8 1.0
OD1 B:ASP28 2.3 25.4 1.0
OD1 B:ASP32 2.4 24.9 1.0
OD1 B:ASN26 2.4 29.1 1.0
CG B:ASP24 2.9 21.9 1.0
C B:LYS30 3.2 25.5 1.0
CG B:ASP28 3.2 24.5 1.0
OD2 B:ASP24 3.5 21.3 1.0
CG B:ASN26 3.5 22.5 1.0
CG B:ASP32 3.6 27.3 1.0
OD2 B:ASP28 3.7 32.2 1.0
CB B:ASP24 3.9 20.6 1.0
N B:LYS30 3.9 23.7 1.0
CA B:LYS30 4.0 23.0 1.0
CB B:LYS30 4.1 18.9 1.0
CA B:ASP24 4.1 21.2 1.0
ND2 B:ASN26 4.1 34.1 1.0
N B:ASN26 4.1 22.9 1.0
N B:GLY25 4.2 19.7 1.0
N B:GLY31 4.3 27.7 1.0
CB B:ASP32 4.3 22.1 1.0
N B:ASP28 4.3 19.4 1.0
C B:GLY31 4.4 21.9 1.0
O B:GLY31 4.5 24.3 1.0
CB B:ASP28 4.5 16.7 1.0
CA B:GLY31 4.5 22.4 1.0
C B:ASP24 4.6 17.5 1.0
N B:GLY27 4.6 17.7 1.0
O B:ASP77 4.6 24.8 1.0
OD2 B:ASP32 4.6 22.8 1.0
CB B:ASN26 4.7 17.5 1.0
CA B:ASP28 4.8 19.7 1.0
CA B:ASN26 4.8 21.3 1.0
N B:GLY29 4.8 16.5 1.0
N B:ASP32 4.9 18.6 1.0
C B:ASN26 4.9 19.4 1.0
C B:ASP28 4.9 21.8 1.0

Magnesium binding site 3 out of 8 in 8z2r

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Magnesium binding site 3 out of 8 in the Crystal Structure of Trehalose Synthase Mutant N253T From Deinococcus Radiodurans


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 Trehalose Synthase Mutant N253T From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:52.9
occ:1.00
 OD1 C:ASN26 1.9 56.1 1.0
O C:LYS30 2.0 47.9 1.0
OD1 C:ASP24 2.3 50.8 1.0
OD1 C:ASP28 2.3 55.6 1.0
CG C:ASN26 2.9 55.5 1.0
C C:LYS30 3.2 46.3 1.0
OD2 C:ASP32 3.2 55.6 1.0
ND2 C:ASN26 3.3 60.7 1.0
CG C:ASP24 3.4 49.3 1.0
CG C:ASP28 3.4 56.0 1.0
CG C:ASP32 3.8 49.8 1.0
N C:LYS30 3.8 48.5 1.0
OD2 C:ASP28 3.8 57.1 1.0
CB C:ASP32 3.9 42.1 1.0
CA C:LYS30 3.9 45.4 1.0
CB C:ASP24 3.9 47.0 1.0
N C:GLY25 4.0 46.9 1.0
CA C:ASP24 4.0 44.9 1.0
N C:ASN26 4.0 46.9 1.0
N C:ASP32 4.1 48.1 1.0
CB C:LYS30 4.1 49.7 1.0
N C:GLY31 4.2 44.5 1.0
CB C:ASN26 4.3 48.0 1.0
OD2 C:ASP24 4.4 45.5 1.0
C C:ASP24 4.4 41.0 1.0
C C:GLY31 4.4 52.8 1.0
N C:ASP28 4.5 49.8 1.0
N C:GLY27 4.5 55.3 1.0
CA C:GLY31 4.5 48.0 1.0
O C:ASP77 4.5 41.6 1.0
CA C:ASP32 4.6 44.8 1.0
CA C:ASN26 4.6 45.4 1.0
CB C:ASP28 4.7 57.5 1.0
OD1 C:ASP32 4.8 51.1 1.0
N C:GLY29 4.9 49.3 1.0
C C:GLY25 4.9 44.3 1.0
CA C:GLY25 5.0 38.3 1.0
CA C:ASP28 5.0 49.0 1.0
C C:ASP28 5.0 53.0 1.0

Magnesium binding site 4 out of 8 in 8z2r

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Magnesium binding site 4 out of 8 in the Crystal Structure of Trehalose Synthase Mutant N253T From Deinococcus Radiodurans


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 Trehalose Synthase Mutant N253T From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:37.9
occ:1.00
 OD2 D:ASP32 2.1 39.8 1.0
OD1 D:ASN26 2.1 50.7 1.0
OD1 D:ASP24 2.2 47.2 1.0
O D:LYS30 2.3 39.4 1.0
OD1 D:ASP28 2.3 40.4 1.0
OD2 D:ASP28 2.9 30.7 1.0
CG D:ASP28 2.9 37.4 1.0
CG D:ASP32 3.2 35.3 1.0
CG D:ASN26 3.3 47.8 1.0
CG D:ASP24 3.3 39.2 1.0
C D:LYS30 3.5 36.8 1.0
CB D:ASP32 3.7 34.3 1.0
N D:GLY25 3.8 43.5 1.0
N D:ASN26 3.8 44.1 1.0
CB D:ASP24 4.0 39.4 1.0
ND2 D:ASN26 4.2 46.9 1.0
OD1 D:ASP32 4.2 31.5 1.0
CA D:ASP24 4.2 44.5 1.0
OD2 D:ASP24 4.3 38.6 1.0
CB D:ASN26 4.3 40.8 1.0
C D:GLY31 4.3 31.2 1.0
O D:ASP77 4.3 43.8 1.0
N D:ASP32 4.3 31.7 1.0
CB D:ASP28 4.4 40.8 1.0
N D:LYS30 4.4 46.1 1.0
CA D:LYS30 4.4 37.1 1.0
N D:ASP28 4.5 42.8 1.0
CA D:ASN26 4.5 42.8 1.0
N D:GLY31 4.5 39.8 1.0
CA D:GLY31 4.5 38.4 1.0
C D:ASP24 4.5 45.1 1.0
CB D:LYS30 4.6 33.0 1.0
CA D:ASP32 4.7 32.7 1.0
O D:GLY31 4.7 36.6 1.0
C D:ASN26 4.7 44.3 1.0
CA D:GLY25 4.7 40.5 1.0
N D:GLY27 4.7 44.1 1.0
C D:GLY25 4.8 45.9 1.0
CA D:ASP28 4.9 43.5 1.0

Magnesium binding site 5 out of 8 in 8z2r

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Magnesium binding site 5 out of 8 in the Crystal Structure of Trehalose Synthase Mutant N253T From Deinococcus Radiodurans


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 Trehalose Synthase Mutant N253T From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:25.4
occ:1.00
 O E:LYS30 2.1 16.2 1.0
OD1 E:ASN26 2.3 31.7 1.0
OD1 E:ASP28 2.4 28.0 1.0
OD2 E:ASP32 2.4 21.9 1.0
OD1 E:ASP24 2.9 23.6 1.0
CG E:ASP24 3.2 22.9 1.0
C E:LYS30 3.2 16.4 1.0
CG E:ASP28 3.3 29.5 1.0
CG E:ASN26 3.5 23.4 1.0
CG E:ASP32 3.5 19.5 1.0
OD2 E:ASP24 3.6 20.7 1.0
OD2 E:ASP28 3.7 33.1 1.0
N E:LYS30 3.8 18.5 1.0
CA E:LYS30 3.9 20.4 1.0
CB E:ASP24 3.9 17.9 1.0
CB E:LYS30 4.0 18.1 1.0
CB E:ASP32 4.0 16.1 1.0
CA E:ASP24 4.2 20.8 1.0
ND2 E:ASN26 4.2 28.2 1.0
N E:ASP28 4.3 21.1 1.0
N E:ASN26 4.3 25.4 1.0
C E:GLY31 4.3 18.7 1.0
N E:GLY31 4.3 20.1 1.0
N E:GLY25 4.3 20.8 1.0
O E:ASP77 4.4 28.0 1.0
O E:GLY31 4.5 23.4 1.0
N E:ASP32 4.5 16.0 1.0
N E:GLY27 4.5 19.2 1.0
OD1 E:ASP32 4.5 20.6 1.0
CA E:GLY31 4.6 18.9 1.0
CB E:ASN26 4.6 26.4 1.0
CB E:ASP28 4.6 20.5 1.0
C E:ASP24 4.7 22.3 1.0
N E:GLY29 4.8 21.4 1.0
CA E:ASN26 4.8 29.4 1.0
CA E:ASP28 4.8 20.0 1.0
CA E:ASP32 4.9 15.6 1.0
C E:ASN26 5.0 24.6 1.0
C E:ASP28 5.0 23.0 1.0

Magnesium binding site 6 out of 8 in 8z2r

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Magnesium binding site 6 out of 8 in the Crystal Structure of Trehalose Synthase Mutant N253T From Deinococcus Radiodurans


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 Trehalose Synthase Mutant N253T From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:33.6
occ:1.00
 OD1 F:ASN26 2.0 39.0 1.0
OD2 F:ASP32 2.2 27.0 1.0
O F:LYS30 2.4 27.9 1.0
OD1 F:ASP24 2.5 32.9 1.0
OD1 F:ASP28 2.6 38.4 1.0
OD2 F:ASP28 2.9 49.3 1.0
CG F:ASP28 3.0 40.0 1.0
CG F:ASN26 3.1 34.1 1.0
CG F:ASP32 3.2 25.1 1.0
CG F:ASP24 3.5 30.9 1.0
C F:LYS30 3.5 24.9 1.0
CB F:ASP32 3.6 25.7 1.0
ND2 F:ASN26 3.8 37.2 1.0
N F:ASN26 4.1 28.6 1.0
O F:GLY31 4.2 28.0 1.0
N F:GLY25 4.2 31.3 1.0
C F:GLY31 4.2 22.6 1.0
N F:LYS30 4.2 30.2 1.0
CB F:ASN26 4.3 31.6 1.0
CA F:LYS30 4.3 28.5 1.0
O F:ASP77 4.3 38.2 1.0
OD1 F:ASP32 4.3 26.8 1.0
CB F:LYS30 4.3 29.4 1.0
CB F:ASP24 4.3 24.2 1.0
CA F:ASP24 4.3 21.7 1.0
OD2 F:ASP24 4.3 29.9 1.0
CB F:ASP28 4.4 35.6 1.0
N F:ASP28 4.4 33.7 1.0
N F:ASP32 4.5 23.2 1.0
N F:GLY31 4.6 26.3 1.0
CA F:ASN26 4.6 27.8 1.0
CA F:ASP32 4.7 20.6 1.0
CA F:GLY31 4.7 22.2 1.0
N F:GLY27 4.7 29.3 1.0
C F:ASP24 4.7 29.0 1.0
C F:ASN26 4.8 30.3 1.0
CA F:ASP28 4.9 37.0 1.0

Magnesium binding site 7 out of 8 in 8z2r

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Magnesium binding site 7 out of 8 in the Crystal Structure of Trehalose Synthase Mutant N253T From Deinococcus Radiodurans


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 Trehalose Synthase Mutant N253T From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg601

b:60.6
occ:1.00
 OD1 G:ASN26 2.1 48.8 1.0
O G:LYS30 2.2 43.1 1.0
OD2 G:ASP32 2.6 45.7 1.0
OD1 G:ASP28 2.6 45.4 1.0
OD1 G:ASP24 3.0 42.9 1.0
CG G:ASN26 3.0 50.4 1.0
CG G:ASP28 3.2 50.1 1.0
C G:LYS30 3.3 48.0 1.0
OD2 G:ASP28 3.4 50.4 1.0
ND2 G:ASN26 3.4 57.5 1.0
CG G:ASP32 3.4 44.9 1.0
CB G:ASP32 3.6 41.6 1.0
CG G:ASP24 3.7 47.4 1.0
CB G:LYS30 4.0 54.4 1.0
CA G:LYS30 4.0 49.3 1.0
N G:LYS30 4.1 45.4 1.0
CB G:ASP24 4.1 49.1 1.0
N G:ASN26 4.2 49.3 1.0
O G:ASP77 4.2 47.7 1.0
CA G:ASP24 4.3 46.4 1.0
N G:ASP32 4.3 51.6 1.0
N G:GLY25 4.3 48.7 1.0
N G:GLY31 4.4 50.3 1.0
CB G:ASN26 4.4 41.6 1.0
C G:GLY31 4.4 51.9 1.0
CB G:ASP28 4.5 48.6 1.0
OD2 G:ASP24 4.5 47.3 1.0
N G:ASP28 4.6 50.6 1.0
CA G:ASP32 4.6 48.2 1.0
OD1 G:ASP32 4.6 49.4 1.0
CA G:GLY31 4.6 50.0 1.0
N G:GLY27 4.6 47.2 1.0
C G:ASP24 4.7 39.4 1.0
CA G:ASN26 4.8 53.8 1.0
CA G:ASP28 5.0 47.2 1.0

Magnesium binding site 8 out of 8 in 8z2r

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Magnesium binding site 8 out of 8 in the Crystal Structure of Trehalose Synthase Mutant N253T From Deinococcus Radiodurans


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 Trehalose Synthase Mutant N253T From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg601

b:47.2
occ:1.00
 O H:LYS30 2.1 48.2 1.0
OD2 H:ASP32 2.2 52.4 1.0
OD1 H:ASN26 2.4 43.1 1.0
OD1 H:ASP28 2.5 44.9 1.0
OD1 H:ASP24 2.8 45.2 1.0
OD2 H:ASP28 3.1 49.0 1.0
CG H:ASP28 3.1 44.5 1.0
C H:LYS30 3.3 41.0 1.0
CG H:ASP32 3.3 53.1 1.0
CG H:ASP24 3.5 42.9 1.0
CG H:ASN26 3.6 46.1 1.0
O H:GLY31 3.7 48.6 1.0
CB H:ASP32 3.8 44.7 1.0
C H:GLY31 3.9 51.6 1.0
O H:ASP77 4.0 53.1 1.0
OD2 H:ASP24 4.1 45.4 1.0
N H:GLY25 4.1 40.1 1.0
CA H:LYS30 4.2 39.4 1.0
ND2 H:ASN26 4.2 52.1 1.0
N H:GLY31 4.2 44.8 1.0
N H:ASN26 4.2 40.7 1.0
CB H:LYS30 4.3 45.3 1.0
N H:LYS30 4.3 44.4 1.0
CA H:GLY31 4.3 44.5 1.0
CA H:ASP24 4.4 38.8 1.0
OD1 H:ASP32 4.4 39.8 1.0
CB H:ASP24 4.4 39.1 1.0
CB H:ASP28 4.5 41.4 1.0
N H:ASP32 4.5 51.8 1.0
CB H:ASN26 4.7 45.2 1.0
CA H:ASP32 4.8 47.8 1.0
N H:ASP28 4.8 47.1 1.0
C H:ASP24 4.8 42.0 1.0
CA H:ASN26 4.9 45.4 1.0

Reference:

L.C.Ye, S.Y.Chow, S.C.Chang, C.H.Kuo, Y.L.Wang, Y.J.Wei, G.C.Lee, S.H.Liaw, W.M.Chen, S.C.Chen. Structural and Mutational Analyses of Trehalose Synthase From Deinococcus Radiodurans Reveal the Interconversion of Maltose-Trehalose Mechanism. J.Agric.Food Chem. V. 72 18649 2024.
ISSN: ESSN 1520-5118
PubMed: 39109746
DOI: 10.1021/ACS.JAFC.4C03661
Page generated: Sat Feb 8 20:53:21 2025

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