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Magnesium in PDB 4tvu: Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization

Enzymatic activity of Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization

All present enzymatic activity of Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization:
5.4.99.16;

Protein crystallography data

The structure of Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization, PDB code: 4tvu was solved by Y.L.Wang, S.Y.Chow, Y.T.Lin, S.H.Liaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.609, 195.896, 130.986, 90.00, 92.89, 90.00
R / Rfree (%) 19.4 / 23.6

Other elements in 4tvu:

The structure of Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization 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 From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization (pdb code 4tvu). 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 From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization, PDB code: 4tvu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4tvu

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Magnesium binding site 1 out of 8 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization


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 From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:14.9
occ:1.00
 OD1 A:ASN26 2.2 36.9 1.0
O A:LYS30 2.3 27.3 1.0
OD1 A:ASP28 2.3 29.1 1.0
OD2 A:ASP32 2.4 20.3 1.0
OD1 A:ASP24 2.5 25.1 1.0
CG A:ASP28 3.1 30.3 1.0
CG A:ASN26 3.2 33.4 1.0
OD2 A:ASP28 3.2 36.5 1.0
C A:LYS30 3.4 24.3 1.0
CG A:ASP32 3.5 22.3 1.0
CG A:ASP24 3.6 24.9 1.0
ND2 A:ASN26 3.6 35.4 1.0
CB A:ASP32 3.9 22.2 1.0
O A:ASP77 3.9 33.5 1.0
CB A:LYS30 4.0 28.0 1.0
CA A:LYS30 4.0 25.9 1.0
N A:LYS30 4.1 25.3 1.0
OD2 A:ASP24 4.3 22.9 1.0
N A:ASN26 4.3 28.2 1.0
CB A:ASP28 4.4 28.6 1.0
C A:GLY31 4.4 22.1 1.0
O A:GLY31 4.5 25.1 1.0
N A:GLY31 4.5 21.3 1.0
CB A:ASP24 4.5 23.7 1.0
N A:GLY25 4.5 27.5 1.0
CB A:ASN26 4.5 30.1 1.0
N A:ASP28 4.6 26.4 1.0
CA A:ASP24 4.6 24.1 1.0
OD1 A:ASP32 4.6 22.0 1.0
N A:ASP32 4.7 21.9 1.0
O A:HOH777 4.7 36.7 1.0
CA A:GLY31 4.8 22.4 1.0
CA A:ASN26 4.8 28.2 1.0
C A:ASN26 4.9 24.8 1.0
CA A:ASP32 4.9 21.6 1.0
CA A:ASP28 4.9 27.0 1.0
N A:GLY27 5.0 23.7 1.0

Magnesium binding site 2 out of 8 in 4tvu

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Magnesium binding site 2 out of 8 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization


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 From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:9.0
occ:1.00
 O B:LYS30 2.2 22.5 1.0
OD2 B:ASP32 2.2 23.4 1.0
OD1 B:ASP24 2.2 18.6 1.0
OD1 B:ASN26 2.3 37.8 1.0
OD1 B:ASP28 2.4 32.4 1.0
CG B:ASP28 3.2 26.6 1.0
CG B:ASN26 3.3 30.8 1.0
C B:LYS30 3.3 24.2 1.0
CG B:ASP32 3.3 22.0 1.0
CG B:ASP24 3.3 20.3 1.0
OD2 B:ASP28 3.4 26.0 1.0
ND2 B:ASN26 3.7 34.7 1.0
O B:HOH725 3.7 23.4 1.0
CB B:ASP32 3.8 20.1 1.0
CA B:LYS30 4.0 24.6 1.0
N B:LYS30 4.1 25.4 1.0
CB B:LYS30 4.1 25.2 1.0
OD2 B:ASP24 4.1 21.1 1.0
O B:ASP77 4.1 27.7 1.0
N B:ASN26 4.2 23.4 1.0
CB B:ASP24 4.2 19.5 1.0
N B:GLY25 4.3 19.4 1.0
C B:GLY31 4.3 20.1 1.0
CA B:ASP24 4.3 19.1 1.0
N B:GLY31 4.4 23.6 1.0
OD1 B:ASP32 4.4 22.6 1.0
O B:GLY31 4.4 19.9 1.0
N B:ASP32 4.5 18.9 1.0
CB B:ASN26 4.5 26.9 1.0
CB B:ASP28 4.5 25.0 1.0
N B:ASP28 4.6 21.9 1.0
CA B:GLY31 4.7 22.1 1.0
C B:ASP24 4.8 18.8 1.0
CA B:ASN26 4.8 25.3 1.0
CA B:ASP32 4.8 19.6 1.0
N B:GLY27 5.0 24.2 1.0
CA B:ASP28 5.0 23.4 1.0
C B:ASN26 5.0 25.8 1.0

Magnesium binding site 3 out of 8 in 4tvu

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Magnesium binding site 3 out of 8 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization


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 From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:12.7
occ:1.00
 OD1 C:ASN26 2.2 34.8 1.0
O C:LYS30 2.3 28.7 1.0
OD2 C:ASP32 2.3 35.0 1.0
OD1 C:ASP28 2.3 30.8 1.0
OD1 C:ASP24 2.3 43.2 1.0
CG C:ASP28 3.1 31.3 1.0
CG C:ASN26 3.2 35.5 1.0
OD2 C:ASP28 3.3 32.9 1.0
C C:LYS30 3.4 27.8 1.0
CG C:ASP32 3.4 37.1 1.0
CG C:ASP24 3.5 34.6 1.0
ND2 C:ASN26 3.6 38.0 1.0
CB C:ASP32 3.9 34.5 1.0
CA C:LYS30 4.1 26.7 1.0
CB C:LYS30 4.1 27.0 1.0
O C:ASP77 4.1 50.9 1.0
N C:LYS30 4.1 28.8 1.0
N C:ASN26 4.2 36.5 1.0
OD2 C:ASP24 4.2 37.7 1.0
N C:GLY25 4.3 33.4 1.0
CB C:ASP24 4.4 31.7 1.0
CB C:ASN26 4.4 35.5 1.0
CA C:ASP24 4.4 30.6 1.0
C C:GLY31 4.5 33.8 1.0
CB C:ASP28 4.5 30.9 1.0
N C:GLY31 4.5 29.4 1.0
O C:GLY31 4.5 33.8 1.0
N C:ASP28 4.5 32.6 1.0
OD1 C:ASP32 4.6 35.0 1.0
N C:ASP32 4.7 36.3 1.0
CA C:ASN26 4.7 36.0 1.0
CA C:GLY31 4.8 32.3 1.0
C C:ASP24 4.8 30.6 1.0
C C:ASN26 4.9 34.7 1.0
N C:GLY27 4.9 34.5 1.0
CA C:ASP32 4.9 34.2 1.0
CA C:ASP28 5.0 31.4 1.0

Magnesium binding site 4 out of 8 in 4tvu

Go back to Magnesium Binding Sites List in 4tvu
Magnesium binding site 4 out of 8 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization


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 From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:10.0
occ:1.00
 OD2 D:ASP32 2.2 18.2 1.0
O D:LYS30 2.2 17.1 1.0
OD1 D:ASN26 2.2 35.2 1.0
OD1 D:ASP24 2.3 29.6 1.0
O D:HOH797 2.3 25.4 1.0
OD1 D:ASP28 2.4 28.6 1.0
CG D:ASP28 3.2 27.3 1.0
CG D:ASN26 3.2 33.0 1.0
CG D:ASP32 3.3 17.5 1.0
C D:LYS30 3.4 19.2 1.0
CG D:ASP24 3.4 27.4 1.0
OD2 D:ASP28 3.4 28.7 1.0
ND2 D:ASN26 3.7 38.4 1.0
CB D:ASP32 3.8 17.3 1.0
CA D:LYS30 4.1 20.5 1.0
O D:ASP77 4.1 25.2 1.0
N D:LYS30 4.1 20.7 1.0
OD2 D:ASP24 4.2 28.6 1.0
CB D:LYS30 4.2 22.4 1.0
N D:ASN26 4.2 27.8 1.0
N D:GLY25 4.3 24.3 1.0
CB D:ASP24 4.3 24.5 1.0
CA D:ASP24 4.4 22.8 1.0
C D:GLY31 4.4 19.9 1.0
OD1 D:ASP32 4.4 16.0 1.0
N D:GLY31 4.4 19.4 1.0
O D:GLY31 4.5 20.8 1.0
CB D:ASN26 4.5 30.0 1.0
CB D:ASP28 4.6 24.4 1.0
N D:ASP32 4.6 18.6 1.0
N D:ASP28 4.6 25.1 1.0
O D:HOH752 4.7 38.9 1.0
CA D:GLY31 4.7 19.6 1.0
CA D:ASN26 4.8 28.3 1.0
C D:ASP24 4.8 22.1 1.0
CA D:ASP32 4.8 17.3 1.0
N D:GLY27 5.0 25.2 1.0
C D:ASN26 5.0 27.4 1.0

Magnesium binding site 5 out of 8 in 4tvu

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Magnesium binding site 5 out of 8 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization


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 From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:7.7
occ:1.00
 O E:LYS30 2.2 23.0 1.0
OD1 E:ASN26 2.2 30.3 1.0
OD2 E:ASP32 2.3 23.7 1.0
OD1 E:ASP28 2.4 33.9 1.0
OD1 E:ASP24 2.4 20.8 1.0
CG E:ASP28 3.2 28.8 1.0
CG E:ASN26 3.2 29.1 1.0
OD2 E:ASP28 3.4 34.7 1.0
C E:LYS30 3.4 21.6 1.0
CG E:ASP32 3.4 23.0 1.0
CG E:ASP24 3.5 21.0 1.0
ND2 E:ASN26 3.6 30.0 1.0
CB E:ASP32 3.8 21.1 1.0
O E:ASP77 4.0 27.4 1.0
CB E:LYS30 4.1 24.9 1.0
CA E:LYS30 4.1 22.9 1.0
N E:LYS30 4.1 23.2 1.0
N E:ASN26 4.3 27.6 1.0
OD2 E:ASP24 4.3 19.9 1.0
N E:GLY25 4.4 25.0 1.0
C E:GLY31 4.4 21.8 1.0
O E:GLY31 4.4 24.1 1.0
N E:GLY31 4.4 20.7 1.0
CB E:ASP24 4.4 21.9 1.0
CB E:ASN26 4.5 28.0 1.0
CA E:ASP24 4.5 22.9 1.0
OD1 E:ASP32 4.5 24.1 1.0
CB E:ASP28 4.6 25.4 1.0
N E:ASP32 4.6 21.6 1.0
N E:ASP28 4.6 22.9 1.0
CA E:GLY31 4.7 21.1 1.0
CA E:ASN26 4.8 26.8 1.0
CA E:ASP32 4.8 20.9 1.0
C E:ASP24 4.9 24.4 1.0
C E:ASN26 4.9 24.0 1.0

Magnesium binding site 6 out of 8 in 4tvu

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Magnesium binding site 6 out of 8 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization


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 From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:20.5
occ:1.00
 OD1 F:ASN26 2.1 49.7 1.0
OD2 F:ASP32 2.2 47.9 1.0
OD1 F:ASP24 2.3 33.9 1.0
OD1 F:ASP28 2.4 46.4 1.0
O F:LYS30 2.4 30.1 1.0
CG F:ASN26 3.1 47.5 1.0
CG F:ASP28 3.2 43.3 1.0
CG F:ASP32 3.3 41.7 1.0
OD2 F:ASP28 3.4 42.4 1.0
CG F:ASP24 3.5 35.2 1.0
ND2 F:ASN26 3.5 50.0 1.0
C F:LYS30 3.5 32.8 1.0
CB F:ASP32 3.8 39.8 1.0
N F:ASN26 4.1 44.9 1.0
O F:ASP77 4.1 47.5 1.0
CA F:LYS30 4.2 34.1 1.0
OD2 F:ASP24 4.2 36.1 1.0
N F:LYS30 4.3 32.1 1.0
CB F:LYS30 4.3 38.8 1.0
N F:GLY25 4.3 37.8 1.0
CB F:ASN26 4.3 46.4 1.0
OD1 F:ASP32 4.4 44.8 1.0
CB F:ASP24 4.4 35.4 1.0
CA F:ASP24 4.5 34.5 1.0
CB F:ASP28 4.5 42.8 1.0
C F:GLY31 4.5 34.8 1.0
N F:ASP28 4.6 42.9 1.0
N F:GLY31 4.6 33.8 1.0
O F:GLY31 4.6 33.0 1.0
CA F:ASN26 4.6 45.9 1.0
N F:ASP32 4.7 37.1 1.0
C F:ASP24 4.9 34.5 1.0
CA F:GLY31 4.9 34.6 1.0
C F:ASN26 4.9 47.0 1.0
CA F:ASP32 4.9 38.2 1.0
N F:GLY27 4.9 46.5 1.0
CA F:ASP28 5.0 42.0 1.0

Magnesium binding site 7 out of 8 in 4tvu

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Magnesium binding site 7 out of 8 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization


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 From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg601

b:16.7
occ:1.00
 OD1 G:ASN26 2.2 35.5 1.0
OD1 G:ASP28 2.2 32.1 1.0
O G:LYS30 2.2 35.9 1.0
OD1 G:ASP24 2.4 26.8 1.0
OD2 G:ASP32 2.4 32.1 1.0
CG G:ASP28 3.0 30.1 1.0
CG G:ASN26 3.2 34.6 1.0
OD2 G:ASP28 3.2 30.2 1.0
C G:LYS30 3.4 34.5 1.0
CG G:ASP24 3.5 28.4 1.0
CG G:ASP32 3.5 31.1 1.0
ND2 G:ASN26 3.6 37.4 1.0
CB G:ASP32 4.0 28.6 1.0
CA G:LYS30 4.0 35.5 1.0
O G:ASP77 4.0 42.2 1.0
CB G:LYS30 4.0 35.4 1.0
N G:LYS30 4.1 39.6 1.0
OD2 G:ASP24 4.2 26.9 1.0
N G:ASN26 4.3 33.9 1.0
CB G:ASP28 4.4 30.1 1.0
CB G:ASP24 4.4 27.8 1.0
N G:GLY25 4.5 33.4 1.0
N G:GLY31 4.5 32.5 1.0
CB G:ASN26 4.5 33.9 1.0
C G:GLY31 4.5 28.6 1.0
O G:GLY31 4.5 27.1 1.0
N G:ASP28 4.5 32.4 1.0
CA G:ASP24 4.6 29.1 1.0
OD1 G:ASP32 4.7 32.1 1.0
O G:HOH806 4.7 25.3 1.0
N G:ASP32 4.7 27.5 1.0
CA G:ASN26 4.8 33.6 1.0
CA G:GLY31 4.8 30.7 1.0
CA G:ASP28 4.9 31.0 1.0
C G:ASN26 4.9 31.8 1.0
N G:GLY27 5.0 30.1 1.0
C G:ASP24 5.0 31.4 1.0
CA G:ASP32 5.0 27.4 1.0

Magnesium binding site 8 out of 8 in 4tvu

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Magnesium binding site 8 out of 8 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization


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 From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg601

b:28.2
occ:1.00
 OD1 H:ASN26 2.1 48.6 1.0
OD2 H:ASP32 2.2 41.9 1.0
OD1 H:ASP24 2.2 48.0 1.0
O H:LYS30 2.3 33.0 1.0
OD1 H:ASP28 2.3 47.3 1.0
CG H:ASN26 3.1 51.2 1.0
CG H:ASP28 3.2 47.0 1.0
CG H:ASP32 3.4 40.0 1.0
CG H:ASP24 3.4 45.9 1.0
OD2 H:ASP28 3.4 50.6 1.0
C H:LYS30 3.5 39.7 1.0
ND2 H:ASN26 3.5 55.0 1.0
CB H:ASP32 3.9 41.3 1.0
N H:ASN26 4.1 50.2 1.0
OD2 H:ASP24 4.1 44.7 1.0
CA H:LYS30 4.2 41.1 1.0
N H:LYS30 4.2 37.9 1.0
O H:ASP77 4.2 43.6 1.0
CB H:LYS30 4.3 46.4 1.0
N H:GLY25 4.3 39.5 1.0
CB H:ASP24 4.3 42.3 1.0
CB H:ASN26 4.4 51.2 1.0
CA H:ASP24 4.4 39.0 1.0
OD1 H:ASP32 4.4 40.5 1.0
CB H:ASP28 4.5 44.0 1.0
N H:ASP28 4.5 45.3 1.0
C H:GLY31 4.5 45.6 1.0
N H:GLY31 4.6 44.2 1.0
O H:GLY31 4.6 45.7 1.0
CA H:ASN26 4.6 52.4 1.0
N H:ASP32 4.7 45.8 1.0
C H:ASP24 4.8 37.2 1.0
CA H:GLY31 4.8 45.4 1.0
N H:GLY27 4.8 53.6 1.0
C H:ASN26 4.9 53.1 1.0
CA H:ASP32 4.9 43.2 1.0
CA H:ASP28 4.9 42.0 1.0

Reference:

Y.L.Wang, S.Y.Chow, Y.T.Lin, Y.C.Hsieh, G.C.Lee, S.H.Liaw. Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in Catalysis of the Intramolecular Isomerization. Acta Crystallogr.,Sect.D V. 70 3144 2014.
ISSN: ESSN 1399-0047
PubMed: 25478833
DOI: 10.1107/S1399004714022500
Page generated: Mon Dec 14 19:35:10 2020

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