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Magnesium in PDB 4wf7: Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis

Enzymatic activity of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis

All present enzymatic activity of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis:
5.4.99.16;

Protein crystallography data

The structure of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis, PDB code: 4wf7 was solved by Y.L.Wang, S.Y.Chow, Y.T.Lin, Y.C.Hsieh, G.C.Lee, S.H.Liaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.21
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.250, 133.705, 196.614, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 20

Other elements in 4wf7:

The structure of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis (pdb code 4wf7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis, PDB code: 4wf7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4wf7

Go back to Magnesium Binding Sites List in 4wf7
Magnesium binding site 1 out of 4 in the Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:20.0
occ:1.00
OD1 A:ASN26 2.0 36.1 1.0
O A:HOH833 2.2 34.4 1.0
OD1 A:ASP24 2.2 22.8 1.0
O A:LYS30 2.2 28.7 1.0
OD2 A:ASP32 2.2 25.2 1.0
OD1 A:ASP28 2.4 29.1 1.0
CG A:ASP24 3.2 23.0 1.0
CG A:ASN26 3.2 35.0 1.0
CG A:ASP32 3.4 25.5 1.0
CG A:ASP28 3.4 28.4 1.0
C A:LYS30 3.4 26.3 1.0
OD2 A:ASP28 3.7 29.3 1.0
N A:ASN26 3.9 30.4 1.0
CB A:ASP32 3.9 26.2 1.0
OD2 A:ASP24 4.0 21.1 1.0
ND2 A:ASN26 4.0 36.8 1.0
CB A:ASP24 4.1 24.7 1.0
CA A:ASP24 4.1 24.4 1.0
N A:LYS30 4.1 25.0 1.0
N A:GLY25 4.1 28.1 1.0
CA A:LYS30 4.1 27.3 1.0
CB A:LYS30 4.2 29.8 1.0
CB A:ASN26 4.3 31.8 1.0
N A:ASP28 4.3 25.7 1.0
OD1 A:ASP32 4.4 26.4 1.0
C A:GLY31 4.4 26.1 1.0
CA A:ASN26 4.4 31.1 1.0
N A:GLY31 4.4 26.6 1.0
C A:ASP24 4.4 26.7 1.0
O A:ASP77 4.5 31.3 1.0
O A:GLY31 4.5 27.0 1.0
CB A:ASP28 4.6 26.9 1.0
N A:ASP32 4.7 23.4 1.0
C A:ASN26 4.7 29.3 1.0
CA A:GLY31 4.7 25.2 1.0
N A:GLY27 4.7 29.4 1.0
C A:GLY25 4.8 30.1 1.0
CA A:ASP28 4.8 26.7 1.0
N A:GLY29 4.9 25.9 1.0
CA A:ASP32 4.9 24.4 1.0
CA A:GLY25 5.0 29.2 1.0

Magnesium binding site 2 out of 4 in 4wf7

Go back to Magnesium Binding Sites List in 4wf7
Magnesium binding site 2 out of 4 in the Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:21.8
occ:1.00
OD2 B:ASP32 2.1 25.6 1.0
O B:HOH747 2.2 25.7 1.0
OD1 B:ASN26 2.2 30.9 1.0
OD1 B:ASP24 2.3 23.1 1.0
O B:LYS30 2.3 26.9 1.0
OD1 B:ASP28 2.3 27.1 1.0
CG B:ASP28 3.1 28.5 1.0
CG B:ASN26 3.2 31.9 1.0
CG B:ASP24 3.3 24.6 1.0
CG B:ASP32 3.3 26.3 1.0
OD2 B:ASP28 3.4 26.4 1.0
C B:LYS30 3.4 26.9 1.0
ND2 B:ASN26 3.8 34.6 1.0
N B:ASN26 3.9 26.8 1.0
CB B:ASP32 4.0 25.2 1.0
N B:LYS30 4.0 27.4 1.0
OD2 B:ASP24 4.0 23.9 1.0
N B:GLY25 4.1 30.8 1.0
CA B:ASP24 4.1 25.8 1.0
CA B:LYS30 4.1 27.9 1.0
CB B:ASP24 4.2 25.1 1.0
CB B:LYS30 4.3 27.1 1.0
CB B:ASN26 4.3 28.3 1.0
OD1 B:ASP32 4.3 29.1 1.0
N B:ASP28 4.3 27.2 1.0
CB B:ASP28 4.4 26.3 1.0
CA B:ASN26 4.4 27.2 1.0
O B:HOH823 4.4 53.6 1.0
N B:GLY31 4.5 25.4 1.0
C B:ASP24 4.5 28.5 1.0
O B:ASP77 4.5 29.8 1.0
C B:GLY31 4.5 24.8 1.0
C B:ASN26 4.6 27.3 1.0
N B:ASP32 4.6 23.3 1.0
N B:GLY27 4.7 27.3 1.0
CA B:GLY31 4.8 24.7 1.0
CA B:ASP28 4.8 26.8 1.0
O B:GLY31 4.8 25.9 1.0
N B:GLY29 4.8 29.6 1.0
C B:GLY25 4.9 30.1 1.0
CA B:ASP32 5.0 24.0 1.0
C B:ASP28 5.0 28.7 1.0

Magnesium binding site 3 out of 4 in 4wf7

Go back to Magnesium Binding Sites List in 4wf7
Magnesium binding site 3 out of 4 in the Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:23.2
occ:1.00
OD1 C:ASN26 2.2 37.0 1.0
O C:HOH832 2.2 23.1 1.0
O C:LYS30 2.3 25.1 1.0
OD2 C:ASP32 2.3 27.2 1.0
OD1 C:ASP28 2.3 32.4 1.0
OD1 C:ASP24 2.4 24.8 1.0
CG C:ASP28 3.1 32.6 1.0
CG C:ASP24 3.3 25.9 1.0
OD2 C:ASP28 3.3 32.9 1.0
CG C:ASN26 3.3 33.1 1.0
C C:LYS30 3.4 25.4 1.0
CG C:ASP32 3.4 27.6 1.0
CB C:ASP32 3.9 27.0 1.0
ND2 C:ASN26 4.0 35.2 1.0
OD2 C:ASP24 4.0 22.9 1.0
N C:LYS30 4.0 25.0 1.0
N C:ASN26 4.0 31.2 1.0
N C:GLY25 4.1 26.0 1.0
CA C:LYS30 4.1 25.5 1.0
CA C:ASP24 4.1 24.9 1.0
CB C:ASP24 4.2 25.1 1.0
N C:ASP28 4.3 28.6 1.0
CB C:LYS30 4.3 29.9 1.0
O C:ASP77 4.4 27.6 1.0
CB C:ASP28 4.4 30.0 1.0
C C:GLY31 4.4 25.0 1.0
N C:GLY31 4.4 25.1 1.0
CB C:ASN26 4.5 31.6 1.0
OD1 C:ASP32 4.5 30.0 1.0
C C:ASP24 4.5 25.1 1.0
N C:GLY27 4.6 32.7 1.0
N C:ASP32 4.6 24.8 1.0
CA C:GLY31 4.6 24.8 1.0
O C:GLY31 4.6 24.6 1.0
CA C:ASN26 4.7 33.3 1.0
CA C:ASP28 4.8 28.6 1.0
N C:GLY29 4.8 28.2 1.0
CA C:ASP32 4.9 26.1 1.0
C C:ASN26 4.9 33.6 1.0
C C:ASP28 5.0 29.0 1.0

Magnesium binding site 4 out of 4 in 4wf7

Go back to Magnesium Binding Sites List in 4wf7
Magnesium binding site 4 out of 4 in the Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:26.7
occ:1.00
O D:LYS30 2.2 26.8 1.0
OD2 D:ASP32 2.2 31.5 1.0
OD1 D:ASN26 2.2 32.9 1.0
O D:HOH825 2.4 32.1 1.0
OD1 D:ASP28 2.4 28.2 1.0
OD1 D:ASP24 2.5 26.6 1.0
CG D:ASP28 3.2 31.8 1.0
CG D:ASP24 3.3 26.1 1.0
CG D:ASN26 3.4 33.4 1.0
C D:LYS30 3.4 28.0 1.0
CG D:ASP32 3.4 30.3 1.0
OD2 D:ASP28 3.4 32.2 1.0
CB D:ASP32 3.9 27.6 1.0
ND2 D:ASN26 4.0 35.2 1.0
OD2 D:ASP24 4.0 27.2 1.0
N D:LYS30 4.0 28.0 1.0
CA D:LYS30 4.1 28.8 1.0
N D:ASN26 4.1 31.2 1.0
CB D:ASP24 4.1 25.2 1.0
CA D:ASP24 4.2 25.5 1.0
N D:GLY25 4.2 29.2 1.0
CB D:LYS30 4.2 31.6 1.0
N D:ASP28 4.3 29.0 1.0
N D:GLY31 4.4 27.5 1.0
O D:ASP77 4.4 34.1 1.0
OD1 D:ASP32 4.4 28.9 1.0
N D:GLY27 4.5 32.0 1.0
C D:GLY31 4.5 28.6 1.0
CB D:ASP28 4.5 29.8 1.0
C D:ASP24 4.5 27.7 1.0
CB D:ASN26 4.5 32.4 1.0
N D:ASP32 4.7 25.8 1.0
CA D:GLY31 4.7 28.9 1.0
CA D:ASN26 4.7 33.0 1.0
O D:GLY31 4.8 28.1 1.0
CA D:ASP28 4.8 29.0 1.0
C D:ASN26 4.9 33.9 1.0
N D:GLY29 4.9 29.4 1.0
CA D:ASP32 4.9 26.3 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: Tue Aug 20 13:12:33 2024

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