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Magnesium in PDB 8z2t: Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa)

Enzymatic activity of Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa)

All present enzymatic activity of Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa):
5.4.99.16;

Protein crystallography data

The structure of Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa), PDB code: 8z2t 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) 29.99 / 2.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 135.276, 153.247, 154.662, 90, 90, 90
R / Rfree (%) 17.8 / 22.8

Other elements in 8z2t:

The structure of Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa) also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa) (pdb code 8z2t). 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 Structure of Trehalose Synthase From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa), PDB code: 8z2t:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8z2t

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Magnesium binding site 1 out of 4 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa)


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 Complexed with Validoxylamine A (Vaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:46.3
occ:1.00
 OD1 A:ASP28 2.2 41.5 1.0
OD1 A:ASN26 2.4 42.6 1.0
OD2 A:ASP32 2.6 32.4 1.0
O A:LYS30 2.7 36.9 1.0
OD1 A:ASP24 2.9 33.0 1.0
CG A:ASP28 3.0 36.6 1.0
OD2 A:ASP28 3.3 43.5 1.0
CG A:ASN26 3.4 36.0 1.0
CG A:ASP32 3.6 33.6 1.0
C A:LYS30 3.6 34.1 1.0
ND2 A:ASN26 3.8 46.6 1.0
CB A:ASP32 3.8 29.5 1.0
O A:ASP77 3.8 38.2 1.0
CG A:ASP24 4.0 35.5 1.0
CB A:LYS30 4.1 31.7 1.0
N A:LYS30 4.2 32.9 1.0
CA A:LYS30 4.2 36.4 1.0
CB A:ASP28 4.4 32.2 1.0
C A:GLY31 4.5 33.6 1.0
N A:ASP32 4.6 35.0 1.0
O A:GLY31 4.6 33.5 1.0
N A:ASP28 4.6 30.2 1.0
N A:GLY31 4.7 34.0 1.0
OD2 A:ASP24 4.7 33.9 1.0
N A:ASN26 4.7 38.3 1.0
CB A:ASN26 4.7 29.8 1.0
OD1 A:ASP32 4.7 33.0 1.0
CA A:ASP32 4.8 34.4 1.0
CB A:ASP24 4.9 31.8 1.0
CA A:GLY31 4.9 32.5 1.0
N A:GLY25 4.9 32.7 1.0
CA A:ASP28 4.9 29.3 1.0
CA A:ASP24 5.0 30.7 1.0

Magnesium binding site 2 out of 4 in 8z2t

Go back to Magnesium Binding Sites List in 8z2t
Magnesium binding site 2 out of 4 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa)


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 Complexed with Validoxylamine A (Vaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:44.5
occ:1.00
 OD1 B:ASP28 2.1 45.7 1.0
OD1 B:ASN26 2.2 51.8 1.0
O B:LYS30 2.3 35.3 1.0
OD2 B:ASP32 2.4 42.6 1.0
OD1 B:ASP24 2.6 37.5 1.0
CG B:ASP28 3.2 46.6 1.0
CG B:ASN26 3.3 44.9 1.0
CG B:ASP32 3.4 41.5 1.0
C B:LYS30 3.4 31.6 1.0
CG B:ASP24 3.6 43.7 1.0
OD2 B:ASP28 3.6 53.6 1.0
ND2 B:ASN26 3.8 44.0 1.0
CB B:ASP32 3.9 36.4 1.0
N B:LYS30 4.1 38.2 1.0
O B:ASP77 4.1 43.1 1.0
CA B:LYS30 4.1 37.5 1.0
CB B:LYS30 4.2 37.0 1.0
C B:GLY31 4.3 38.5 1.0
N B:ASN26 4.3 44.8 1.0
OD2 B:ASP24 4.3 44.8 1.0
O B:GLY31 4.3 39.8 1.0
CB B:ASP28 4.4 42.1 1.0
CB B:ASP24 4.4 41.7 1.0
N B:GLY25 4.5 35.8 1.0
CA B:ASP24 4.5 39.4 1.0
CB B:ASN26 4.5 43.9 1.0
N B:GLY31 4.5 34.1 1.0
OD1 B:ASP32 4.5 42.9 1.0
N B:ASP28 4.5 38.7 1.0
N B:ASP32 4.5 39.0 1.0
CA B:GLY31 4.7 33.9 1.0
CA B:ASP32 4.8 36.2 1.0
CA B:ASN26 4.8 49.0 1.0
C B:ASP24 4.9 38.7 1.0
CA B:ASP28 4.9 37.2 1.0

Magnesium binding site 3 out of 4 in 8z2t

Go back to Magnesium Binding Sites List in 8z2t
Magnesium binding site 3 out of 4 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa)


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 Complexed with Validoxylamine A (Vaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:38.2
occ:1.00
 OD1 C:ASP28 2.2 47.2 1.0
OD1 C:ASN26 2.3 45.7 1.0
O C:LYS30 2.4 41.2 1.0
OD2 C:ASP32 2.5 37.9 1.0
OD1 C:ASP24 2.7 40.4 1.0
CG C:ASP28 3.1 42.9 1.0
OD2 C:ASP28 3.3 43.0 1.0
CG C:ASN26 3.4 36.6 1.0
C C:LYS30 3.5 37.3 1.0
CG C:ASP32 3.6 41.4 1.0
CG C:ASP24 3.8 37.6 1.0
ND2 C:ASN26 3.8 39.9 1.0
O C:ASP77 3.9 44.7 1.0
CB C:ASP32 4.0 37.4 1.0
N C:LYS30 4.0 35.7 1.0
CB C:LYS30 4.1 35.5 1.0
CA C:LYS30 4.1 38.9 1.0
CB C:ASP28 4.5 36.7 1.0
N C:ASN26 4.5 34.9 1.0
C C:GLY31 4.5 40.6 1.0
OD2 C:ASP24 4.5 35.5 1.0
O C:GLY31 4.6 42.3 1.0
N C:GLY31 4.6 34.6 1.0
N C:ASP28 4.6 35.3 1.0
CB C:ASP24 4.7 35.8 1.0
OD1 C:ASP32 4.7 44.0 1.0
CB C:ASN26 4.7 31.9 1.0
N C:GLY25 4.7 38.5 1.0
N C:ASP32 4.8 39.9 1.0
CA C:ASP24 4.8 34.5 1.0
CA C:GLY31 4.9 36.3 1.0
N C:GLY27 4.9 38.2 1.0
CA C:ASP28 5.0 38.1 1.0

Magnesium binding site 4 out of 4 in 8z2t

Go back to Magnesium Binding Sites List in 8z2t
Magnesium binding site 4 out of 4 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa)


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 Complexed with Validoxylamine A (Vaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:52.3
occ:1.00
 OD1 D:ASP28 2.1 49.9 1.0
O D:LYS30 2.2 47.6 1.0
OD1 D:ASN26 2.3 59.3 1.0
OD2 D:ASP32 2.4 53.4 1.0
OD1 D:ASP24 2.7 48.3 1.0
CG D:ASP28 2.9 52.2 1.0
OD2 D:ASP28 3.0 55.8 1.0
C D:LYS30 3.4 49.0 1.0
CG D:ASN26 3.4 55.8 1.0
CG D:ASP32 3.5 46.9 1.0
CG D:ASP24 3.7 49.0 1.0
O D:ASP77 3.8 52.5 1.0
ND2 D:ASN26 3.9 52.2 1.0
N D:LYS30 3.9 40.4 1.0
CB D:ASP32 4.0 42.3 1.0
CA D:LYS30 4.0 47.5 1.0
CB D:LYS30 4.0 49.6 1.0
CB D:ASP28 4.3 45.2 1.0
C D:GLY31 4.4 47.4 1.0
CB D:ASP24 4.5 45.9 1.0
N D:GLY31 4.5 49.5 1.0
CA D:ASP24 4.5 41.1 1.0
O D:GLY31 4.5 51.0 1.0
N D:GLY25 4.5 45.8 1.0
N D:ASN26 4.6 50.4 1.0
OD2 D:ASP24 4.6 41.1 1.0
OD1 D:ASP32 4.6 44.4 1.0
N D:ASP32 4.6 48.2 1.0
CB D:ASN26 4.7 50.5 1.0
N D:ASP28 4.7 49.0 1.0
CA D:GLY31 4.8 45.6 1.0
C D:ASP24 4.9 49.0 1.0
CA D:ASP28 4.9 46.4 1.0
CG D:LYS30 4.9 47.2 1.0
CA D:ASP32 4.9 45.3 1.0
C D:ASP28 5.0 49.1 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 21:19:39 2025

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