Magnesium in PDB 8z2u: Crystal Structure of Trehalose Synthase Mutamt E324D From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa)

Enzymatic activity of Crystal Structure of Trehalose Synthase Mutamt E324D From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa)

All present enzymatic activity of Crystal Structure of Trehalose Synthase Mutamt E324D From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa):
5.4.99.16;

Protein crystallography data

The structure of Crystal Structure of Trehalose Synthase Mutamt E324D From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa), PDB code: 8z2u 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) 29.14 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 134.731, 152.031, 153.213, 90, 90, 90
R / Rfree (%) 18 / 25.2

Other elements in 8z2u:

The structure of Crystal Structure of Trehalose Synthase Mutamt E324D 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 Mutamt E324D From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa) (pdb code 8z2u). 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 Mutamt E324D From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa), PDB code: 8z2u:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8z2u

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Magnesium binding site 1 out of 4 in the Crystal Structure of Trehalose Synthase Mutamt E324D 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 Mutamt E324D From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:18.7
occ:1.00
 OD1 A:ASN26 2.3 30.2 1.0
O A:LYS30 2.5 26.1 1.0
OD1 A:ASP28 2.8 26.7 1.0
OD1 A:ASP24 2.9 19.9 1.0
CG A:ASP32 3.0 21.0 1.0
OD2 A:ASP32 3.0 25.3 1.0
CB A:ASP32 3.1 20.0 1.0
CG A:ASN26 3.4 21.0 1.0
CG A:ASP28 3.5 32.9 1.0
C A:LYS30 3.5 21.3 1.0
OD2 A:ASP28 3.6 30.7 1.0
OD1 A:ASP32 3.7 23.0 1.0
C A:GLY31 3.8 17.0 1.0
O A:ASP77 3.8 20.6 1.0
O A:GLY31 3.8 22.1 1.0
N A:ASP32 3.9 17.7 1.0
CG A:ASP24 3.9 23.1 1.0
CA A:ASP32 4.0 16.5 1.0
ND2 A:ASN26 4.2 18.7 1.0
CB A:ASN26 4.3 20.5 1.0
CA A:GLY31 4.3 16.9 1.0
N A:GLY31 4.4 15.5 1.0
CA A:LYS30 4.4 23.0 1.0
N A:GLY25 4.4 20.7 1.0
N A:ASN26 4.4 20.9 1.0
CB A:LYS30 4.4 20.9 1.0
CA A:ASP24 4.5 18.8 1.0
CB A:ASP24 4.6 19.6 1.0
N A:LYS30 4.6 20.8 1.0
CB A:ASP28 4.8 16.5 1.0
OD2 A:ASP24 4.8 18.1 1.0
CA A:ASN26 4.9 19.1 1.0
C A:ASP24 4.9 20.8 1.0

Magnesium binding site 2 out of 4 in 8z2u

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Magnesium binding site 2 out of 4 in the Crystal Structure of Trehalose Synthase Mutamt E324D 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 Mutamt E324D From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:27.5
occ:1.00
 OD1 B:ASN26 2.3 20.6 1.0
OD1 B:ASP28 2.3 25.3 1.0
O B:LYS30 2.7 14.6 1.0
CG B:ASP28 3.0 25.9 1.0
OD1 B:ASP24 3.0 18.2 1.0
OD2 B:ASP28 3.1 26.3 1.0
CG B:ASN26 3.3 17.6 1.0
CG B:ASP32 3.3 20.0 1.0
OD1 B:ASP32 3.4 22.0 1.0
CB B:ASP32 3.7 19.2 1.0
OD2 B:ASP32 3.7 21.2 1.0
C B:LYS30 3.8 14.8 1.0
O B:ASP77 3.9 17.2 1.0
ND2 B:ASN26 3.9 18.1 1.0
CG B:ASP24 4.0 20.0 1.0
CB B:ASN26 4.4 23.9 1.0
CB B:ASP28 4.4 18.2 1.0
CB B:LYS30 4.5 17.1 1.0
C B:GLY31 4.5 21.0 1.0
CA B:LYS30 4.5 15.9 1.0
N B:ASP28 4.5 20.3 1.0
N B:ASN26 4.5 19.6 1.0
N B:LYS30 4.6 17.4 1.0
N B:ASP32 4.6 21.0 1.0
OD2 B:ASP24 4.7 15.8 1.0
O B:GLY31 4.7 23.9 1.0
CA B:ASP32 4.7 14.3 1.0
N B:GLY31 4.8 15.5 1.0
N B:GLY27 4.9 22.2 1.0
CA B:ASN26 4.9 18.2 1.0
CA B:GLY31 4.9 14.5 1.0
CB B:ASP24 4.9 20.1 1.0
CA B:ASP28 4.9 21.2 1.0
N B:GLY25 5.0 22.0 1.0

Magnesium binding site 3 out of 4 in 8z2u

Go back to Magnesium Binding Sites List in 8z2u
Magnesium binding site 3 out of 4 in the Crystal Structure of Trehalose Synthase Mutamt E324D 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 Mutamt E324D From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:23.8
occ:1.00
 OD1 C:ASP28 2.7 22.8 1.0
O C:ASP77 2.9 22.7 1.0
OD1 C:ASN26 2.9 27.8 1.0
O C:LYS30 2.9 32.8 1.0
OD2 C:ASP28 3.0 31.4 1.0
CG C:ASP28 3.1 26.3 1.0
CB C:ASP32 3.5 20.4 1.0
OD1 C:ASP24 3.7 26.1 1.0
CG C:ASN26 3.8 19.8 1.0
C C:LYS30 3.8 21.1 1.0
CB C:LYS30 3.8 21.9 1.0
CG C:ASP32 3.9 29.1 1.0
ND2 C:ASN26 3.9 16.8 1.0
C C:ASP77 4.1 21.6 1.0
OD1 C:ASP32 4.2 35.8 1.0
CA C:LYS30 4.3 22.6 1.0
OD2 C:ASP32 4.4 31.0 1.0
CA C:ASP32 4.4 16.9 1.0
C C:GLY31 4.5 20.2 1.0
N C:ASP32 4.5 17.3 1.0
O C:GLY31 4.5 26.2 1.0
N C:LYS30 4.5 23.1 1.0
CB C:ASP28 4.6 17.7 1.0
CG C:ASP24 4.7 30.0 1.0
N C:GLY31 4.8 16.9 1.0
CA C:ASP77 4.9 24.1 1.0

Magnesium binding site 4 out of 4 in 8z2u

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Magnesium binding site 4 out of 4 in the Crystal Structure of Trehalose Synthase Mutamt E324D 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 Mutamt E324D From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:20.3
occ:1.00
 OD1 D:ASP32 2.5 24.5 1.0
O D:LYS30 2.6 15.5 1.0
OD1 D:ASP28 2.7 23.2 1.0
OD1 D:ASN26 2.8 20.2 1.0
CG D:ASP32 2.9 17.2 1.0
OD2 D:ASP28 3.0 28.6 1.0
CB D:ASP32 3.1 14.4 1.0
CG D:ASP28 3.2 24.0 1.0
O D:ASP77 3.3 16.2 1.0
CG D:ASN26 3.3 23.5 1.0
ND2 D:ASN26 3.4 21.7 1.0
OD1 D:ASP24 3.6 21.6 1.0
C D:LYS30 3.6 18.3 1.0
OD2 D:ASP32 3.9 19.9 1.0
C D:GLY31 4.0 15.8 1.0
N D:ASP32 4.0 18.0 1.0
O D:GLY31 4.1 15.5 1.0
CA D:ASP32 4.1 15.8 1.0
CB D:LYS30 4.3 19.4 1.0
CA D:LYS30 4.3 19.7 1.0
N D:GLY31 4.4 16.1 1.0
CG D:ASP24 4.5 22.5 1.0
C D:ASP77 4.5 18.9 1.0
CA D:GLY31 4.5 14.1 1.0
N D:LYS30 4.6 17.1 1.0
CB D:ASN26 4.6 17.4 1.0
CB D:ASP28 4.7 16.8 1.0
N D:ASN26 4.9 16.5 1.0
N D:GLY25 4.9 19.7 1.0
CA D:ASP24 5.0 17.2 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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