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Calcium 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:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Trehalose Synthase Mutamt E324D From Deinococcus Radiodurans Complexed with Validoxylamine A (Vaa), PDB code: 8z2u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8z2u

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Calcium 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 Calcium with other atoms in the Ca 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:Ca601

b:29.0
occ:1.00
 OD1 A:ASN105 2.4 23.1 1.0
O A:TYR213 2.5 20.5 1.0
OE2 A:GLU216 2.6 23.4 1.0
OD2 A:ASP179 2.6 17.4 1.0
O A:LEU214 2.6 26.3 1.0
CG A:ASP179 3.4 23.5 1.0
C A:LEU214 3.4 22.8 1.0
CG A:ASN105 3.6 20.7 1.0
CA A:LEU214 3.6 27.1 1.0
C A:TYR213 3.6 16.5 1.0
CB A:ASP179 3.7 18.4 1.0
CD A:GLU216 3.8 25.9 1.0
O A:LEU180 3.8 32.0 1.0
O A:ASN105 3.9 15.5 1.0
N A:LEU214 4.1 20.4 1.0
ND2 A:ASN105 4.2 18.0 1.0
OE1 A:GLU216 4.4 28.2 1.0
OD1 A:ASP179 4.5 20.7 1.0
N A:ILE215 4.7 27.1 1.0
CB A:ASN105 4.7 19.5 1.0
CA A:ASP179 4.7 15.6 1.0
N A:LEU180 4.8 23.7 1.0
C A:ASN105 4.8 23.0 1.0
CA A:ASN105 4.8 25.1 1.0
CA A:TYR213 4.9 18.0 1.0
CB A:LEU214 4.9 28.1 1.0
CD1 A:TRP170 4.9 21.1 1.0
NE1 A:TRP170 4.9 19.8 1.0
CD2 A:LEU214 4.9 25.2 1.0
CB A:TYR213 4.9 16.3 1.0
CG A:GLU216 4.9 25.7 1.0
C A:LEU180 5.0 23.4 1.0
C A:ASP179 5.0 20.5 1.0

Calcium binding site 2 out of 4 in 8z2u

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Calcium 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 Calcium with other atoms in the Ca 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:Ca601

b:32.5
occ:1.00
 OE2 B:GLU216 2.3 30.0 1.0
O B:TYR213 2.4 23.9 1.0
OD2 B:ASP179 2.4 17.4 1.0
O B:LEU214 2.4 27.3 1.0
OD1 B:ASN105 2.7 28.5 1.0
C B:LEU214 3.2 25.6 1.0
CG B:ASP179 3.4 18.5 1.0
C B:TYR213 3.5 24.4 1.0
CA B:LEU214 3.5 26.0 1.0
CD B:GLU216 3.5 31.8 1.0
O B:LEU180 3.7 21.7 1.0
CB B:ASP179 3.7 23.8 1.0
CG B:ASN105 3.8 25.2 1.0
O B:ASN105 3.9 24.6 1.0
N B:LEU214 3.9 24.4 1.0
OE1 B:GLU216 4.0 29.7 1.0
N B:ILE215 4.3 30.6 1.0
OD1 B:ASP179 4.5 20.1 1.0
ND2 B:ASN105 4.5 20.9 1.0
CG B:GLU216 4.6 39.3 1.0
CA B:TYR213 4.7 22.2 1.0
CA B:ASP179 4.8 23.0 1.0
NE1 B:TRP170 4.8 22.4 1.0
CB B:LEU214 4.8 22.7 1.0
CB B:TYR213 4.8 24.6 1.0
C B:ASN105 4.9 23.7 1.0
C B:LEU180 4.9 24.0 1.0
CB B:ASN105 4.9 29.8 1.0
CA B:ILE215 4.9 30.8 1.0
N B:LEU180 4.9 23.3 1.0
CA B:ASN105 5.0 27.4 1.0

Calcium binding site 3 out of 4 in 8z2u

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Calcium 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 Calcium with other atoms in the Ca 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:Ca601

b:41.1
occ:1.00
 OD2 C:ASP179 2.2 44.1 1.0
O C:LEU214 2.3 43.7 1.0
OE2 C:GLU216 2.6 43.6 1.0
O C:TYR213 2.7 35.4 1.0
OD1 C:ASN105 2.8 40.8 1.0
CG C:ASP179 3.3 43.3 1.0
C C:LEU214 3.3 49.3 1.0
CD C:GLU216 3.4 47.9 1.0
OE1 C:GLU216 3.5 46.0 1.0
CA C:LEU214 3.7 45.8 1.0
CG C:ASN105 3.7 36.9 1.0
CB C:ASP179 3.8 47.6 1.0
O C:LEU180 3.8 55.2 1.0
C C:TYR213 3.8 35.9 1.0
O C:ASN105 4.1 40.6 1.0
ND2 C:ASN105 4.3 32.2 1.0
N C:LEU214 4.3 35.4 1.0
OD1 C:ASP179 4.4 35.2 1.0
N C:LEU180 4.4 42.8 1.0
N C:ILE215 4.5 51.1 1.0
NE1 C:TRP170 4.6 38.2 1.0
CD1 C:TRP170 4.7 39.3 1.0
CA C:ASP179 4.7 42.2 1.0
C C:LEU180 4.8 51.3 1.0
CG C:GLU216 4.9 46.4 1.0
CB C:ASN105 4.9 38.5 1.0
C C:ASP179 4.9 42.0 1.0
C C:ASN105 5.0 35.9 1.0

Calcium binding site 4 out of 4 in 8z2u

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Calcium 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 Calcium with other atoms in the Ca 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:Ca601

b:28.3
occ:1.00
 O D:TYR213 2.4 24.2 1.0
OD1 D:ASN105 2.4 42.8 1.0
OD2 D:ASP179 2.5 25.4 1.0
OE2 D:GLU216 2.5 35.8 1.0
O D:LEU214 2.7 25.0 1.0
CG D:ASN105 3.4 29.2 1.0
CG D:ASP179 3.4 27.4 1.0
C D:TYR213 3.4 29.1 1.0
C D:LEU214 3.5 28.8 1.0
CB D:ASP179 3.6 25.4 1.0
CA D:LEU214 3.6 31.7 1.0
CD D:GLU216 3.7 36.9 1.0
ND2 D:ASN105 3.8 23.6 1.0
N D:LEU214 4.0 29.6 1.0
O D:LEU180 4.0 41.3 1.0
O D:ASN105 4.0 32.3 1.0
OE1 D:GLU216 4.3 51.3 1.0
OD1 D:ASP179 4.5 28.2 1.0
CB D:TYR213 4.6 33.1 1.0
CA D:TYR213 4.6 34.1 1.0
CB D:ASN105 4.6 25.2 1.0
NE1 D:TRP170 4.6 29.6 1.0
CA D:ASP179 4.6 27.7 1.0
CD1 D:TRP170 4.7 29.1 1.0
N D:ILE215 4.7 31.9 1.0
CG D:ARG172 4.7 27.4 1.0
CA D:ASN105 4.8 25.7 1.0
CG D:GLU216 4.8 38.2 1.0
C D:ASN105 4.9 28.0 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 16:17:06 2025

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