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Calcium 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:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 8z2t

Go back to Calcium Binding Sites List in 8z2t
Calcium 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 Calcium with other atoms in the Ca 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:Ca601

b:46.8
occ:1.00
 O A:LEU214 2.3 50.0 1.0
OE2 A:GLU216 2.3 48.2 1.0
OD2 A:ASP179 2.4 39.8 1.0
OD1 A:ASN105 2.4 42.0 1.0
O A:TYR213 2.6 42.1 1.0
C A:LEU214 3.2 46.7 1.0
CD A:GLU216 3.3 46.9 1.0
CG A:ASP179 3.4 37.2 1.0
OE1 A:GLU216 3.5 56.3 1.0
CA A:LEU214 3.5 47.7 1.0
CG A:ASN105 3.6 37.5 1.0
C A:TYR213 3.7 42.8 1.0
O A:LEU180 3.8 46.4 1.0
CB A:ASP179 3.8 39.4 1.0
O A:ASN105 3.8 37.7 1.0
N A:LEU214 4.1 47.2 1.0
ND2 A:ASN105 4.3 34.2 1.0
N A:ILE215 4.4 46.5 1.0
OD1 A:ASP179 4.5 36.9 1.0
CB A:ASN105 4.6 39.2 1.0
CG A:GLU216 4.7 41.8 1.0
C A:ASN105 4.7 40.7 1.0
CA A:ASN105 4.8 38.9 1.0
CB A:LEU214 4.9 46.7 1.0
CA A:ASP179 4.9 40.6 1.0
CD1 A:TRP170 4.9 41.5 1.0
C A:LEU180 4.9 39.7 1.0
CA A:ILE215 5.0 48.6 1.0
N A:LEU180 5.0 38.2 1.0
CD1 A:TYR182 5.0 45.3 1.0
CA A:TYR213 5.0 39.8 1.0

Calcium binding site 2 out of 4 in 8z2t

Go back to Calcium Binding Sites List in 8z2t
Calcium 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 Calcium with other atoms in the Ca 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:Ca601

b:55.7
occ:1.00
 OD2 B:ASP179 2.1 50.7 1.0
OE2 B:GLU216 2.2 59.1 1.0
O B:LEU214 2.3 57.9 1.0
OD1 B:ASN105 2.6 51.5 1.0
O B:TYR213 2.7 55.2 1.0
C B:LEU214 3.1 57.2 1.0
CD B:GLU216 3.2 58.9 1.0
CG B:ASP179 3.2 54.1 1.0
CA B:LEU214 3.4 51.5 1.0
OE1 B:GLU216 3.6 57.9 1.0
CG B:ASN105 3.7 42.4 1.0
O B:LEU180 3.7 57.7 1.0
C B:TYR213 3.7 53.9 1.0
CB B:ASP179 3.8 53.1 1.0
N B:LEU214 4.0 50.0 1.0
ND2 B:ASN105 4.1 42.3 1.0
O B:ASN105 4.3 44.5 1.0
OD1 B:ASP179 4.3 50.6 1.0
N B:ILE215 4.3 57.6 1.0
CD1 B:TRP170 4.5 50.3 1.0
CG B:GLU216 4.6 54.4 1.0
NE1 B:TRP170 4.7 48.8 1.0
CB B:LEU214 4.8 52.7 1.0
CA B:ASP179 4.8 44.6 1.0
C B:LEU180 4.9 55.4 1.0
CB B:ASN105 4.9 42.3 1.0
CA B:ILE215 4.9 53.5 1.0
N B:LEU180 5.0 48.3 1.0

Calcium binding site 3 out of 4 in 8z2t

Go back to Calcium Binding Sites List in 8z2t
Calcium 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 Calcium with other atoms in the Ca 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:Ca601

b:72.1
occ:1.00
 OD2 C:ASP179 2.1 56.6 1.0
OE2 C:GLU216 2.3 74.3 1.0
O C:LEU214 2.3 71.6 1.0
O C:TYR213 2.4 60.5 1.0
OD1 C:ASN105 2.9 68.3 1.0
C C:LEU214 3.1 70.5 1.0
CG C:ASP179 3.2 59.8 1.0
CA C:LEU214 3.4 66.9 1.0
CD C:GLU216 3.4 77.7 1.0
C C:TYR213 3.5 63.8 1.0
CG C:ASN105 3.6 59.9 1.0
CB C:ASP179 3.8 60.2 1.0
N C:LEU214 3.9 68.0 1.0
ND2 C:ASN105 3.9 58.4 1.0
O C:ASN105 4.0 59.4 1.0
O C:LEU180 4.0 71.4 1.0
OE1 C:GLU216 4.1 81.1 1.0
OD1 C:ASP179 4.3 60.5 1.0
N C:ILE215 4.3 73.0 1.0
CG C:GLU216 4.6 77.4 1.0
CB C:ASN105 4.7 62.1 1.0
CB C:LEU214 4.7 65.4 1.0
CA C:TYR213 4.8 60.7 1.0
CD1 C:TRP170 4.8 63.5 1.0
CA C:ASP179 4.9 57.1 1.0
CA C:ASN105 4.9 58.2 1.0
C C:ASN105 4.9 56.0 1.0
NE1 C:TRP170 4.9 65.8 1.0
N C:LEU180 4.9 67.6 1.0
CA C:ILE215 4.9 79.3 1.0
CD2 C:LEU214 5.0 61.5 1.0
CB C:TYR213 5.0 65.3 1.0

Calcium binding site 4 out of 4 in 8z2t

Go back to Calcium Binding Sites List in 8z2t
Calcium 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 Calcium with other atoms in the Ca 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:Ca601

b:82.3
occ:1.00
 OD2 D:ASP179 2.0 64.7 1.0
O D:LEU214 2.2 69.6 1.0
OE2 D:GLU216 2.4 80.8 1.0
O D:TYR213 2.7 66.6 1.0
OD1 D:ASN105 2.8 72.8 1.0
C D:LEU214 3.0 75.2 1.0
CG D:ASP179 3.2 68.9 1.0
CA D:LEU214 3.3 71.4 1.0
CD D:GLU216 3.3 82.1 1.0
O D:LEU180 3.5 76.8 1.0
OE1 D:GLU216 3.5 80.1 1.0
C D:TYR213 3.7 72.9 1.0
CG D:ASN105 3.8 66.4 1.0
N D:LEU214 3.9 70.7 1.0
OD1 D:ASP179 4.1 68.4 1.0
CB D:ASP179 4.1 70.5 1.0
N D:ILE215 4.2 80.7 1.0
O D:ASN105 4.3 64.9 1.0
ND2 D:ASN105 4.3 62.3 1.0
CB D:LEU214 4.5 70.2 1.0
CD1 D:TYR182 4.6 81.5 1.0
CG D:GLU216 4.7 80.4 1.0
C D:LEU180 4.7 75.4 1.0
N D:LEU180 4.7 69.8 1.0
CA D:ILE215 4.9 80.1 1.0
CA D:ASP179 4.9 67.0 1.0
CD2 D:LEU214 4.9 64.8 1.0
CD1 D:TRP170 4.9 75.0 1.0
CB D:ASN105 5.0 65.5 1.0
CE1 D:TYR182 5.0 80.1 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: Thu Jul 10 08:40:33 2025

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