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Calcium in PDB 8ywd: Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans

Enzymatic activity of Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans

All present enzymatic activity of Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans:
5.4.99.16;

Protein crystallography data

The structure of Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans, PDB code: 8ywd 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) 22.33 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.321, 196.852, 131.188, 90, 93.07, 90
R / Rfree (%) 17.2 / 23.4

Other elements in 8ywd:

The structure of Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans (pdb code 8ywd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans, PDB code: 8ywd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 8ywd

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Calcium binding site 1 out of 8 in the Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans


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 Mutant N253C From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca600

b:58.0
occ:1.00
 OD2 A:ASP179 2.3 34.8 1.0
O A:TYR213 2.4 43.6 1.0
OE2 A:GLU216 2.4 42.8 1.0
OD1 A:ASN105 2.4 37.7 1.0
O A:LEU214 2.6 43.5 1.0
CG A:ASP179 3.3 32.7 1.0
C A:LEU214 3.3 37.5 1.0
CD A:GLU216 3.4 36.5 1.0
CG A:ASN105 3.4 30.0 1.0
C A:TYR213 3.5 37.6 1.0
CA A:LEU214 3.6 32.9 1.0
OE1 A:GLU216 3.6 34.0 1.0
CB A:ASP179 3.8 31.8 1.0
ND2 A:ASN105 3.9 28.4 1.0
N A:LEU214 4.0 33.4 1.0
O A:ASN105 4.1 33.2 1.0
O A:LEU180 4.1 42.0 1.0
O A:HOH705 4.2 35.3 1.0
OD1 A:ASP179 4.3 38.8 1.0
N A:ILE215 4.5 40.5 1.0
NE1 A:TRP170 4.7 28.9 1.0
CB A:ASN105 4.7 31.4 1.0
CA A:TYR213 4.7 35.3 1.0
CD1 A:TRP170 4.7 28.0 1.0
CG A:GLU216 4.8 35.8 1.0
CB A:TYR213 4.8 33.8 1.0
CA A:ASP179 4.8 30.8 1.0
CA A:ASN105 4.9 31.9 1.0
C A:ASN105 4.9 33.9 1.0
CG A:ARG172 4.9 38.2 1.0
CD2 A:LEU214 4.9 39.9 1.0
CB A:LEU214 4.9 36.1 1.0

Calcium binding site 2 out of 8 in 8ywd

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Calcium binding site 2 out of 8 in the Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans


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 Mutant N253C From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:35.0
occ:1.00
 OD2 B:ASP179 2.3 36.0 1.0
OE2 B:GLU216 2.3 40.0 1.0
O B:TYR213 2.4 31.0 1.0
O B:LEU214 2.5 35.0 1.0
OD1 B:ASN105 2.7 36.5 1.0
C B:LEU214 3.1 37.1 1.0
CD B:GLU216 3.4 35.7 1.0
CA B:LEU214 3.4 31.5 1.0
CG B:ASP179 3.4 34.4 1.0
C B:TYR213 3.4 29.3 1.0
OE1 B:GLU216 3.7 40.8 1.0
CG B:ASN105 3.7 33.6 1.0
CB B:ASP179 3.9 31.3 1.0
N B:LEU214 3.9 28.0 1.0
O B:LEU180 4.1 35.9 1.0
ND2 B:ASN105 4.2 33.8 1.0
N B:ILE215 4.2 37.4 1.0
O B:ASN105 4.4 35.2 1.0
OD1 B:ASP179 4.5 37.8 1.0
NE1 B:TRP170 4.6 31.0 1.0
CD1 B:TRP170 4.6 32.2 1.0
CG B:GLU216 4.7 33.8 1.0
CA B:TYR213 4.7 27.9 1.0
CB B:TYR213 4.7 28.1 1.0
CB B:LEU214 4.8 33.9 1.0
CG B:ARG172 4.8 32.3 1.0
CB B:ASN105 4.9 34.1 1.0
CA B:ILE215 4.9 35.7 1.0
CA B:ASP179 5.0 29.6 1.0

Calcium binding site 3 out of 8 in 8ywd

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Calcium binding site 3 out of 8 in the Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans


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 Mutant N253C From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:38.2
occ:1.00
 OD2 C:ASP179 2.2 38.1 1.0
O C:TYR213 2.3 34.8 1.0
OE2 C:GLU216 2.5 38.8 1.0
O C:LEU214 2.5 40.6 1.0
OD1 C:ASN105 2.7 41.4 1.0
C C:LEU214 3.2 39.4 1.0
CG C:ASP179 3.4 40.4 1.0
CD C:GLU216 3.4 43.4 1.0
C C:TYR213 3.4 37.7 1.0
CA C:LEU214 3.5 37.1 1.0
OE1 C:GLU216 3.6 46.1 1.0
CG C:ASN105 3.6 38.9 1.0
CB C:ASP179 3.9 32.5 1.0
ND2 C:ASN105 3.9 39.1 1.0
N C:LEU214 3.9 36.9 1.0
O C:LEU180 4.2 42.8 1.0
N C:ILE215 4.3 36.4 1.0
O C:ASN105 4.3 40.2 1.0
OD1 C:ASP179 4.4 45.1 1.0
CD1 C:TRP170 4.7 35.5 1.0
CA C:TYR213 4.7 35.7 1.0
NE1 C:TRP170 4.7 38.8 1.0
CB C:TYR213 4.8 34.3 1.0
CG C:ARG172 4.8 35.7 1.0
CG C:GLU216 4.8 48.7 1.0
CB C:LEU214 4.9 37.1 1.0
CA C:ILE215 4.9 39.8 1.0
CA C:ASP179 4.9 34.1 1.0
CB C:ASN105 5.0 37.3 1.0

Calcium binding site 4 out of 8 in 8ywd

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Calcium binding site 4 out of 8 in the Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans


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 Mutant N253C From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:35.3
occ:1.00
 O D:LEU214 2.4 34.2 1.0
O D:TYR213 2.5 41.1 1.0
OD2 D:ASP179 2.5 39.7 1.0
OE1 D:GLU216 2.7 39.7 1.0
ND2 D:ASN105 2.8 38.5 1.0
OE2 D:GLU216 2.8 41.9 1.0
CD D:GLU216 3.2 40.5 1.0
C D:LEU214 3.3 37.8 1.0
CG D:ASP179 3.4 38.0 1.0
C D:TYR213 3.6 35.8 1.0
CB D:ASP179 3.7 32.9 1.0
CA D:LEU214 3.7 39.0 1.0
CG D:ASN105 3.9 41.1 1.0
N D:LEU214 4.2 34.3 1.0
O D:LEU180 4.2 36.6 1.0
OD1 D:ASN105 4.2 40.2 1.0
N D:ILE215 4.5 35.3 1.0
O D:ASN105 4.5 35.9 1.0
OD1 D:ASP179 4.6 43.5 1.0
CD1 D:TRP170 4.6 34.2 1.0
NE1 D:TRP170 4.6 35.6 1.0
CG D:GLU216 4.7 47.0 1.0
CA D:TYR213 4.8 39.0 1.0
CA D:ASP179 4.9 28.0 1.0
CB D:TYR213 4.9 37.3 1.0
CG D:ARG172 5.0 39.9 1.0
CA D:ILE215 5.0 36.5 1.0

Calcium binding site 5 out of 8 in 8ywd

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Calcium binding site 5 out of 8 in the Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca601

b:43.1
occ:1.00
 OD1 E:ASN105 2.4 51.3 1.0
OD2 E:ASP179 2.6 45.2 1.0
OE2 E:GLU216 2.7 48.1 1.0
O E:TYR213 2.8 50.8 1.0
O E:LEU214 2.9 56.2 1.0
CG E:ASN105 3.4 46.8 1.0
CG E:ASP179 3.4 47.2 1.0
OE1 E:GLU216 3.5 45.2 1.0
CD E:GLU216 3.5 48.2 1.0
C E:LEU214 3.5 51.2 1.0
O E:LEU180 3.6 48.4 1.0
CB E:ASP179 3.6 43.7 1.0
CA E:LEU214 3.7 48.4 1.0
C E:TYR213 3.8 50.2 1.0
O E:ASN105 3.8 46.2 1.0
ND2 E:ASN105 3.9 48.6 1.0
N E:LEU214 4.2 47.6 1.0
OD1 E:ASP179 4.5 50.1 1.0
CA E:ASP179 4.5 45.0 1.0
CB E:ASN105 4.6 38.2 1.0
N E:ILE215 4.6 46.4 1.0
C E:ASN105 4.7 43.1 1.0
N E:LEU180 4.7 44.5 1.0
C E:LEU180 4.7 46.4 1.0
C E:ASP179 4.7 47.1 1.0
CA E:ASN105 4.7 44.1 1.0
CD1 E:TRP170 4.9 38.0 1.0
CG E:GLU216 5.0 51.6 1.0

Calcium binding site 6 out of 8 in 8ywd

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Calcium binding site 6 out of 8 in the Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca601

b:55.2
occ:1.00
 OE2 F:GLU216 2.2 59.2 1.0
O F:TYR213 2.4 46.2 1.0
OD1 F:ASN105 2.5 59.2 1.0
OD2 F:ASP179 2.5 47.1 1.0
O F:LEU214 2.8 55.5 1.0
CG F:ASP179 3.4 50.0 1.0
CG F:ASN105 3.4 57.1 1.0
CD F:GLU216 3.4 60.1 1.0
C F:LEU214 3.5 56.9 1.0
C F:TYR213 3.6 52.9 1.0
CB F:ASP179 3.7 43.8 1.0
ND2 F:ASN105 3.7 52.9 1.0
CA F:LEU214 3.8 55.9 1.0
O F:LEU180 4.1 54.0 1.0
OE1 F:GLU216 4.1 64.5 1.0
N F:LEU214 4.2 54.2 1.0
O F:ASN105 4.2 49.8 1.0
OD1 F:ASP179 4.4 56.0 1.0
N F:ILE215 4.5 51.3 1.0
CG F:GLU216 4.5 64.8 1.0
CD1 F:TRP170 4.7 45.6 1.0
CA F:TYR213 4.8 47.5 1.0
CB F:TYR213 4.8 43.6 1.0
NE1 F:TRP170 4.8 44.1 1.0
CB F:ASN105 4.8 57.3 1.0
CA F:ASP179 4.9 48.5 1.0
CG F:ARG172 5.0 45.7 1.0

Calcium binding site 7 out of 8 in 8ywd

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Calcium binding site 7 out of 8 in the Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca601

b:51.1
occ:1.00
 OD2 G:ASP179 2.0 45.2 1.0
O G:TYR213 2.3 45.5 1.0
OE2 G:GLU216 2.3 51.8 1.0
OD1 G:ASN105 2.5 49.6 1.0
O G:LEU214 2.7 49.2 1.0
CD G:GLU216 3.0 50.5 1.0
OE1 G:GLU216 3.0 51.7 1.0
CG G:ASP179 3.2 48.7 1.0
C G:LEU214 3.3 51.0 1.0
C G:TYR213 3.4 46.4 1.0
CG G:ASN105 3.5 46.1 1.0
CA G:LEU214 3.5 48.3 1.0
CB G:ASP179 3.8 47.0 1.0
ND2 G:ASN105 3.9 43.6 1.0
N G:LEU214 3.9 47.6 1.0
OD1 G:ASP179 4.2 49.6 1.0
O G:LEU180 4.2 58.5 1.0
O G:ASN105 4.3 48.2 1.0
N G:ILE215 4.4 49.5 1.0
CG G:GLU216 4.5 46.9 1.0
NE1 G:TRP170 4.7 42.0 1.0
CD1 G:TRP170 4.7 39.5 1.0
CA G:TYR213 4.7 44.6 1.0
CB G:TYR213 4.8 43.5 1.0
CB G:ASN105 4.8 45.2 1.0
CA G:ASP179 4.9 43.9 1.0
CB G:LEU214 4.9 46.5 1.0
CG G:ARG172 4.9 46.4 1.0

Calcium binding site 8 out of 8 in 8ywd

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Calcium binding site 8 out of 8 in the Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Trehalose Synthase Mutant N253C From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca601

b:64.5
occ:1.00
 OD1 H:ASP179 2.1 69.8 1.0
O H:TYR213 2.3 61.4 1.0
CG H:ASP179 2.6 67.6 1.0
O H:LEU214 2.7 73.0 1.0
OD2 H:ASP179 2.7 67.9 1.0
OD1 H:ASN105 2.7 64.2 1.0
OE2 H:GLU216 2.8 67.6 1.0
OE1 H:GLU216 3.0 75.6 1.0
C H:LEU214 3.2 66.8 1.0
CD H:GLU216 3.2 73.8 1.0
C H:TYR213 3.4 65.1 1.0
CA H:LEU214 3.4 66.1 1.0
CG H:ASN105 3.8 62.6 1.0
N H:LEU214 3.9 70.3 1.0
CB H:ASP179 4.0 53.8 1.0
N H:ILE215 4.1 62.8 1.0
ND2 H:ASN105 4.1 59.9 1.0
O H:LEU180 4.2 67.8 1.0
O H:ASN105 4.5 62.4 1.0
CA H:TYR213 4.6 57.9 1.0
CG H:GLU216 4.7 66.5 1.0
CB H:TYR213 4.7 61.1 1.0
CA H:ILE215 4.8 69.8 1.0
NE1 H:TRP170 4.8 58.2 1.0
CB H:LEU214 4.9 69.3 1.0
N H:LEU180 4.9 67.8 1.0
CD1 H:TRP170 4.9 58.8 1.0
C H:ILE215 4.9 73.9 1.0
CA H:ASP179 5.0 53.0 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: Thu Jul 10 08:37:25 2025

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