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Calcium in PDB 4tvu: Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization

Enzymatic activity of Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization

All present enzymatic activity of Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization:
5.4.99.16;

Protein crystallography data

The structure of Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization, PDB code: 4tvu was solved by Y.L.Wang, S.Y.Chow, Y.T.Lin, S.H.Liaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.609, 195.896, 130.986, 90.00, 92.89, 90.00
R / Rfree (%) 19.4 / 23.6

Other elements in 4tvu:

The structure of Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization 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 From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization (pdb code 4tvu). 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 From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization, PDB code: 4tvu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4tvu

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Calcium binding site 1 out of 8 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization


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 Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca600

b:32.0
occ:1.00
 OD2 A:ASP179 2.2 25.0 1.0
O A:TYR213 2.4 30.7 1.0
OD1 A:ASN105 2.4 30.4 1.0
O A:LEU214 2.5 25.1 1.0
OE2 A:GLU216 2.8 37.1 1.0
OE1 A:GLU216 2.9 37.5 1.0
CD A:GLU216 3.2 37.3 1.0
CG A:ASP179 3.3 26.3 1.0
C A:LEU214 3.3 29.3 1.0
CG A:ASN105 3.5 28.2 1.0
C A:TYR213 3.5 30.2 1.0
CA A:LEU214 3.5 30.7 1.0
CB A:ASP179 3.7 26.2 1.0
ND2 A:ASN105 3.8 27.6 1.0
O A:LEU180 4.0 28.2 1.0
N A:LEU214 4.0 30.1 1.0
O A:HOH855 4.2 18.2 1.0
O A:ASN105 4.2 29.8 1.0
OD1 A:ASP179 4.3 26.6 1.0
N A:ILE215 4.4 30.6 1.0
O A:HOH706 4.5 13.7 1.0
CD1 A:TRP170 4.5 23.5 1.0
NE1 A:TRP170 4.5 22.9 1.0
CG A:GLU216 4.7 37.5 1.0
CA A:TYR213 4.8 29.9 1.0
CB A:ASN105 4.8 27.7 1.0
CA A:ASP179 4.8 25.8 1.0
CB A:TYR213 4.9 31.2 1.0
CG A:ARG172 4.9 26.5 1.0
CB A:LEU214 4.9 31.4 1.0

Calcium binding site 2 out of 8 in 4tvu

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Calcium binding site 2 out of 8 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization


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 Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca600

b:36.7
occ:1.00
 OE1 B:GLU216 2.1 49.3 1.0
O B:LEU214 2.3 43.0 1.0
OD2 B:ASP179 2.4 30.2 1.0
OD1 B:ASN105 2.5 40.3 1.0
O B:TYR213 2.7 27.9 1.0
CD B:GLU216 3.1 44.7 1.0
C B:LEU214 3.1 37.0 1.0
OE2 B:GLU216 3.4 42.9 1.0
CG B:ASP179 3.4 30.4 1.0
CA B:LEU214 3.4 37.2 1.0
CG B:ASN105 3.5 33.8 1.0
O B:LEU180 3.6 34.6 1.0
C B:TYR213 3.7 31.0 1.0
CB B:ASP179 3.7 29.3 1.0
ND2 B:ASN105 4.0 34.6 1.0
O B:ASN105 4.0 28.3 1.0
N B:LEU214 4.0 32.5 1.0
N B:ILE215 4.3 35.6 1.0
CG B:GLU216 4.3 44.0 1.0
OD1 B:ASP179 4.5 33.1 1.0
CD1 B:TRP170 4.7 29.1 1.0
CA B:ASP179 4.8 27.9 1.0
CB B:LEU214 4.8 37.7 1.0
CB B:ASN105 4.8 32.6 1.0
C B:LEU180 4.8 32.8 1.0
NE1 B:TRP170 4.8 30.2 1.0
N B:LEU180 4.9 29.6 1.0
CA B:ILE215 4.9 36.0 1.0
C B:ASN105 4.9 28.7 1.0

Calcium binding site 3 out of 8 in 4tvu

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Calcium binding site 3 out of 8 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization


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 Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca600

b:38.5
occ:1.00
 OD2 C:ASP179 2.2 38.6 1.0
O C:HOH807 2.2 32.6 1.0
O C:TYR213 2.4 35.0 1.0
OD1 C:ASN105 2.5 49.8 1.0
O C:LEU214 2.5 40.1 1.0
OE1 C:GLU216 2.7 49.8 1.0
OE2 C:GLU216 2.9 49.0 1.0
CD C:GLU216 3.2 48.7 1.0
CG C:ASP179 3.3 39.0 1.0
C C:LEU214 3.3 41.0 1.0
C C:TYR213 3.5 37.9 1.0
CG C:ASN105 3.5 47.1 1.0
CA C:LEU214 3.5 43.7 1.0
CB C:ASP179 3.7 37.8 1.0
ND2 C:ASN105 3.8 48.9 1.0
N C:LEU214 4.0 42.7 1.0
O C:LEU180 4.0 35.2 1.0
O C:ASN105 4.2 40.8 1.0
OD1 C:ASP179 4.3 42.9 1.0
N C:ILE215 4.4 40.8 1.0
CD1 C:TRP170 4.5 30.1 1.0
NE1 C:TRP170 4.5 29.9 1.0
CG C:GLU216 4.7 48.3 1.0
CA C:TYR213 4.7 36.5 1.0
CB C:TYR213 4.8 39.9 1.0
CB C:ASN105 4.8 44.0 1.0
CG C:ARG172 4.8 49.4 1.0
CA C:ASP179 4.9 35.8 1.0
CB C:LEU214 4.9 45.5 1.0
CA C:ILE215 5.0 41.9 1.0

Calcium binding site 4 out of 8 in 4tvu

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Calcium binding site 4 out of 8 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization


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 Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca600

b:44.3
occ:1.00
 OD2 D:ASP179 2.2 40.3 1.0
O D:TYR213 2.4 32.1 1.0
OD1 D:ASN105 2.4 55.4 1.0
O D:LEU214 2.5 48.0 1.0
OE2 D:GLU216 2.8 43.0 1.0
OE1 D:GLU216 2.9 39.3 1.0
C D:LEU214 3.3 49.9 1.0
CG D:ASP179 3.3 42.7 1.0
CD D:GLU216 3.3 45.1 1.0
CG D:ASN105 3.4 54.5 1.0
C D:TYR213 3.4 37.5 1.0
CA D:LEU214 3.5 45.7 1.0
CB D:ASP179 3.8 41.1 1.0
ND2 D:ASN105 3.8 57.8 1.0
N D:LEU214 3.9 41.5 1.0
O D:LEU180 4.0 47.1 1.0
O D:ASN105 4.1 48.2 1.0
OD1 D:ASP179 4.3 52.2 1.0
N D:ILE215 4.4 51.8 1.0
O D:HOH750 4.6 27.9 1.0
NE1 D:TRP170 4.6 39.6 1.0
CD1 D:TRP170 4.6 38.0 1.0
CA D:TYR213 4.7 38.1 1.0
CB D:ASN105 4.7 49.5 1.0
CB D:TYR213 4.8 39.0 1.0
CG D:GLU216 4.8 47.6 1.0
CA D:ASP179 4.8 40.6 1.0
CG D:ARG172 4.9 51.6 1.0
CB D:LEU214 4.9 42.9 1.0

Calcium binding site 5 out of 8 in 4tvu

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Calcium binding site 5 out of 8 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization


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 From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca600

b:25.6
occ:1.00
 OD2 E:ASP179 2.2 25.4 1.0
O E:HOH893 2.4 17.1 1.0
O E:TYR213 2.5 27.2 1.0
OD1 E:ASN105 2.5 31.4 1.0
O E:LEU214 2.5 29.5 1.0
OE2 E:GLU216 2.7 29.5 1.0
OE1 E:GLU216 2.9 24.7 1.0
CD E:GLU216 3.2 26.6 1.0
CG E:ASP179 3.2 24.9 1.0
C E:LEU214 3.3 26.5 1.0
CG E:ASN105 3.5 31.6 1.0
C E:TYR213 3.5 24.8 1.0
CA E:LEU214 3.6 24.9 1.0
CB E:ASP179 3.7 22.7 1.0
ND2 E:ASN105 3.8 31.0 1.0
O E:LEU180 3.9 22.5 1.0
N E:LEU214 4.0 23.9 1.0
O E:ASN105 4.1 29.9 1.0
O E:HOH768 4.3 14.8 1.0
OD1 E:ASP179 4.3 24.9 1.0
N E:ILE215 4.4 25.6 1.0
CD1 E:TRP170 4.5 21.8 1.0
O E:HOH733 4.5 7.7 1.0
NE1 E:TRP170 4.6 21.5 1.0
CG E:GLU216 4.7 27.5 1.0
CB E:ASN105 4.8 30.4 1.0
CA E:ASP179 4.8 21.3 1.0
CA E:TYR213 4.8 23.9 1.0
CB E:TYR213 4.9 25.2 1.0
CG E:ARG172 4.9 26.1 1.0
CB E:LEU214 4.9 23.8 1.0

Calcium binding site 6 out of 8 in 4tvu

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Calcium binding site 6 out of 8 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization


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 From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca600

b:39.0
occ:1.00
 OD1 F:ASN105 2.3 40.1 1.0
OD2 F:ASP179 2.4 52.0 1.0
O F:LEU214 2.5 72.2 1.0
O F:TYR213 2.8 58.1 1.0
OE2 F:GLU216 2.9 38.5 1.0
C F:LEU214 3.3 62.4 1.0
CG F:ASP179 3.3 51.5 1.0
CG F:ASN105 3.3 36.8 1.0
OE1 F:GLU216 3.4 41.4 1.0
O F:LEU180 3.5 55.5 1.0
CA F:LEU214 3.5 61.9 1.0
CD F:GLU216 3.6 44.2 1.0
CB F:ASP179 3.6 50.1 1.0
O F:ASN105 3.7 32.3 1.0
C F:TYR213 3.8 54.7 1.0
ND2 F:ASN105 3.8 38.9 1.0
N F:LEU214 4.1 56.8 1.0
OD1 F:ASP179 4.4 56.4 1.0
N F:ILE215 4.5 60.3 1.0
CB F:ASN105 4.6 34.8 1.0
CA F:ASP179 4.6 49.4 1.0
N F:LEU180 4.6 58.0 1.0
C F:LEU180 4.6 57.9 1.0
C F:ASN105 4.7 34.2 1.0
CA F:ASN105 4.7 34.9 1.0
CB F:LEU214 4.8 58.9 1.0
CD1 F:TRP170 4.9 28.9 1.0
C F:ASP179 4.9 54.8 1.0
CD1 F:TYR182 4.9 52.7 1.0
NE1 F:TRP170 5.0 26.8 1.0

Calcium binding site 7 out of 8 in 4tvu

Go back to Calcium Binding Sites List in 4tvu
Calcium binding site 7 out of 8 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization


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 From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca600

b:30.2
occ:1.00
 O G:TYR213 2.2 32.9 1.0
OD2 G:ASP179 2.3 27.0 1.0
O G:LEU214 2.5 31.3 1.0
OD1 G:ASN105 2.5 43.0 1.0
O G:HOH833 2.6 24.2 1.0
OE1 G:GLU216 2.7 36.0 1.0
OE2 G:GLU216 2.8 45.8 1.0
CD G:GLU216 3.1 39.2 1.0
C G:LEU214 3.2 32.3 1.0
CG G:ASP179 3.3 30.0 1.0
C G:TYR213 3.3 33.6 1.0
CA G:LEU214 3.5 33.9 1.0
CG G:ASN105 3.5 39.3 1.0
CB G:ASP179 3.9 30.5 1.0
ND2 G:ASN105 3.9 38.0 1.0
N G:LEU214 3.9 33.7 1.0
O G:LEU180 4.2 44.4 1.0
O G:HOH727 4.2 17.7 1.0
N G:ILE215 4.3 32.5 1.0
O G:ASN105 4.3 31.8 1.0
OD1 G:ASP179 4.4 32.1 1.0
NE1 G:TRP170 4.5 25.8 1.0
CD1 G:TRP170 4.5 26.6 1.0
CA G:TYR213 4.6 32.9 1.0
CG G:GLU216 4.6 37.6 1.0
CB G:TYR213 4.7 36.3 1.0
CG G:ARG172 4.8 31.5 1.0
CB G:ASN105 4.9 35.6 1.0
CA G:ILE215 4.9 35.6 1.0
CB G:LEU214 4.9 33.2 1.0
C G:ILE215 4.9 34.7 1.0

Calcium binding site 8 out of 8 in 4tvu

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Calcium binding site 8 out of 8 in the Crystal Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization


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 From Deinococcus Radiodurans Reveals A Closed Conformation For Catalysis of the Intramolecular Isomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca600

b:67.7
occ:1.00
 OD2 H:ASP179 2.3 61.0 1.0
OD1 H:ASN105 2.4 62.2 1.0
O H:LEU214 2.6 79.9 1.0
OE2 H:GLU216 2.9 73.9 1.0
O H:TYR213 2.9 63.5 1.0
CG H:ASP179 3.2 67.6 1.0
C H:LEU214 3.4 81.5 1.0
CG H:ASN105 3.4 60.4 1.0
OE1 H:GLU216 3.4 80.6 1.0
O H:LEU180 3.4 71.7 1.0
CB H:ASP179 3.5 66.0 1.0
CD H:GLU216 3.5 77.4 1.0
CA H:LEU214 3.6 79.0 1.0
O H:ASN105 3.7 45.3 1.0
ND2 H:ASN105 3.9 61.1 1.0
C H:TYR213 3.9 71.3 1.0
N H:LEU214 4.2 76.1 1.0
OD1 H:ASP179 4.3 75.9 1.0
CA H:ASP179 4.5 62.7 1.0
N H:LEU180 4.5 76.0 1.0
C H:LEU180 4.6 77.3 1.0
N H:ILE215 4.6 89.8 1.0
CB H:ASN105 4.6 59.4 1.0
C H:ASN105 4.7 51.6 1.0
C H:ASP179 4.7 72.4 1.0
CD1 H:TRP170 4.8 67.0 1.0
CA H:ASN105 4.8 56.5 1.0
CD2 H:TYR182 4.9 81.4 1.0
CB H:LEU214 4.9 78.6 1.0
NE1 H:TRP170 4.9 66.9 1.0

Reference:

Y.L.Wang, S.Y.Chow, Y.T.Lin, Y.C.Hsieh, G.C.Lee, S.H.Liaw. Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in Catalysis of the Intramolecular Isomerization. Acta Crystallogr.,Sect.D V. 70 3144 2014.
ISSN: ESSN 1399-0047
PubMed: 25478833
DOI: 10.1107/S1399004714022500
Page generated: Sun Jul 14 13:32:47 2024

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