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Calcium in PDB 4wf7: Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis

Enzymatic activity of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis

All present enzymatic activity of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis:
5.4.99.16;

Protein crystallography data

The structure of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis, PDB code: 4wf7 was solved by Y.L.Wang, S.Y.Chow, Y.T.Lin, Y.C.Hsieh, G.C.Lee, S.H.Liaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.21
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.250, 133.705, 196.614, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 20

Other elements in 4wf7:

The structure of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis (pdb code 4wf7). 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 Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis, PDB code: 4wf7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4wf7

Go back to Calcium Binding Sites List in 4wf7
Calcium binding site 1 out of 4 in the Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca600

b:29.6
occ:1.00
 O A:TYR213 2.3 26.7 1.0
OD2 A:ASP179 2.3 28.7 1.0
O A:HOH784 2.4 24.0 1.0
OD1 A:ASN105 2.4 21.9 1.0
OE2 A:GLU216 2.5 31.2 1.0
O A:HOH785 2.5 23.8 1.0
O A:LEU214 2.5 25.9 1.0
C A:LEU214 3.3 28.6 1.0
CG A:ASP179 3.4 26.5 1.0
C A:TYR213 3.4 29.8 1.0
CD A:GLU216 3.4 30.9 1.0
CG A:ASN105 3.4 25.8 1.0
CA A:LEU214 3.6 28.7 1.0
OE1 A:GLU216 3.7 32.3 1.0
ND2 A:ASN105 3.9 26.6 1.0
CB A:ASP179 4.0 26.7 1.0
N A:LEU214 4.0 29.0 1.0
O A:HOH808 4.2 25.6 1.0
O A:LEU180 4.2 28.7 1.0
O A:ASN105 4.3 29.9 1.0
O A:HOH742 4.3 26.2 1.0
N A:ILE215 4.4 28.7 1.0
OD1 A:ASP179 4.4 28.8 1.0
CD1 A:TRP170 4.6 25.9 1.0
CB A:TYR213 4.6 32.5 1.0
NE1 A:TRP170 4.6 25.9 1.0
CA A:TYR213 4.6 30.2 1.0
CB A:ASN105 4.8 25.7 1.0
CG A:GLU216 4.8 31.7 1.0
CG A:ARG172 4.9 31.7 1.0
CB A:LEU214 4.9 30.3 1.0
CA A:ILE215 5.0 28.7 1.0

Calcium binding site 2 out of 4 in 4wf7

Go back to Calcium Binding Sites List in 4wf7
Calcium binding site 2 out of 4 in the Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca600

b:26.6
occ:1.00
 O B:HOH865 2.3 20.5 1.0
OD2 B:ASP179 2.3 26.1 1.0
O B:HOH788 2.3 23.1 1.0
O B:TYR213 2.4 29.0 1.0
OD1 B:ASN105 2.5 23.7 1.0
O B:LEU214 2.5 25.2 1.0
OE2 B:GLU216 2.5 30.6 1.0
C B:LEU214 3.3 26.2 1.0
CG B:ASP179 3.4 25.9 1.0
C B:TYR213 3.4 28.3 1.0
CD B:GLU216 3.5 29.2 1.0
CG B:ASN105 3.5 23.2 1.0
CA B:LEU214 3.6 26.7 1.0
OE1 B:GLU216 3.8 29.2 1.0
N B:LEU214 4.0 26.8 1.0
CB B:ASP179 4.0 25.1 1.0
ND2 B:ASN105 4.0 22.0 1.0
O B:ASN105 4.1 25.0 1.0
O B:LEU180 4.2 27.4 1.0
O B:HOH824 4.2 26.1 1.0
O B:HOH826 4.4 26.8 1.0
N B:ILE215 4.4 27.2 1.0
OD1 B:ASP179 4.5 26.5 1.0
NE1 B:TRP170 4.6 24.0 1.0
CB B:TYR213 4.6 29.5 1.0
CA B:TYR213 4.7 28.3 1.0
CD1 B:TRP170 4.7 25.0 1.0
CB B:ASN105 4.8 25.7 1.0
CG B:GLU216 4.9 27.2 1.0
CB B:LEU214 5.0 26.8 1.0
CG B:ARG172 5.0 25.9 1.0

Calcium binding site 3 out of 4 in 4wf7

Go back to Calcium Binding Sites List in 4wf7
Calcium binding site 3 out of 4 in the Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca600

b:35.1
occ:1.00
 O C:TYR213 2.3 34.0 1.0
OE2 C:GLU216 2.3 36.6 1.0
O C:HOH743 2.3 23.2 1.0
O C:HOH845 2.5 34.2 1.0
OD2 C:ASP179 2.5 36.4 1.0
OD1 C:ASN105 2.5 38.0 1.0
O C:LEU214 2.6 33.8 1.0
C C:LEU214 3.2 35.3 1.0
CD C:GLU216 3.3 39.3 1.0
C C:TYR213 3.4 34.5 1.0
CA C:LEU214 3.5 34.4 1.0
CG C:ASP179 3.5 37.8 1.0
CG C:ASN105 3.5 38.0 1.0
OE1 C:GLU216 3.6 34.3 1.0
N C:LEU214 3.9 33.5 1.0
CB C:ASP179 4.0 34.5 1.0
ND2 C:ASN105 4.0 36.3 1.0
O C:HOH854 4.1 30.7 1.0
O C:LEU180 4.2 35.9 1.0
O C:HOH756 4.2 32.6 1.0
O C:ASN105 4.2 37.9 1.0
N C:ILE215 4.3 35.5 1.0
NE1 C:TRP170 4.5 32.9 1.0
CD1 C:TRP170 4.6 33.6 1.0
OD1 C:ASP179 4.6 35.3 1.0
CA C:TYR213 4.6 37.3 1.0
CB C:TYR213 4.6 35.5 1.0
CG C:GLU216 4.7 42.5 1.0
CB C:ASN105 4.8 38.8 1.0
CG C:ARG172 4.9 33.3 1.0
CB C:LEU214 4.9 35.7 1.0
CA C:ILE215 5.0 36.4 1.0

Calcium binding site 4 out of 4 in 4wf7

Go back to Calcium Binding Sites List in 4wf7
Calcium binding site 4 out of 4 in the Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca600

b:30.9
occ:1.00
 O D:TYR213 2.3 31.2 1.0
OD2 D:ASP179 2.3 30.5 1.0
OE2 D:GLU216 2.5 38.6 1.0
O D:HOH839 2.5 29.3 1.0
O D:LEU214 2.6 31.6 1.0
OD1 D:ASN105 2.6 29.4 1.0
C D:LEU214 3.3 30.9 1.0
CG D:ASP179 3.4 31.1 1.0
C D:TYR213 3.4 32.2 1.0
CD D:GLU216 3.5 40.1 1.0
CG D:ASN105 3.5 30.2 1.0
CA D:LEU214 3.5 31.3 1.0
OE1 D:GLU216 3.8 39.3 1.0
CB D:ASP179 3.8 29.5 1.0
ND2 D:ASN105 3.9 30.8 1.0
N D:LEU214 3.9 30.6 1.0
O D:HOH789 4.2 27.6 1.0
O D:ASN105 4.2 30.8 1.0
O D:LEU180 4.3 29.1 1.0
O D:HOH744 4.3 24.5 1.0
N D:ILE215 4.4 30.5 1.0
OD1 D:ASP179 4.4 29.9 1.0
NE1 D:TRP170 4.5 33.2 1.0
CD1 D:TRP170 4.5 34.3 1.0
CA D:TYR213 4.6 33.2 1.0
CB D:TYR213 4.7 35.3 1.0
CG D:ARG172 4.8 31.7 1.0
CB D:ASN105 4.8 30.3 1.0
CG D:GLU216 4.8 39.3 1.0
CB D:LEU214 5.0 32.0 1.0
CA D:ILE215 5.0 32.3 1.0
CA D:ASP179 5.0 29.4 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 14:04:25 2024

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