Atomistry » Calcium » PDB 4wa3-4wn0 » 4wf7
Atomistry »
  Calcium »
    PDB 4wa3-4wn0 »
      4wf7 »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy