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Calcium in PDB 5gtw: The N253R Mutant Structures of Trehalose Synthase From Deinococcus Radiodurans Display Two Different Active-Site Conformations

Enzymatic activity of The N253R Mutant Structures of Trehalose Synthase From Deinococcus Radiodurans Display Two Different Active-Site Conformations

All present enzymatic activity of The N253R Mutant Structures of Trehalose Synthase From Deinococcus Radiodurans Display Two Different Active-Site Conformations:
5.4.99.16;

Protein crystallography data

The structure of The N253R Mutant Structures of Trehalose Synthase From Deinococcus Radiodurans Display Two Different Active-Site Conformations, PDB code: 5gtw was solved by S.Y.Chow, Y.J.Wei, S.H.Liaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.383, 134.058, 197.198, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 26.7

Other elements in 5gtw:

The structure of The N253R Mutant Structures of Trehalose Synthase From Deinococcus Radiodurans Display Two Different Active-Site Conformations also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The N253R Mutant Structures of Trehalose Synthase From Deinococcus Radiodurans Display Two Different Active-Site Conformations (pdb code 5gtw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The N253R Mutant Structures of Trehalose Synthase From Deinococcus Radiodurans Display Two Different Active-Site Conformations, PDB code: 5gtw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5gtw

Go back to Calcium Binding Sites List in 5gtw
Calcium binding site 1 out of 4 in the The N253R Mutant Structures of Trehalose Synthase From Deinococcus Radiodurans Display Two Different Active-Site Conformations


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The N253R Mutant Structures of Trehalose Synthase From Deinococcus Radiodurans Display Two Different Active-Site Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:57.6
occ:1.00
 OD2 A:ASP179 2.3 54.2 1.0
OD1 A:ASN105 2.4 73.2 1.0
O A:LEU214 2.5 55.5 1.0
O A:TYR213 2.6 52.5 1.0
OE1 A:GLU216 2.8 92.4 1.0
OE2 A:GLU216 2.9 81.2 1.0
CD A:GLU216 3.2 85.2 1.0
CG A:ASP179 3.4 61.1 1.0
CG A:ASN105 3.4 67.6 1.0
C A:LEU214 3.4 57.7 1.0
CA A:LEU214 3.6 56.1 1.0
C A:TYR213 3.7 55.5 1.0
ND2 A:ASN105 3.7 61.2 1.0
CB A:ASP179 3.9 63.3 1.0
O A:LEU180 3.9 78.8 1.0
N A:LEU214 4.1 55.4 1.0
O A:ASN105 4.2 46.5 1.0
OD1 A:ASP179 4.3 68.1 1.0
NE1 A:TRP170 4.5 60.9 1.0
CD1 A:TRP170 4.5 58.9 1.0
N A:ILE215 4.6 66.3 1.0
O A:HOH719 4.6 33.5 1.0
N A:LEU180 4.7 66.5 1.0
CB A:ASN105 4.7 59.5 1.0
CG A:GLU216 4.7 80.7 1.0
CA A:ASP179 4.9 64.1 1.0
CA A:TYR213 5.0 55.9 1.0
C A:LEU180 5.0 73.7 1.0

Calcium binding site 2 out of 4 in 5gtw

Go back to Calcium Binding Sites List in 5gtw
Calcium binding site 2 out of 4 in the The N253R Mutant Structures of Trehalose Synthase From Deinococcus Radiodurans Display Two Different Active-Site Conformations


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The N253R Mutant Structures of Trehalose Synthase From Deinococcus Radiodurans Display Two Different Active-Site Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:78.5
occ:1.00
 OE2 B:GLU216 2.3 66.5 1.0
OD1 B:ASN105 2.4 73.2 1.0
O B:LEU214 2.6 77.0 1.0
OD2 B:ASP179 2.8 67.4 1.0
O B:TYR213 2.8 66.5 1.0
O B:LEU180 3.3 72.4 1.0
CD B:GLU216 3.3 70.5 1.0
C B:LEU214 3.4 67.8 1.0
CB B:ASP179 3.5 64.4 1.0
CG B:ASN105 3.5 70.2 1.0
CG B:ASP179 3.6 71.1 1.0
OE1 B:GLU216 3.6 65.9 1.0
CA B:LEU214 3.7 69.6 1.0
O B:ASN105 3.8 57.9 1.0
C B:TYR213 3.8 70.6 1.0
ND2 B:ASN105 4.1 72.3 1.0
N B:LEU180 4.1 53.7 1.0
N B:LEU214 4.2 70.7 1.0
C B:LEU180 4.4 63.8 1.0
CA B:ASP179 4.4 59.4 1.0
N B:ILE215 4.5 64.1 1.0
C B:ASP179 4.5 55.7 1.0
CG B:GLU216 4.6 71.0 1.0
C B:ASN105 4.7 60.7 1.0
CB B:ASN105 4.7 67.0 1.0
CD1 B:TRP170 4.7 60.6 1.0
CD2 B:TYR182 4.7 64.1 1.0
OD1 B:ASP179 4.8 68.7 1.0
CA B:ASN105 4.8 65.4 1.0
CA B:LEU180 4.9 57.2 1.0

Calcium binding site 3 out of 4 in 5gtw

Go back to Calcium Binding Sites List in 5gtw
Calcium binding site 3 out of 4 in the The N253R Mutant Structures of Trehalose Synthase From Deinococcus Radiodurans Display Two Different Active-Site Conformations


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The N253R Mutant Structures of Trehalose Synthase From Deinococcus Radiodurans Display Two Different Active-Site Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:60.0
occ:1.00
 OE2 C:GLU216 1.8 0.2 1.0
OD2 C:ASP179 2.1 64.8 1.0
OD1 C:ASN105 2.3 88.5 1.0
O C:TYR213 2.4 56.4 1.0
O C:LEU214 2.5 69.7 1.0
CD C:GLU216 3.0 0.5 1.0
CG C:ASP179 3.2 73.4 1.0
C C:LEU214 3.3 71.5 1.0
CG C:ASN105 3.4 78.2 1.0
C C:TYR213 3.6 59.0 1.0
OE1 C:GLU216 3.6 97.8 1.0
O C:LEU180 3.6 75.0 1.0
CA C:LEU214 3.7 67.3 1.0
CB C:ASP179 3.8 71.6 1.0
ND2 C:ASN105 3.8 68.0 1.0
N C:LEU214 4.1 60.8 1.0
CG C:GLU216 4.2 99.4 1.0
O C:ASN105 4.2 62.1 1.0
OD1 C:ASP179 4.3 83.7 1.0
N C:ILE215 4.5 74.0 1.0
N C:LEU180 4.6 66.7 1.0
CD1 C:TRP170 4.7 55.5 1.0
CB C:ASN105 4.7 78.4 1.0
CA C:ASP179 4.7 68.8 1.0
C C:LEU180 4.8 70.2 1.0
NE1 C:TRP170 4.8 56.7 1.0
CB C:TYR213 4.8 63.1 1.0
CA C:TYR213 4.8 61.2 1.0
C C:ASP179 5.0 72.7 1.0

Calcium binding site 4 out of 4 in 5gtw

Go back to Calcium Binding Sites List in 5gtw
Calcium binding site 4 out of 4 in the The N253R Mutant Structures of Trehalose Synthase From Deinococcus Radiodurans Display Two Different Active-Site Conformations


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The N253R Mutant Structures of Trehalose Synthase From Deinococcus Radiodurans Display Two Different Active-Site Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca600

b:56.8
occ:1.00
 OD1 D:ASN105 2.3 76.3 1.0
OD2 D:ASP179 2.3 63.4 1.0
OE2 D:GLU216 2.4 79.9 1.0
O D:LEU214 2.4 54.7 1.0
O D:TYR213 2.7 64.7 1.0
OE1 D:GLU216 3.0 86.3 1.0
CD D:GLU216 3.1 80.7 1.0
CG D:ASP179 3.3 60.8 1.0
CG D:ASN105 3.3 63.9 1.0
C D:LEU214 3.4 56.2 1.0
CB D:ASP179 3.6 55.4 1.0
C D:TYR213 3.7 60.1 1.0
CA D:LEU214 3.8 55.6 1.0
ND2 D:ASN105 3.8 61.8 1.0
O D:LEU180 3.8 64.3 1.0
O D:ASN105 4.0 66.0 1.0
N D:LEU214 4.2 53.9 1.0
OD1 D:ASP179 4.4 64.4 1.0
CG D:GLU216 4.5 76.8 1.0
CD1 D:TRP170 4.6 68.3 1.0
CA D:ASP179 4.6 52.3 1.0
N D:ILE215 4.6 60.5 1.0
CB D:ASN105 4.6 60.6 1.0
NE1 D:TRP170 4.6 73.2 1.0
N D:LEU180 4.8 52.5 1.0
C D:ASN105 4.9 59.7 1.0
C D:ASP179 4.9 48.0 1.0
CB D:TYR213 5.0 64.7 1.0
CA D:TYR213 5.0 61.6 1.0
CA D:ASN105 5.0 59.2 1.0
C D:LEU180 5.0 59.5 1.0

Reference:

S.Y.Chow, Y.J.Wei, S.H.Liaw. The N253R Mutant Structures of Trehalose Synthase From Deinococcus Radiodurans Display Two Different Active-Site Conformations To Be Published.
Page generated: Sun Jul 14 19:44:48 2024

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