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Calcium in PDB 5ykb: The N253F Mutant Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals An Open Active-Site Conformation

Enzymatic activity of The N253F Mutant Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals An Open Active-Site Conformation

All present enzymatic activity of The N253F Mutant Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals An Open Active-Site Conformation:
5.4.99.16;

Protein crystallography data

The structure of The N253F Mutant Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals An Open Active-Site Conformation, PDB code: 5ykb was solved by S.Y.Chow, Y.C.Hsieh, S.H.Liaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.401, 132.422, 196.013, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 25.1

Other elements in 5ykb:

The structure of The N253F Mutant Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals An Open Active-Site Conformation also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The N253F Mutant Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals An Open Active-Site Conformation (pdb code 5ykb). 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 N253F Mutant Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals An Open Active-Site Conformation, PDB code: 5ykb:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5ykb

Go back to Calcium Binding Sites List in 5ykb
Calcium binding site 1 out of 4 in the The N253F Mutant Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals An Open Active-Site Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The N253F Mutant Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals An Open Active-Site Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca600

b:87.4
occ:1.00
 O A:LEU214 2.4 81.6 1.0
OD1 A:ASN105 2.4 77.5 1.0
OE2 A:GLU216 2.5 94.3 1.0
OD2 A:ASP179 2.5 71.9 1.0
O A:TYR213 2.8 71.3 1.0
C A:LEU214 3.3 78.9 1.0
CG A:ASP179 3.4 74.0 1.0
O A:LEU180 3.5 66.8 1.0
CG A:ASN105 3.5 65.0 1.0
CD A:GLU216 3.5 92.7 1.0
CA A:LEU214 3.6 76.9 1.0
CB A:ASP179 3.7 72.1 1.0
C A:TYR213 3.8 73.6 1.0
OE1 A:GLU216 3.9 89.2 1.0
O A:ASN105 3.9 54.6 1.0
ND2 A:ASN105 4.0 66.9 1.0
N A:LEU214 4.2 75.2 1.0
N A:ILE215 4.5 80.5 1.0
OD1 A:ASP179 4.5 81.0 1.0
N A:LEU180 4.6 70.3 1.0
CA A:ASP179 4.6 68.7 1.0
C A:LEU180 4.6 68.5 1.0
CB A:ASN105 4.7 61.2 1.0
C A:ASN105 4.8 56.0 1.0
C A:ASP179 4.8 69.6 1.0
CG A:GLU216 4.8 92.5 1.0
CA A:ASN105 4.9 56.7 1.0
CD2 A:TYR182 4.9 73.7 1.0
NE1 A:TRP170 4.9 97.0 1.0
CD1 A:TRP170 4.9 96.5 1.0
CB A:LEU214 4.9 76.5 1.0

Calcium binding site 2 out of 4 in 5ykb

Go back to Calcium Binding Sites List in 5ykb
Calcium binding site 2 out of 4 in the The N253F Mutant Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals An Open Active-Site Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The N253F Mutant Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals An Open Active-Site Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca600

b:81.8
occ:1.00
 O B:LEU214 2.5 88.3 1.0
OD1 B:ASN105 2.7 99.6 1.0
O B:LEU180 2.7 81.2 1.0
OE1 B:GLU216 3.0 0.8 1.0
O B:TYR213 3.1 78.9 1.0
OD2 B:ASP179 3.2 84.0 1.0
C B:LEU214 3.4 87.5 1.0
CA B:LEU214 3.7 84.8 1.0
OE2 B:GLU216 3.7 0.7 1.0
CB B:ASP179 3.8 75.0 1.0
O B:ASN105 3.8 82.7 1.0
CD B:GLU216 3.8 0.2 1.0
C B:LEU180 3.8 83.1 1.0
CG B:ASN105 3.9 88.6 1.0
CG B:ASP179 3.9 77.3 1.0
N B:LEU180 4.0 78.0 1.0
C B:TYR213 4.1 77.5 1.0
CD2 B:TYR182 4.4 88.8 1.0
N B:LEU214 4.4 77.3 1.0
C B:ASP179 4.5 77.9 1.0
CA B:LEU180 4.5 79.0 1.0
N B:ILE215 4.5 91.1 1.0
CA B:ASP179 4.5 76.7 1.0
ND2 B:ASN105 4.6 94.8 1.0
C B:ASN105 4.7 79.8 1.0
CA B:ASN105 4.7 74.9 1.0
CE2 B:TYR182 4.8 84.7 1.0
CB B:ASN105 4.9 80.1 1.0
N B:ASN181 4.9 82.3 1.0
CB B:LEU214 5.0 85.3 1.0
CB B:LEU180 5.0 79.7 1.0
CA B:ILE215 5.0 86.5 1.0

Calcium binding site 3 out of 4 in 5ykb

Go back to Calcium Binding Sites List in 5ykb
Calcium binding site 3 out of 4 in the The N253F Mutant Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals An Open Active-Site Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The N253F Mutant Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals An Open Active-Site Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca600

b:60.4
occ:1.00
 O C:TYR213 1.9 71.8 1.0
OD1 C:ASP179 2.3 82.4 1.0
OD1 C:ASN105 2.4 81.9 1.0
OD2 C:ASP179 2.7 74.4 1.0
CG C:ASP179 2.8 77.7 1.0
O C:LEU214 2.8 74.1 1.0
C C:TYR213 3.1 70.2 1.0
OE2 C:GLU216 3.2 77.8 1.0
C C:LEU214 3.3 75.2 1.0
OE1 C:GLU216 3.3 79.8 1.0
CG C:ASN105 3.5 72.2 1.0
CA C:LEU214 3.6 73.5 1.0
CD C:GLU216 3.7 82.2 1.0
N C:LEU214 3.8 72.5 1.0
ND2 C:ASN105 3.8 73.3 1.0
NH2 C:ARG172 4.2 98.7 1.0
N C:ILE215 4.2 83.1 1.0
CB C:ASP179 4.2 77.0 1.0
CB C:TYR213 4.3 70.1 1.0
CA C:TYR213 4.3 68.5 1.0
O C:LEU180 4.3 84.0 1.0
NE1 C:TRP170 4.6 0.1 1.0
O C:ASN105 4.7 64.0 1.0
CD1 C:TRP170 4.8 0.2 1.0
CB C:ASN105 4.8 68.7 1.0
CA C:ILE215 4.8 86.3 1.0
NE C:ARG172 4.9 0.8 1.0
C C:ILE215 5.0 83.2 1.0

Calcium binding site 4 out of 4 in 5ykb

Go back to Calcium Binding Sites List in 5ykb
Calcium binding site 4 out of 4 in the The N253F Mutant Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals An Open Active-Site Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The N253F Mutant Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals An Open Active-Site Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca600

b:68.8
occ:1.00
 OE2 D:GLU216 1.7 20.0 1.0
O D:TYR213 2.1 84.3 1.0
OD1 D:ASP179 2.4 68.4 1.0
O D:LEU214 2.8 0.7 1.0
OD1 D:ASN105 2.8 82.2 1.0
OD2 D:ASP179 2.9 64.9 1.0
CD D:GLU216 2.9 20.0 1.0
CG D:ASP179 3.0 67.4 1.0
C D:LEU214 3.1 0.6 1.0
C D:TYR213 3.2 87.0 1.0
CA D:LEU214 3.3 98.1 1.0
N D:LEU214 3.6 93.8 1.0
OE1 D:GLU216 3.7 20.0 1.0
O D:LEU180 3.8 91.1 1.0
CZ3 D:TRP170 3.8 95.3 1.0
CG D:ASN105 3.9 73.8 1.0
CG D:GLU216 4.0 20.0 1.0
N D:ILE215 4.1 0.7 1.0
CH2 D:TRP170 4.3 99.2 1.0
CB D:ASP179 4.5 66.9 1.0
CA D:TYR213 4.5 81.0 1.0
ND2 D:ASN105 4.5 72.2 1.0
O D:ASN105 4.6 63.6 1.0
CB D:TYR213 4.6 81.8 1.0
CA D:ILE215 4.7 0.4 1.0
CB D:LEU214 4.7 95.3 1.0
CE3 D:TRP170 4.7 91.6 1.0
N D:LEU180 4.9 79.8 1.0
C D:ILE215 4.9 0.4 1.0
C D:LEU180 4.9 85.3 1.0

Reference:

S.Y.Chow, Y.L.Wang, Y.C.Hsieh, G.C.Lee, S.H.Liaw. The N253F Mutant Structure of Trehalose Synthase From Deinococcus Radiodurans Reveals An Open Active-Site Topology Acta Crystallogr F Struct V. 73 588 2017BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 29095151
DOI: 10.1107/S2053230X17014303
Page generated: Mon Jul 15 15:27:11 2024

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