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Magnesium 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:

Calcium (Ca) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5ykb

Go back to Magnesium Binding Sites List in 5ykb
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg601

b:20.4
occ:1.00
 OD2 A:ASP32 2.1 28.2 1.0
O A:LYS30 2.2 34.9 1.0
OD1 A:ASP24 2.3 34.5 1.0
OD1 A:ASN26 2.3 32.4 1.0
OD1 A:ASP28 2.4 34.3 1.0
CG A:ASP28 3.0 33.8 1.0
OD2 A:ASP28 3.1 37.8 1.0
CG A:ASP32 3.3 30.2 1.0
C A:LYS30 3.4 35.8 1.0
CG A:ASN26 3.4 29.9 1.0
CG A:ASP24 3.4 32.8 1.0
CB A:ASP32 3.9 30.2 1.0
ND2 A:ASN26 4.0 30.6 1.0
N A:GLY25 4.0 30.0 1.0
N A:LYS30 4.1 35.6 1.0
CA A:LYS30 4.1 37.8 1.0
N A:ASN26 4.2 28.3 1.0
O A:GLY31 4.2 32.1 1.0
OD2 A:ASP24 4.3 31.0 1.0
C A:GLY31 4.3 31.8 1.0
CA A:ASP24 4.3 30.1 1.0
OD1 A:ASP32 4.3 32.1 1.0
CB A:ASP24 4.3 31.2 1.0
CB A:LYS30 4.3 43.3 1.0
CB A:ASP28 4.4 31.0 1.0
N A:GLY31 4.4 34.1 1.0
CB A:ASN26 4.5 28.9 1.0
CA A:GLY31 4.6 32.4 1.0
N A:ASP32 4.6 32.5 1.0
N A:ASP28 4.6 30.4 1.0
C A:ASP24 4.6 30.2 1.0
O A:ASP77 4.7 47.4 1.0
CA A:ASN26 4.7 28.9 1.0
CA A:ASP32 4.9 31.1 1.0
CA A:ASP28 4.9 30.1 1.0
N A:GLY27 5.0 27.8 1.0

Magnesium binding site 2 out of 4 in 5ykb

Go back to Magnesium Binding Sites List in 5ykb
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg601

b:19.9
occ:1.00
 OD1 B:ASN26 2.1 41.6 1.0
OD1 B:ASP28 2.2 40.5 1.0
OD2 B:ASP32 2.3 29.2 1.0
O B:LYS30 2.3 33.6 1.0
OD1 B:ASP24 2.3 29.2 1.0
CG B:ASP28 3.0 36.2 1.0
CG B:ASN26 3.1 38.2 1.0
OD2 B:ASP28 3.2 36.6 1.0
CG B:ASP32 3.5 31.7 1.0
CG B:ASP24 3.5 29.3 1.0
C B:LYS30 3.5 33.8 1.0
ND2 B:ASN26 3.6 39.8 1.0
CB B:ASP32 4.0 31.3 1.0
N B:LYS30 4.1 32.2 1.0
CA B:LYS30 4.2 34.9 1.0
OD2 B:ASP24 4.2 28.0 1.0
N B:ASN26 4.2 36.7 1.0
N B:GLY25 4.3 33.0 1.0
CB B:LYS30 4.3 38.3 1.0
O B:GLY31 4.3 32.0 1.0
C B:GLY31 4.4 30.9 1.0
CB B:ASP28 4.4 34.0 1.0
O B:ASP77 4.4 46.1 1.0
CB B:ASN26 4.4 37.9 1.0
CB B:ASP24 4.4 28.3 1.0
CA B:ASP24 4.5 28.9 1.0
OD1 B:ASP32 4.5 33.4 1.0
N B:GLY31 4.5 32.3 1.0
N B:ASP28 4.5 34.7 1.0
O B:ASN26 4.7 42.2 1.0
C B:ASN26 4.7 37.4 1.0
N B:ASP32 4.7 31.1 1.0
CA B:ASN26 4.7 36.9 1.0
CA B:GLY31 4.7 31.6 1.0
C B:ASP24 4.8 30.9 1.0
CA B:ASP28 4.9 33.5 1.0

Magnesium binding site 3 out of 4 in 5ykb

Go back to Magnesium Binding Sites List in 5ykb
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg601

b:38.6
occ:1.00
 OD1 C:ASN26 2.3 48.5 1.0
OD1 C:ASP28 2.3 40.2 1.0
OD2 C:ASP32 2.3 39.1 1.0
O C:LYS30 2.5 44.2 1.0
OD1 C:ASP24 2.6 35.4 1.0
CG C:ASP28 2.9 40.0 1.0
OD2 C:ASP28 2.9 40.7 1.0
CG C:ASN26 3.2 44.6 1.0
CG C:ASP32 3.4 38.3 1.0
ND2 C:ASN26 3.6 48.1 1.0
C C:LYS30 3.7 44.6 1.0
CG C:ASP24 3.7 35.1 1.0
CB C:ASP32 3.9 36.0 1.0
O C:ASP77 4.2 45.9 1.0
CB C:ASP28 4.2 37.4 1.0
CB C:LYS30 4.3 57.0 1.0
N C:LYS30 4.3 42.5 1.0
CA C:LYS30 4.3 46.7 1.0
O C:ASN26 4.4 43.6 1.0
N C:ASN26 4.4 42.2 1.0
N C:GLY25 4.4 38.4 1.0
O C:GLY31 4.4 37.8 1.0
OD1 C:ASP32 4.5 39.4 1.0
C C:GLY31 4.5 39.8 1.0
OD2 C:ASP24 4.5 30.0 1.0
N C:ASP28 4.6 34.4 1.0
CB C:ASN26 4.6 41.4 1.0
C C:ASN26 4.7 39.6 1.0
CB C:ASP24 4.7 35.4 1.0
CA C:ASP24 4.7 34.6 1.0
N C:GLY31 4.7 43.4 1.0
N C:ASP32 4.7 38.6 1.0
CA C:ASN26 4.8 40.5 1.0
CA C:ASP28 4.9 36.3 1.0
CA C:ASP32 4.9 37.3 1.0
CA C:GLY31 4.9 41.1 1.0

Magnesium binding site 4 out of 4 in 5ykb

Go back to Magnesium Binding Sites List in 5ykb
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg601

b:32.6
occ:1.00
 OD2 D:ASP32 2.2 42.1 1.0
OD1 D:ASN26 2.2 56.3 1.0
O D:LYS30 2.3 45.3 1.0
OD1 D:ASP28 2.5 44.3 1.0
OD1 D:ASP24 2.5 40.5 1.0
CG D:ASP28 3.2 44.3 1.0
OD2 D:ASP28 3.2 46.6 1.0
CG D:ASP32 3.2 44.5 1.0
CG D:ASN26 3.2 49.5 1.0
C D:LYS30 3.4 45.6 1.0
CG D:ASP24 3.6 39.0 1.0
CB D:ASP32 3.7 42.1 1.0
ND2 D:ASN26 3.8 51.5 1.0
O D:GLY31 4.1 43.8 1.0
C D:GLY31 4.1 45.6 1.0
O D:ASP77 4.2 58.0 1.0
N D:LYS30 4.2 41.7 1.0
CA D:LYS30 4.2 45.8 1.0
N D:ASN26 4.3 43.6 1.0
OD1 D:ASP32 4.3 46.5 1.0
CB D:LYS30 4.3 50.8 1.0
N D:GLY25 4.4 38.2 1.0
N D:ASP32 4.4 44.9 1.0
N D:GLY31 4.4 47.8 1.0
OD2 D:ASP24 4.5 37.0 1.0
CB D:ASN26 4.5 45.4 1.0
CA D:ASP24 4.5 35.8 1.0
CB D:ASP24 4.5 37.2 1.0
CB D:ASP28 4.6 41.4 1.0
CA D:GLY31 4.6 47.0 1.0
CA D:ASP32 4.7 41.7 1.0
N D:ASP28 4.8 43.5 1.0
CA D:ASN26 4.8 42.9 1.0
C D:ASP24 4.9 37.2 1.0
N D:GLY27 5.0 39.1 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 Sep 30 11:20:21 2024

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