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Magnesium 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:

Calcium (Ca) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 5gtw

Go back to Magnesium Binding Sites List in 5gtw
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg602

b:30.0
occ:1.00
 OD1 A:ASP28 2.2 51.6 1.0
OD1 A:ASN26 2.3 41.1 1.0
O A:LYS30 2.4 46.8 1.0
OD2 A:ASP32 2.5 47.6 1.0
OD1 A:ASP24 2.9 37.8 1.0
CG A:ASP28 3.0 50.7 1.0
OD2 A:ASP28 3.1 52.7 1.0
CG A:ASP32 3.4 48.7 1.0
CG A:ASN26 3.5 40.8 1.0
C A:LYS30 3.5 44.0 1.0
CB A:ASP32 3.6 48.8 1.0
O A:GLY31 3.7 47.7 1.0
CG A:ASP24 3.8 42.2 1.0
O A:ASP77 3.9 48.0 1.0
C A:GLY31 4.1 45.7 1.0
ND2 A:ASN26 4.2 43.1 1.0
N A:LYS30 4.2 44.8 1.0
CA A:LYS30 4.2 44.7 1.0
CB A:LYS30 4.3 46.6 1.0
CB A:ASP28 4.4 50.8 1.0
N A:GLY25 4.6 42.6 1.0
N A:GLY31 4.6 41.7 1.0
N A:ASP32 4.6 47.1 1.0
CB A:ASP24 4.6 42.2 1.0
OD1 A:ASP32 4.6 46.5 1.0
CB A:ASN26 4.6 41.4 1.0
N A:ASN26 4.6 42.0 1.0
OD2 A:ASP24 4.7 39.5 1.0
CA A:ASP32 4.7 47.4 1.0
CA A:ASP24 4.7 39.4 1.0
CA A:GLY31 4.8 42.5 1.0
N A:ASP28 4.8 51.9 1.0

Magnesium binding site 2 out of 4 in 5gtw

Go back to Magnesium Binding Sites List in 5gtw
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg602

b:63.6
occ:1.00
 OD1 B:ASN26 2.3 49.9 1.0
OD2 B:ASP32 2.6 53.8 1.0
O B:LYS30 2.7 37.1 1.0
OD1 B:ASP28 2.7 49.1 1.0
OD2 B:ASP28 2.8 51.3 1.0
CG B:ASP28 3.0 44.5 1.0
OD1 B:ASP24 3.0 39.5 1.0
CG B:ASN26 3.3 43.5 1.0
CG B:ASP32 3.4 53.4 1.0
CB B:ASP32 3.5 48.9 1.0
C B:LYS30 3.6 37.3 1.0
O B:GLY31 3.7 45.9 1.0
ND2 B:ASN26 3.7 45.0 1.0
O B:ASP77 3.8 44.4 1.0
CG B:ASP24 4.0 40.1 1.0
C B:GLY31 4.0 42.0 1.0
CB B:LYS30 4.3 42.2 1.0
CA B:LYS30 4.3 39.4 1.0
N B:ASP32 4.3 44.4 1.0
N B:LYS30 4.4 40.8 1.0
CB B:ASP28 4.4 40.9 1.0
CA B:ASP32 4.5 43.5 1.0
OD1 B:ASP32 4.5 53.2 1.0
N B:ASN26 4.5 40.1 1.0
N B:GLY31 4.6 37.9 1.0
N B:GLY25 4.6 38.5 1.0
CA B:ASP24 4.7 38.6 1.0
CB B:ASP24 4.7 40.6 1.0
CB B:ASN26 4.7 41.8 1.0
CA B:GLY31 4.7 38.8 1.0
OD2 B:ASP24 4.8 39.3 1.0
N B:ASP28 4.8 38.5 1.0
C B:ASP24 5.0 39.8 1.0

Magnesium binding site 3 out of 4 in 5gtw

Go back to Magnesium Binding Sites List in 5gtw
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg602

b:40.5
occ:1.00
 OD2 C:ASP32 2.0 53.9 1.0
OD1 C:ASP28 2.1 47.8 1.0
OD2 C:ASP28 2.2 53.4 1.0
OD1 C:ASN26 2.3 66.1 1.0
O C:LYS30 2.4 48.4 1.0
CG C:ASP28 2.5 52.0 1.0
OD1 C:ASP24 3.0 43.8 1.0
CG C:ASP32 3.1 50.7 1.0
CG C:ASN26 3.4 59.2 1.0
C C:LYS30 3.6 43.6 1.0
CB C:ASP32 3.6 47.6 1.0
O C:ASP77 3.8 44.6 1.0
CG C:ASP24 3.9 42.5 1.0
ND2 C:ASN26 3.9 59.5 1.0
CB C:ASP28 4.0 49.4 1.0
N C:GLY25 4.1 46.0 1.0
O C:GLY31 4.1 38.1 1.0
OD1 C:ASP32 4.2 51.3 1.0
N C:LYS30 4.2 40.1 1.0
CA C:LYS30 4.3 43.5 1.0
C C:GLY31 4.3 41.9 1.0
N C:ASN26 4.3 48.9 1.0
CB C:LYS30 4.3 47.1 1.0
CA C:ASP24 4.5 41.2 1.0
N C:ASP28 4.5 46.4 1.0
OD2 C:ASP24 4.5 43.5 1.0
N C:ASP32 4.6 43.5 1.0
N C:GLY31 4.6 42.4 1.0
CB C:ASP24 4.7 41.2 1.0
CB C:ASN26 4.7 53.1 1.0
CA C:ASP32 4.7 44.8 1.0
CA C:ASP28 4.8 46.7 1.0
CA C:GLY31 4.8 42.3 1.0
C C:ASP24 4.8 43.8 1.0
CA C:ASN26 5.0 50.2 1.0

Magnesium binding site 4 out of 4 in 5gtw

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

b:35.3
occ:1.00
 OD1 D:ASP28 1.9 57.6 1.0
OD1 D:ASN26 2.3 44.6 1.0
OD2 D:ASP32 2.3 41.0 1.0
O D:LYS30 2.3 31.6 1.0
OD1 D:ASP24 2.6 33.7 1.0
CG D:ASP28 2.6 54.2 1.0
OD2 D:ASP28 2.7 54.0 1.0
C D:LYS30 3.4 33.6 1.0
CG D:ASP32 3.4 39.4 1.0
CG D:ASN26 3.4 39.0 1.0
CG D:ASP24 3.6 37.2 1.0
CB D:ASP32 3.9 37.5 1.0
N D:LYS30 4.0 39.1 1.0
ND2 D:ASN26 4.0 41.1 1.0
CA D:LYS30 4.0 38.5 1.0
CB D:ASP28 4.1 47.8 1.0
CB D:LYS30 4.2 40.3 1.0
O D:ASP77 4.2 43.5 1.0
N D:ASN26 4.2 40.9 1.0
O D:GLY31 4.4 35.5 1.0
C D:GLY31 4.4 33.7 1.0
N D:ASP28 4.4 44.6 1.0
N D:GLY25 4.5 41.1 1.0
CB D:ASP24 4.5 37.8 1.0
OD1 D:ASP32 4.5 45.4 1.0
N D:GLY31 4.5 32.1 1.0
OD2 D:ASP24 4.5 33.9 1.0
CA D:ASP24 4.5 37.4 1.0
CB D:ASN26 4.6 38.2 1.0
CA D:ASP28 4.7 45.4 1.0
CA D:GLY31 4.7 33.1 1.0
N D:ASP32 4.8 34.1 1.0
C D:ASP24 4.8 40.1 1.0
N D:GLY29 4.8 45.3 1.0
CA D:ASN26 4.9 37.5 1.0
N D:GLY27 4.9 35.5 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 Sep 29 15:26:02 2024

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