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Magnesium in PDB 5brp: Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea), Mutant R201Q, in Complex with Png

Enzymatic activity of Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea), Mutant R201Q, in Complex with Png

All present enzymatic activity of Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea), Mutant R201Q, in Complex with Png:
3.2.1.93;

Protein crystallography data

The structure of Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea), Mutant R201Q, in Complex with Png, PDB code: 5brp was solved by C.-D.Hsiao, M.-G.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.252, 97.388, 108.539, 80.30, 88.15, 72.18
R / Rfree (%) 17.1 / 21.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea), Mutant R201Q, in Complex with Png (pdb code 5brp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea), Mutant R201Q, in Complex with Png, PDB code: 5brp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5brp

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Magnesium binding site 1 out of 4 in the Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea), Mutant R201Q, in Complex with Png


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea), Mutant R201Q, in Complex with Png within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:18.4
occ:1.00
 OD1 A:ASN28 2.3 18.1 1.0
O A:HOH798 2.3 25.1 1.0
OD1 A:ASP24 2.3 14.0 1.0
O A:VAL30 2.3 15.0 1.0
OG1 A:THR26 2.4 16.1 1.0
OD2 A:ASP32 2.5 18.2 1.0
CG A:ASP24 3.2 19.9 1.0
CG A:ASN28 3.2 19.9 1.0
C A:VAL30 3.5 16.8 1.0
CG A:ASP32 3.6 16.2 1.0
CB A:THR26 3.6 20.7 1.0
ND2 A:ASN28 3.6 17.7 1.0
N A:THR26 3.8 20.4 1.0
CG2 A:THR26 3.9 24.2 1.0
CB A:ASP32 3.9 15.9 1.0
OD2 A:ASP24 4.0 19.2 1.0
CB A:ASP24 4.0 16.8 1.0
CA A:ASP24 4.1 12.5 1.0
N A:VAL30 4.1 15.4 1.0
N A:THR25 4.2 19.4 1.0
CA A:THR26 4.2 19.0 1.0
CA A:VAL30 4.3 17.4 1.0
C A:GLY31 4.3 15.6 1.0
O A:GLY31 4.3 15.7 1.0
N A:ASN28 4.4 21.4 1.0
N A:GLY27 4.5 18.3 1.0
N A:ASP32 4.5 16.2 1.0
C A:ASP24 4.5 19.3 1.0
CB A:VAL30 4.5 21.1 1.0
N A:GLY31 4.5 15.4 1.0
CB A:ASN28 4.6 16.6 1.0
CA A:GLY31 4.7 13.6 1.0
OD1 A:ASP32 4.7 18.3 1.0
C A:THR26 4.7 20.9 1.0
O A:GLU77 4.8 26.5 1.0
CA A:ASP32 4.8 16.1 1.0
N A:GLY29 4.8 20.6 1.0
CA A:ASN28 4.9 18.0 1.0
C A:THR25 4.9 19.3 1.0

Magnesium binding site 2 out of 4 in 5brp

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Magnesium binding site 2 out of 4 in the Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea), Mutant R201Q, in Complex with Png


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea), Mutant R201Q, in Complex with Png within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:25.7
occ:1.00
 OD1 B:ASP24 2.2 22.8 1.0
O B:VAL30 2.3 23.7 1.0
O B:HOH742 2.3 29.6 1.0
OD1 B:ASN28 2.5 26.2 1.0
OG1 B:THR26 2.5 26.1 1.0
OD2 B:ASP32 2.5 25.5 1.0
CG B:ASP24 3.2 26.8 1.0
CG B:ASN28 3.4 28.9 1.0
CB B:THR26 3.5 29.0 1.0
CG B:ASP32 3.5 21.4 1.0
C B:VAL30 3.5 21.8 1.0
CG2 B:THR26 3.6 26.4 1.0
N B:THR26 3.7 27.1 1.0
CB B:ASP32 3.8 22.8 1.0
ND2 B:ASN28 3.9 23.3 1.0
CB B:ASP24 3.9 24.4 1.0
CA B:ASP24 4.0 21.4 1.0
OD2 B:ASP24 4.0 23.9 1.0
N B:THR25 4.1 24.2 1.0
CA B:THR26 4.1 29.9 1.0
N B:VAL30 4.2 23.6 1.0
C B:GLY31 4.2 23.8 1.0
N B:GLY27 4.4 28.2 1.0
CA B:VAL30 4.4 23.9 1.0
O B:GLY31 4.4 25.0 1.0
N B:ASP32 4.4 19.2 1.0
N B:ASN28 4.4 27.4 1.0
C B:ASP24 4.5 24.1 1.0
N B:GLY31 4.5 22.5 1.0
CA B:GLY31 4.6 20.7 1.0
C B:THR26 4.6 29.7 1.0
CB B:ASN28 4.7 24.4 1.0
OD1 B:ASP32 4.7 22.7 1.0
CA B:ASP32 4.7 21.2 1.0
CB B:VAL30 4.7 24.7 1.0
O B:GLU77 4.8 30.2 1.0
C B:THR25 4.8 26.9 1.0
O B:HOH994 4.9 33.9 1.0
N B:GLY29 4.9 25.0 1.0
CA B:ASN28 5.0 24.2 1.0

Magnesium binding site 3 out of 4 in 5brp

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Magnesium binding site 3 out of 4 in the Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea), Mutant R201Q, in Complex with Png


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea), Mutant R201Q, in Complex with Png within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:22.1
occ:1.00
 OD1 C:ASP24 2.2 22.4 1.0
O C:VAL30 2.3 22.6 1.0
O C:HOH830 2.3 24.3 1.0
OD1 C:ASN28 2.4 21.3 1.0
OD2 C:ASP32 2.5 25.2 1.0
OG1 C:THR26 2.5 24.7 1.0
CG C:ASP24 3.2 23.8 1.0
CG C:ASN28 3.3 22.4 1.0
C C:VAL30 3.5 20.8 1.0
CG C:ASP32 3.6 24.0 1.0
CB C:THR26 3.7 23.3 1.0
ND2 C:ASN28 3.7 27.6 1.0
N C:THR26 3.8 27.6 1.0
CB C:ASP24 3.9 19.9 1.0
CB C:ASP32 3.9 20.8 1.0
CA C:ASP24 4.0 19.1 1.0
CG2 C:THR26 4.1 23.9 1.0
OD2 C:ASP24 4.1 24.4 1.0
N C:THR25 4.1 17.6 1.0
N C:VAL30 4.2 20.2 1.0
C C:GLY31 4.2 19.9 1.0
CA C:THR26 4.2 25.7 1.0
CA C:VAL30 4.3 23.8 1.0
N C:ASP32 4.4 19.7 1.0
N C:GLY27 4.4 23.4 1.0
O C:GLY31 4.4 20.4 1.0
N C:ASN28 4.4 20.8 1.0
N C:GLY31 4.5 20.7 1.0
C C:ASP24 4.5 20.4 1.0
CA C:GLY31 4.5 19.1 1.0
CB C:VAL30 4.6 24.4 1.0
CB C:ASN28 4.7 22.3 1.0
O C:HOH812 4.7 34.8 1.0
OD1 C:ASP32 4.7 21.3 1.0
C C:THR26 4.7 25.9 1.0
CA C:ASP32 4.8 19.8 1.0
O C:GLU77 4.8 27.9 1.0
N C:GLY29 4.9 21.1 1.0
C C:THR25 4.9 22.6 1.0
CA C:ASN28 5.0 20.0 1.0

Magnesium binding site 4 out of 4 in 5brp

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Magnesium binding site 4 out of 4 in the Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea), Mutant R201Q, in Complex with Png


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea), Mutant R201Q, in Complex with Png within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:23.7
occ:1.00
 O D:VAL30 2.2 21.8 1.0
OD2 D:ASP32 2.3 24.1 1.0
O D:HOH913 2.3 25.4 1.0
OD1 D:ASP24 2.3 21.8 1.0
OD1 D:ASN28 2.3 23.9 1.0
OG1 D:THR26 2.7 25.6 1.0
CG D:ASP24 3.2 24.4 1.0
CG D:ASN28 3.3 28.2 1.0
CG D:ASP32 3.4 24.2 1.0
C D:VAL30 3.4 22.6 1.0
ND2 D:ASN28 3.7 28.4 1.0
CB D:ASP32 3.7 20.1 1.0
CB D:THR26 3.8 27.8 1.0
N D:THR26 3.8 24.8 1.0
CB D:ASP24 3.9 23.6 1.0
CG2 D:THR26 4.0 27.3 1.0
CA D:ASP24 4.0 20.8 1.0
OD2 D:ASP24 4.0 22.1 1.0
C D:GLY31 4.1 20.4 1.0
N D:THR25 4.1 24.1 1.0
N D:VAL30 4.2 18.9 1.0
O D:GLY31 4.2 20.4 1.0
CA D:VAL30 4.2 24.4 1.0
CA D:THR26 4.3 26.5 1.0
N D:ASP32 4.3 18.9 1.0
N D:GLY31 4.4 21.1 1.0
CB D:VAL30 4.5 25.0 1.0
N D:ASN28 4.5 24.1 1.0
CA D:GLY31 4.5 19.1 1.0
OD1 D:ASP32 4.5 24.6 1.0
C D:ASP24 4.5 26.5 1.0
N D:GLY27 4.5 24.6 1.0
O D:HOH824 4.6 37.4 1.0
CA D:ASP32 4.6 21.9 1.0
CB D:ASN28 4.6 24.1 1.0
C D:THR26 4.7 25.0 1.0
O D:GLU77 4.7 24.5 1.0
C D:THR25 4.9 25.0 1.0
CA D:ASN28 5.0 24.1 1.0

Reference:

M.-G.Lin, M.-C.Chi, V.Naveen, Y.-C.Li, L.-L.Lin, C.-D.Hsiao. Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase Structures Suggest Keys to Substrate Specificity Acta Crystallogr D Struct V. 72 59 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 26894535
DOI: 10.1107/S2059798315020756
Page generated: Mon Dec 14 20:03:06 2020

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