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Magnesium in PDB 5brq: Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea)

Enzymatic activity of Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea)

All present enzymatic activity of Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea):
3.2.1.93;

Protein crystallography data

The structure of Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea), PDB code: 5brq 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) 24.30 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.802, 97.584, 108.336, 98.20, 91.44, 108.15
R / Rfree (%) 18.1 / 24.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea) (pdb code 5brq). 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), PDB code: 5brq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5brq

Go back to Magnesium Binding Sites List in 5brq
Magnesium binding site 1 out of 4 in the Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:19.5
occ:1.00
 OD1 A:ASP24 2.3 15.3 1.0
O A:VAL30 2.4 16.0 1.0
OD2 A:ASP32 2.4 18.4 1.0
O A:HOH798 2.4 21.4 1.0
OD1 A:ASN28 2.6 16.7 1.0
OG1 A:THR26 2.6 18.6 1.0
CG A:ASP24 3.2 17.8 1.0
CG A:ASN28 3.5 19.4 1.0
CG A:ASP32 3.5 17.5 1.0
C A:VAL30 3.6 18.7 1.0
CB A:THR26 3.6 22.3 1.0
N A:THR26 3.7 23.2 1.0
CG2 A:THR26 3.8 23.6 1.0
ND2 A:ASN28 3.9 19.9 1.0
CA A:ASP24 4.0 16.6 1.0
CB A:ASP24 4.0 14.6 1.0
CB A:ASP32 4.0 14.8 1.0
N A:THR25 4.0 16.6 1.0
OD2 A:ASP24 4.1 17.1 1.0
CA A:THR26 4.1 24.2 1.0
N A:VAL30 4.2 17.1 1.0
O A:HOH814 4.3 29.0 1.0
C A:ASP24 4.4 17.3 1.0
C A:GLY31 4.4 14.0 1.0
CA A:VAL30 4.4 15.2 1.0
N A:GLY27 4.4 20.4 1.0
N A:ASN28 4.5 17.1 1.0
N A:ASP32 4.5 14.4 1.0
N A:GLY31 4.5 12.4 1.0
O A:GLY31 4.6 15.0 1.0
OD1 A:ASP32 4.6 19.2 1.0
C A:THR26 4.6 29.5 1.0
CA A:GLY31 4.6 11.7 1.0
CB A:VAL30 4.6 17.7 1.0
CB A:ASN28 4.7 14.7 1.0
C A:THR25 4.8 19.9 1.0
O A:GLU77 4.9 24.2 1.0
CA A:ASP32 4.9 16.1 1.0
N A:GLY29 4.9 21.8 1.0
CA A:THR25 5.0 20.8 1.0

Magnesium binding site 2 out of 4 in 5brq

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Magnesium binding site 2 out of 4 in the Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:11.1
occ:1.00
 O B:VAL30 2.3 13.0 1.0
OD1 B:ASP24 2.3 12.5 1.0
O B:HOH727 2.3 21.9 1.0
OD1 B:ASN28 2.4 16.0 1.0
OD2 B:ASP32 2.4 16.2 1.0
OG1 B:THR26 2.6 16.2 1.0
CG B:ASP24 3.2 16.5 1.0
CG B:ASN28 3.3 19.7 1.0
C B:VAL30 3.4 13.5 1.0
CG B:ASP32 3.5 14.7 1.0
ND2 B:ASN28 3.7 18.7 1.0
CB B:THR26 3.8 17.4 1.0
N B:THR26 3.9 14.3 1.0
CB B:ASP24 4.0 10.2 1.0
CB B:ASP32 4.0 13.2 1.0
OD2 B:ASP24 4.1 16.6 1.0
CA B:ASP24 4.1 8.8 1.0
N B:VAL30 4.1 12.0 1.0
N B:THR25 4.2 10.6 1.0
CA B:VAL30 4.2 14.2 1.0
CG2 B:THR26 4.3 16.8 1.0
C B:GLY31 4.3 11.0 1.0
CA B:THR26 4.3 17.3 1.0
N B:GLY27 4.4 13.0 1.0
N B:ASN28 4.4 15.1 1.0
N B:GLY31 4.4 10.1 1.0
O B:GLY31 4.5 13.4 1.0
CB B:VAL30 4.5 15.3 1.0
N B:ASP32 4.5 11.0 1.0
CA B:GLY31 4.5 10.5 1.0
C B:ASP24 4.5 12.3 1.0
OD1 B:ASP32 4.6 12.9 1.0
CB B:ASN28 4.6 15.0 1.0
O B:HOH839 4.7 25.4 1.0
C B:THR26 4.7 16.1 1.0
O B:GLU77 4.8 20.2 1.0
N B:GLY29 4.9 15.8 1.0
CA B:ASP32 4.9 12.0 1.0
CA B:ASN28 4.9 16.2 1.0
C B:THR25 5.0 18.1 1.0

Magnesium binding site 3 out of 4 in 5brq

Go back to Magnesium Binding Sites List in 5brq
Magnesium binding site 3 out of 4 in the Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:27.2
occ:1.00
 OD1 C:ASP24 2.1 21.8 1.0
O C:VAL30 2.3 25.6 1.0
OD1 C:ASN28 2.4 22.1 1.0
OD2 C:ASP32 2.5 27.3 1.0
OG1 C:THR26 2.6 27.3 1.0
CG C:ASP24 3.1 23.9 1.0
CG C:ASN28 3.3 26.9 1.0
CG C:ASP32 3.5 25.4 1.0
C C:VAL30 3.5 29.0 1.0
ND2 C:ASN28 3.7 21.1 1.0
CB C:THR26 3.8 30.3 1.0
N C:THR26 3.9 31.3 1.0
CB C:ASP32 3.9 25.1 1.0
OD2 C:ASP24 3.9 23.5 1.0
CB C:ASP24 4.0 23.3 1.0
N C:THR25 4.1 23.6 1.0
CA C:ASP24 4.2 19.5 1.0
CG2 C:THR26 4.2 28.8 1.0
N C:VAL30 4.2 21.9 1.0
CA C:THR26 4.3 28.6 1.0
CA C:VAL30 4.3 25.4 1.0
N C:GLY27 4.3 26.7 1.0
C C:GLY31 4.3 22.0 1.0
N C:ASN28 4.5 23.6 1.0
N C:ASP32 4.5 21.2 1.0
O C:GLY31 4.5 20.9 1.0
N C:GLY31 4.5 22.1 1.0
CB C:VAL30 4.6 26.1 1.0
C C:ASP24 4.6 19.0 1.0
CB C:ASN28 4.6 22.6 1.0
OD1 C:ASP32 4.6 24.5 1.0
O C:GLU77 4.6 34.3 1.0
CA C:GLY31 4.7 19.3 1.0
C C:THR26 4.7 30.4 1.0
CA C:ASP32 4.8 24.4 1.0
C C:THR25 5.0 28.8 1.0
CA C:ASN28 5.0 23.3 1.0

Magnesium binding site 4 out of 4 in 5brq

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Magnesium binding site 4 out of 4 in the Crystal Structure of Bacillus Licheniformis Trehalose-6-Phosphate Hydrolase (Trea)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:26.4
occ:1.00
 O D:VAL30 2.3 21.2 1.0
OD2 D:ASP32 2.3 27.9 1.0
OD1 D:ASN28 2.4 28.1 1.0
OD1 D:ASP24 2.5 25.7 1.0
OG1 D:THR26 2.8 32.2 1.0
CG D:ASN28 3.4 28.6 1.0
CG D:ASP32 3.4 25.2 1.0
C D:VAL30 3.4 28.7 1.0
CG D:ASP24 3.5 29.8 1.0
ND2 D:ASN28 3.6 24.5 1.0
CB D:ASP32 3.8 25.7 1.0
CB D:THR26 3.9 34.9 1.0
CG2 D:THR26 4.0 32.4 1.0
C D:GLY31 4.1 16.4 1.0
N D:THR26 4.2 30.2 1.0
O D:GLY31 4.2 19.1 1.0
N D:VAL30 4.2 18.2 1.0
CA D:VAL30 4.2 22.2 1.0
CB D:ASP24 4.3 24.9 1.0
N D:ASP32 4.3 22.3 1.0
O D:GLU77 4.4 23.7 1.0
CB D:VAL30 4.4 25.5 1.0
N D:GLY31 4.4 21.7 1.0
CA D:ASP24 4.4 19.5 1.0
OD2 D:ASP24 4.4 26.5 1.0
N D:GLY27 4.5 31.0 1.0
OD1 D:ASP32 4.5 28.9 1.0
CA D:GLY31 4.5 18.6 1.0
N D:THR25 4.5 28.5 1.0
CA D:THR26 4.5 29.0 1.0
N D:ASN28 4.6 23.1 1.0
CA D:ASP32 4.7 19.5 1.0
CB D:ASN28 4.7 22.2 1.0
C D:ASP24 4.9 23.8 1.0
CG1 D:VAL30 4.9 27.6 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: Tue Aug 12 05:46:01 2025

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