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Arsenic in PDB 5naq: Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum

Enzymatic activity of Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum

All present enzymatic activity of Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum:
3.2.1.21;

Protein crystallography data

The structure of Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum, PDB code: 5naq was solved by I.Acebron, J.M.Mancheno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.23 / 2.48
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 196.688, 191.683, 105.931, 90.00, 102.75, 90.00
R / Rfree (%) 15.9 / 21.7

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum (pdb code 5naq). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 6 binding sites of Arsenic where determined in the Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum, PDB code: 5naq:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6;

Arsenic binding site 1 out of 6 in 5naq

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Arsenic binding site 1 out of 6 in the Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As292

b:0.5
occ:1.00
 AS A:CAS292 0.0 0.5 1.0
CE2 A:CAS292 2.0 0.1 1.0
CE1 A:CAS292 2.0 0.3 1.0
SG A:CAS292 2.3 33.6 1.0
O A:HOH657 3.5 34.2 1.0
CB A:CAS292 3.5 26.6 1.0
OH A:TYR161 3.9 16.3 1.0
CE2 A:TYR161 4.0 19.0 1.0
CZ A:TYR161 4.2 22.1 1.0
O A:HOH642 4.4 38.5 1.0
CD2 A:HIS159 4.6 29.7 1.0
CB A:GLN217 4.7 29.8 1.0
CA A:CAS292 4.8 21.7 1.0
CB A:HIS159 4.8 11.6 1.0
O A:TRP160 4.9 17.5 1.0
CD2 A:TYR161 4.9 13.7 1.0

Arsenic binding site 2 out of 6 in 5naq

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Arsenic binding site 2 out of 6 in the Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As292

b:0.8
occ:1.00
 AS B:CAS292 0.0 0.8 1.0
CE1 B:CAS292 2.0 0.5 1.0
CE2 B:CAS292 2.0 0.2 1.0
SG B:CAS292 2.3 87.2 1.0
CB B:CAS292 3.4 50.1 1.0
O B:HOH837 3.5 46.4 1.0
CE B:MET362 3.8 43.0 1.0
O B:HOH755 4.0 58.2 1.0
CD2 B:HIS159 4.4 37.4 1.0
CA B:CAS292 4.6 36.7 1.0
CB B:GLN217 4.8 37.4 1.0
NE2 B:GLN410 5.0 34.9 1.0

Arsenic binding site 3 out of 6 in 5naq

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Arsenic binding site 3 out of 6 in the Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As292

b:0.6
occ:1.00
 AS C:CAS292 0.0 0.6 1.0
CE1 C:CAS292 2.0 0.6 1.0
CE2 C:CAS292 2.0 0.1 1.0
SG C:CAS292 2.3 32.3 1.0
CB C:CAS292 3.4 28.0 1.0
O C:HOH746 3.9 33.5 1.0
CB C:GLN217 4.3 39.8 1.0
ND1 C:HIS159 4.3 44.7 1.0
OH C:TYR161 4.4 33.2 1.0
CZ C:TYR161 4.7 35.1 1.0
CA C:CAS292 4.8 34.6 1.0
CE2 C:TYR161 4.8 35.8 1.0
CB C:HIS159 4.9 35.2 1.0
CG C:GLN217 4.9 55.6 1.0
O C:GLN217 5.0 28.2 1.0

Arsenic binding site 4 out of 6 in 5naq

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Arsenic binding site 4 out of 6 in the Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As292

b:0.1
occ:1.00
 AS D:CAS292 0.0 0.1 1.0
CE1 D:CAS292 2.0 0.4 1.0
CE2 D:CAS292 2.0 0.4 1.0
SG D:CAS292 2.2 52.2 1.0
CB D:CAS292 3.4 39.8 1.0
OH D:TYR161 3.9 28.6 1.0
CZ D:TYR161 4.3 22.9 1.0
ND1 D:HIS159 4.4 36.3 1.0
CE2 D:TYR161 4.4 26.0 1.0
O D:HOH606 4.5 49.0 1.0
CB D:GLN217 4.7 40.0 1.0
CA D:CAS292 4.8 31.6 1.0
O D:TRP160 5.0 29.8 1.0

Arsenic binding site 5 out of 6 in 5naq

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Arsenic binding site 5 out of 6 in the Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:As292

b:0.0
occ:1.00
 AS E:CAS292 0.0 0.0 1.0
CE1 E:CAS292 2.0 0.6 1.0
CE2 E:CAS292 2.0 0.1 1.0
SG E:CAS292 2.3 78.3 1.0
CB E:CAS292 3.1 46.0 1.0
CB E:GLN217 4.3 44.1 1.0
CD2 E:HIS159 4.4 53.1 1.0
CE E:MET362 4.5 38.3 1.0
CA E:CAS292 4.5 31.4 1.0
O E:HOH678 4.7 45.6 1.0
CG E:GLN217 4.8 52.1 1.0
OE1 E:GLN217 4.9 59.7 1.0

Arsenic binding site 6 out of 6 in 5naq

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Arsenic binding site 6 out of 6 in the Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of Crystal Structure of Native 6-Phospho-Glucosidase Lpbgl From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
F:As292

b:0.1
occ:1.00
 AS F:CAS292 0.0 0.1 1.0
CE2 F:CAS292 2.0 0.9 1.0
CE1 F:CAS292 2.0 0.3 1.0
SG F:CAS292 2.2 56.2 1.0
CB F:CAS292 3.4 43.1 1.0
OH F:TYR161 4.0 38.5 1.0
CG F:GLN217 4.1 88.7 1.0
OE1 F:GLN217 4.1 99.7 1.0
CE2 F:TYR161 4.2 30.0 1.0
CZ F:TYR161 4.3 35.9 1.0
CD F:GLN217 4.3 98.6 1.0
CD2 F:HIS159 4.4 54.0 1.0
CA F:CAS292 4.8 40.6 1.0
CB F:HIS159 4.9 56.7 1.0
CE2 F:TYR114 4.9 53.3 1.0
O F:TRP160 4.9 27.2 1.0

Reference:

I.Acebron, L.Plaza-Vinuesa, B.De Las Rivas, R.Munoz, J.Cumella, F.Sanchez-Sancho, J.M.Mancheno. Structural Basis of the Substrate Specificity and Instability in Solution of A Glycosidase From Lactobacillus Plantarum. Biochim. Biophys. Acta V.1865 1227 2017.
ISSN: ISSN 0006-3002
PubMed: 28734976
DOI: 10.1016/J.BBAPAP.2017.07.007
Page generated: Wed Jul 10 12:54:22 2024

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