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Magnesium in PDB 6lgi: Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Covalent Intermediate Complexed with Fructose

Protein crystallography data

The structure of Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Covalent Intermediate Complexed with Fructose, PDB code: 6lgi was solved by T.Miyazaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.04 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.405, 147.055, 153.544, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.7

Other elements in 6lgi:

The structure of Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Covalent Intermediate Complexed with Fructose also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Covalent Intermediate Complexed with Fructose (pdb code 6lgi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Covalent Intermediate Complexed with Fructose, PDB code: 6lgi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6lgi

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Magnesium binding site 1 out of 5 in the Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Covalent Intermediate Complexed with Fructose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Covalent Intermediate Complexed with Fructose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:28.8
occ:1.00
 OD2 A:ASP71 2.1 32.1 1.0
OD1 A:ASP65 2.1 29.7 1.0
O A:HOH832 2.1 29.9 1.0
OD1 A:ASP67 2.1 36.4 1.0
OD1 A:ASP63 2.1 29.3 1.0
O A:ILE69 2.1 27.8 1.0
CG A:ASP67 3.0 33.7 1.0
CG A:ASP63 3.1 27.5 1.0
CG A:ASP65 3.1 37.0 1.0
CG A:ASP71 3.2 27.2 1.0
OD2 A:ASP67 3.3 34.3 1.0
C A:ILE69 3.3 29.2 1.0
OD2 A:ASP65 3.6 40.5 1.0
CB A:ASP71 3.8 25.4 1.0
OD2 A:ASP63 3.9 29.6 1.0
CB A:ASP63 3.9 30.6 1.0
N A:ASP65 4.0 30.0 1.0
CA A:ASP63 4.1 31.0 1.0
CA A:ILE69 4.1 29.6 1.0
N A:ILE69 4.1 26.9 1.0
N A:SER64 4.2 29.5 1.0
CB A:ILE69 4.3 29.2 1.0
OD1 A:ASP71 4.3 30.4 1.0
N A:ASP67 4.3 30.6 1.0
CB A:ASP65 4.4 36.5 1.0
CB A:ASP67 4.4 32.7 1.0
N A:GLY70 4.4 27.7 1.0
C A:GLY70 4.4 27.7 1.0
C A:ASP63 4.5 34.6 1.0
CA A:ASP65 4.5 35.5 1.0
N A:ASP71 4.6 28.8 1.0
N A:GLY66 4.6 28.6 1.0
O A:GLY70 4.6 30.9 1.0
CA A:GLY70 4.7 31.2 1.0
C A:ASP65 4.7 32.1 1.0
O A:GLU116 4.7 30.7 1.0
CA A:ASP67 4.8 32.0 1.0
CA A:ASP71 4.8 29.4 1.0
N A:GLY68 4.8 29.5 1.0
CG2 A:ILE69 4.9 28.8 1.0

Magnesium binding site 2 out of 5 in 6lgi

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Magnesium binding site 2 out of 5 in the Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Covalent Intermediate Complexed with Fructose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Covalent Intermediate Complexed with Fructose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:37.1
occ:1.00
 O A:HOH1130 2.0 43.2 1.0
O A:HOH889 2.0 37.0 1.0
O A:HOH1145 2.0 51.0 1.0
O A:HOH1214 2.1 40.0 1.0
O A:HOH899 2.2 38.4 1.0
O A:HOH878 2.3 37.4 1.0
O6 A:FRU705 3.9 32.8 1.0
O A:ASP389 4.0 28.5 1.0
O A:HOH1151 4.2 38.0 1.0
OE2 A:GLU440 4.2 30.4 1.0
O A:TYR453 4.3 39.2 1.0
OE1 A:GLU440 4.3 34.0 1.0
CD A:GLU440 4.6 31.9 1.0
O A:HOH958 4.8 34.0 1.0
O A:HOH834 4.9 47.9 1.0
CG A:ARG455 4.9 24.6 1.0
O A:LEU452 4.9 42.0 1.0
ND2 A:ASN390 5.0 25.3 1.0

Magnesium binding site 3 out of 5 in 6lgi

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Magnesium binding site 3 out of 5 in the Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Covalent Intermediate Complexed with Fructose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Covalent Intermediate Complexed with Fructose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg708

b:24.7
occ:1.00
 O B:HOH913 1.9 21.7 1.0
O B:HOH985 2.0 22.6 1.0
O A:HOH920 2.1 22.6 1.0
O A:HOH1178 2.1 27.5 1.0
O B:HOH1259 2.2 25.2 1.0
O A:HOH1171 2.2 25.9 1.0
NE2 A:HIS564 4.0 30.9 1.0
OD1 A:ASP523 4.0 27.6 1.0
OD1 B:ASP523 4.1 23.3 1.0
NE2 B:HIS564 4.1 28.5 1.0
OD2 A:ASP523 4.2 26.6 1.0
O A:HOH1189 4.2 30.5 1.0
OD2 B:ASP523 4.2 25.3 1.0
O B:HOH1294 4.2 31.9 1.0
O B:HOH1300 4.2 36.8 1.0
O B:HOH1310 4.3 25.6 1.0
O A:HOH1215 4.3 27.9 1.0
O A:HOH1220 4.3 32.8 1.0
O A:HOH1219 4.3 30.3 1.0
O B:HOH1282 4.4 29.1 1.0
CG A:ASP523 4.4 27.1 1.0
CG B:ASP523 4.5 23.7 1.0
O B:HOH1209 4.5 28.1 1.0
O A:HOH1103 4.6 28.3 1.0
CE1 A:HIS564 4.7 33.9 1.0
CE1 B:HIS564 4.7 28.3 1.0

Magnesium binding site 4 out of 5 in 6lgi

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Magnesium binding site 4 out of 5 in the Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Covalent Intermediate Complexed with Fructose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Covalent Intermediate Complexed with Fructose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:23.1
occ:1.00
 OD1 B:ASP65 2.0 25.0 1.0
OD1 B:ASP63 2.1 26.2 1.0
O B:HOH869 2.1 25.1 1.0
O B:ILE69 2.1 23.8 1.0
OD2 B:ASP71 2.1 21.4 1.0
OD1 B:ASP67 2.2 24.6 1.0
CG B:ASP67 3.1 30.6 1.0
CG B:ASP65 3.2 30.4 1.0
CG B:ASP63 3.2 28.9 1.0
C B:ILE69 3.3 23.3 1.0
CG B:ASP71 3.3 21.8 1.0
OD2 B:ASP67 3.4 29.7 1.0
OD2 B:ASP65 3.7 36.9 1.0
CB B:ASP71 3.9 25.7 1.0
CB B:ASP63 3.9 26.3 1.0
N B:ILE69 4.0 29.8 1.0
CA B:ASP63 4.0 24.9 1.0
CA B:ILE69 4.0 25.1 1.0
OD2 B:ASP63 4.0 28.2 1.0
N B:ASP65 4.1 26.1 1.0
N B:SER64 4.2 28.4 1.0
CB B:ILE69 4.2 23.9 1.0
CB B:ASP65 4.3 28.9 1.0
C B:GLY70 4.4 22.6 1.0
N B:ASP67 4.4 29.4 1.0
N B:GLY70 4.4 22.3 1.0
OD1 B:ASP71 4.4 25.9 1.0
CB B:ASP67 4.4 28.2 1.0
C B:ASP63 4.4 26.8 1.0
O B:HOH1090 4.5 42.4 1.0
CA B:ASP65 4.6 28.6 1.0
N B:GLY66 4.6 28.4 1.0
N B:ASP71 4.6 22.9 1.0
CA B:GLY70 4.6 24.2 1.0
O B:GLY70 4.6 25.8 1.0
C B:ASP65 4.7 31.8 1.0
O B:GLU116 4.7 27.2 1.0
CA B:ASP67 4.8 27.5 1.0
CA B:ASP71 4.9 24.8 1.0
CG2 B:ILE69 4.9 25.5 1.0
N B:GLY68 4.9 27.4 1.0

Magnesium binding site 5 out of 5 in 6lgi

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Magnesium binding site 5 out of 5 in the Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Covalent Intermediate Complexed with Fructose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Covalent Intermediate Complexed with Fructose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:33.0
occ:1.00
 O B:HOH926 1.9 31.9 1.0
O B:HOH1237 2.0 42.0 1.0
O B:HOH1096 2.1 36.4 1.0
O B:HOH1309 2.1 44.1 1.0
O B:HOH1249 2.1 38.4 1.0
O B:HOH908 2.2 35.0 1.0
O6 B:FRU705 3.9 31.7 1.0
O B:ASP389 4.1 26.1 1.0
OE2 B:GLU440 4.1 30.4 1.0
O B:TYR453 4.2 36.2 1.0
OE1 B:GLU440 4.3 31.2 1.0
O B:HOH1235 4.3 33.7 1.0
O B:HOH1292 4.5 43.6 1.0
CD B:GLU440 4.6 30.9 1.0
O B:HOH907 4.7 31.9 1.0
O B:HOH922 4.8 42.5 1.0
CG B:ARG455 4.9 25.6 1.0
ND2 B:ASN390 5.0 21.9 1.0

Reference:

T.Miyazaki, E.Y.Park. Structure-Function Analysis of Silkworm Sucrose Hydrolase Uncovers the Mechanism of Substrate Specificity in GH13 Subfamily 17EXO-Alpha-Glucosidases. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32381508
DOI: 10.1074/JBC.RA120.013595
Page generated: Tue Oct 1 10:27:05 2024

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