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Magnesium in PDB 3e1f: E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose

Enzymatic activity of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose

All present enzymatic activity of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose:
3.2.1.23;

Protein crystallography data

The structure of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose, PDB code: 3e1f was solved by R.E.Huber, M.L.Dugdale, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 98.54 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 128.370, 152.870, 132.120, 90.00, 102.68, 90.00
R / Rfree (%) 21.8 / 24.9

Other elements in 3e1f:

The structure of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose also contains other interesting chemical elements:

Sodium (Na) 13 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose (pdb code 3e1f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose, PDB code: 3e1f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3e1f

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Magnesium binding site 1 out of 10 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg3000

b:18.2
occ:1.00
 OE1 1:GLU418 2.2 30.7 1.0
OE1 1:GLU461 2.3 31.8 1.0
OE2 1:GLU416 2.4 34.4 1.0
O 1:HOH8614 2.8 8.9 1.0
O4 1:GAL2001 2.9 43.8 1.0
CB 1:ASP201 3.4 42.7 1.0
CD 1:GLU461 3.4 31.1 1.0
CD 1:GLU416 3.4 31.1 1.0
CD 1:GLU418 3.4 31.3 1.0
N 1:ASP201 3.6 40.8 1.0
OD1 1:ASN102 3.7 57.1 1.0
OE1 1:GLU416 3.7 28.5 1.0
OE2 1:GLU461 3.9 31.3 1.0
CA 1:ASP201 4.0 42.5 1.0
C2 1:GAL2001 4.0 40.0 1.0
O3 1:GAL2001 4.0 39.2 1.0
OE2 1:GLU418 4.1 31.5 1.0
C4 1:GAL2001 4.1 41.5 1.0
O 1:ASP199 4.2 34.5 1.0
O 1:ASN102 4.3 51.9 1.0
C3 1:GAL2001 4.3 40.6 1.0
C 1:GLN200 4.4 39.0 1.0
CB 1:GLU418 4.5 31.5 1.0
CG 1:GLU418 4.6 30.9 1.0
CG 1:ASP201 4.6 42.8 1.0
CA 1:GLN200 4.6 36.9 1.0
CG 1:GLU461 4.7 30.1 1.0
ND2 1:ASN460 4.8 33.4 1.0
CG 1:GLU416 4.8 30.3 1.0
C 1:ASN102 4.8 51.7 1.0
O5 1:GAL2001 4.8 42.5 1.0
O2 1:GAL2001 4.9 37.8 1.0
CG 1:ASN102 4.9 56.6 1.0
CB 1:GLU461 4.9 29.3 1.0
C1 1:GAL2001 5.0 40.6 1.0
CG2 1:VAL103 5.0 46.9 1.0

Magnesium binding site 2 out of 10 in 3e1f

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Magnesium binding site 2 out of 10 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg3001

b:0.3
occ:1.00
 OD2 1:ASP193 2.0 27.8 1.0
O 1:ASP15 2.0 43.1 1.0
NE2 1:GLN163 2.2 38.2 1.0
O 1:VAL21 2.5 37.4 1.0
O 1:ASN18 2.6 39.8 1.0
CG 1:ASP193 3.1 30.3 1.0
CD 1:GLN163 3.2 40.7 1.0
C 1:ASP15 3.2 42.6 1.0
C 1:ASN18 3.4 38.5 1.0
OE1 1:GLN163 3.5 42.6 1.0
OD1 1:ASP193 3.6 30.7 1.0
N 1:ASN18 3.6 39.2 1.0
C 1:VAL21 3.7 36.3 1.0
CA 1:TRP16 3.7 41.3 1.0
OH 1:TYR161 3.8 38.0 1.0
C 1:TRP16 3.9 40.2 1.0
N 1:TRP16 3.9 42.1 1.0
CA 1:ASN18 4.0 38.1 1.0
N 1:GLU17 4.1 40.4 1.0
CE2 1:TYR161 4.1 39.3 1.0
N 1:PRO19 4.4 38.1 1.0
CA 1:ASP15 4.4 41.7 1.0
O 1:TRP16 4.4 38.7 1.0
CB 1:ASP193 4.4 30.3 1.0
CB 1:VAL21 4.4 34.3 1.0
CB 1:ASN18 4.4 36.0 1.0
CZ 1:TYR161 4.4 39.3 1.0
CA 1:VAL21 4.5 36.3 1.0
CG 1:GLN163 4.5 40.3 1.0
N 1:VAL21 4.6 37.9 1.0
CA 1:PRO19 4.7 38.7 1.0
N 1:THR22 4.7 35.2 1.0
C 1:GLU17 4.7 39.3 1.0
CG1 1:VAL21 4.8 33.4 1.0
CB 1:ASP15 4.8 39.4 1.0
CA 1:THR22 4.8 34.2 1.0
CA 1:GLU17 4.9 39.5 1.0

Magnesium binding site 3 out of 10 in 3e1f

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Magnesium binding site 3 out of 10 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg3002

b:63.1
occ:1.00
 NE2 1:GLN623 3.2 49.8 1.0
C2 1:DMS8402 3.2 67.1 1.0
CB 1:THR911 4.1 54.9 1.0
CD 1:GLN623 4.2 49.5 1.0
CG2 1:THR911 4.2 54.4 1.0
NE2 1:HIS622 4.3 47.0 1.0
C1 1:DMS8402 4.3 67.4 1.0
S 1:DMS8402 4.3 66.9 1.0
OE1 1:GLN623 4.4 51.8 1.0
OG1 1:THR911 4.8 55.8 1.0
CD2 1:HIS622 4.8 47.0 1.0

Magnesium binding site 4 out of 10 in 3e1f

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Magnesium binding site 4 out of 10 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg3000

b:30.3
occ:1.00
 OE2 2:GLU416 1.8 37.9 1.0
OE1 2:GLU418 2.2 37.8 1.0
O 2:HOH8661 2.2 27.3 1.0
OE1 2:GLU461 2.8 27.3 1.0
O 2:HOH8602 2.8 38.8 1.0
CD 2:GLU416 2.9 37.3 1.0
O 2:ASP199 3.2 28.6 1.0
CD 2:GLU418 3.4 36.0 1.0
N 2:ASP201 3.4 29.8 1.0
OE1 2:GLU416 3.5 39.1 1.0
O 2:ASN102 3.7 38.2 1.0
CB 2:ASP201 3.8 31.6 1.0
CD 2:GLU461 3.9 29.2 1.0
CB 2:GLU418 3.9 32.9 1.0
C 2:GLN200 4.0 29.1 1.0
OD1 2:ASN102 4.0 40.9 1.0
CA 2:ASP201 4.1 29.9 1.0
CA 2:GLN200 4.1 28.7 1.0
CG 2:GLU416 4.2 34.4 1.0
CG 2:GLU418 4.2 34.4 1.0
C 2:ASP199 4.3 27.8 1.0
OE2 2:GLU418 4.3 34.5 1.0
C 2:ASN102 4.5 39.5 1.0
OE2 2:GLU461 4.5 29.6 1.0
O4 2:GAL2001 4.6 41.6 1.0
O 2:HOH8623 4.7 21.3 1.0
CA 2:VAL103 4.7 40.9 1.0
N 2:GLN200 4.7 28.1 1.0
OD2 2:ASP199 4.8 28.6 1.0
CB 2:GLU461 4.9 28.2 1.0
N 2:VAL103 4.9 40.4 1.0
O 2:GLN200 4.9 27.6 1.0
CG2 2:VAL103 4.9 42.2 1.0
CG 2:GLU461 4.9 29.7 1.0
O3 2:GAL2001 4.9 41.2 1.0

Magnesium binding site 5 out of 10 in 3e1f

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Magnesium binding site 5 out of 10 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg3001

b:57.3
occ:1.00
 OD2 2:ASP193 1.8 35.3 1.0
O 2:ASN18 2.3 35.9 1.0
O 2:VAL21 2.3 28.0 1.0
NE2 2:GLN163 2.4 32.9 1.0
CG 2:ASP193 2.7 36.4 1.0
OD1 2:ASP193 2.9 38.9 1.0
O 2:ASP15 2.9 37.6 1.0
C 2:ASN18 3.1 34.4 1.0
OE1 2:GLN163 3.1 33.9 1.0
CD 2:GLN163 3.1 33.1 1.0
C 2:VAL21 3.5 28.4 1.0
N 2:ASN18 3.8 35.8 1.0
N 2:PRO19 3.8 33.3 1.0
CA 2:PRO19 3.9 31.9 1.0
CA 2:ASN18 4.0 35.1 1.0
CB 2:ASP193 4.1 35.1 1.0
C 2:ASP15 4.1 37.4 1.0
N 2:VAL21 4.3 28.9 1.0
CA 2:VAL21 4.3 27.9 1.0
N 2:THR22 4.4 27.9 1.0
C 2:PRO19 4.4 31.0 1.0
C 2:TRP16 4.4 37.7 1.0
OH 2:TYR161 4.5 28.5 1.0
CA 2:TRP16 4.5 37.9 1.0
CA 2:THR22 4.5 26.7 1.0
CG 2:GLN163 4.6 31.8 1.0
CB 2:ASN18 4.6 34.8 1.0
CB 2:VAL21 4.6 27.8 1.0
N 2:GLU17 4.6 36.9 1.0
CE2 2:TYR161 4.7 26.2 1.0
N 2:GLY20 4.8 30.5 1.0
O 2:TRP16 4.8 39.3 1.0
CG2 2:THR22 4.8 24.9 1.0
N 2:TRP16 4.8 37.5 1.0
C 2:GLU17 4.9 36.4 1.0
O 2:PRO19 5.0 29.4 1.0

Magnesium binding site 6 out of 10 in 3e1f

Go back to Magnesium Binding Sites List in 3e1f
Magnesium binding site 6 out of 10 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg3002

b:26.1
occ:0.50
 OE1 2:GLN718 2.2 53.0 1.0
C2 2:DMS8427 2.8 79.0 1.0
CD 2:GLN718 3.2 51.2 1.0
O 2:GLN719 3.3 50.5 1.0
N 2:GLN719 3.6 47.7 1.0
NE2 2:GLN718 4.0 51.2 1.0
CG 2:GLN718 4.1 49.3 1.0
C 2:GLN719 4.1 50.4 1.0
CA 2:GLN719 4.2 49.9 1.0
CB 2:GLN719 4.4 51.9 1.0
S 2:DMS8427 4.4 80.7 1.0
C 2:GLN718 4.6 46.7 1.0
CA 2:GLN718 4.7 45.7 1.0
O 2:DMS8427 4.7 78.8 1.0
O 2:THR911 5.0 40.2 1.0
CB 2:GLN718 5.0 46.9 1.0

Magnesium binding site 7 out of 10 in 3e1f

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Magnesium binding site 7 out of 10 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg3000

b:9.7
occ:1.00
 OE1 3:GLU418 1.7 29.2 1.0
O 3:HOH8746 2.3 21.5 1.0
OE1 3:GLU461 2.3 24.2 1.0
OE2 3:GLU416 2.4 27.3 1.0
O 3:HOH8747 2.9 13.9 1.0
CD 3:GLU418 2.9 28.0 1.0
CD 3:GLU461 3.4 25.1 1.0
OD1 3:ASN102 3.5 42.1 1.0
CD 3:GLU416 3.6 28.4 1.0
OE2 3:GLU418 3.6 27.5 1.0
O4 3:GAL2001 3.7 33.2 1.0
CB 3:ASP201 3.7 35.8 1.0
OE2 3:GLU461 3.8 24.6 1.0
N 3:ASP201 3.9 36.6 1.0
OE1 3:GLU416 4.0 30.6 1.0
CG 3:GLU418 4.0 25.0 1.0
O 3:ASN102 4.1 37.4 1.0
CB 3:GLU418 4.1 25.6 1.0
O 3:ASP199 4.2 32.4 1.0
CA 3:ASP201 4.4 36.9 1.0
CG2 3:VAL103 4.5 36.5 1.0
C 3:ASN102 4.5 38.4 1.0
C2 3:GAL2001 4.6 32.0 1.0
CG 3:GLU461 4.6 24.6 1.0
CG 3:ASN102 4.7 41.9 1.0
C 3:GLN200 4.7 35.7 1.0
CA 3:VAL103 4.7 38.3 1.0
CG 3:GLU416 4.8 26.8 1.0
CB 3:GLU461 4.8 25.4 1.0
O3 3:GAL2001 4.8 35.2 1.0
N 3:VAL103 4.9 38.5 1.0
CG 3:ASP201 4.9 35.1 1.0
CA 3:GLN200 4.9 34.3 1.0
C4 3:GAL2001 5.0 32.7 1.0

Magnesium binding site 8 out of 10 in 3e1f

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Magnesium binding site 8 out of 10 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg3001

b:48.2
occ:1.00
 O 3:VAL21 1.9 36.4 1.0
NE2 3:GLN163 2.1 43.7 1.0
OD2 3:ASP193 2.4 32.8 1.0
O 3:ASP15 2.5 42.6 1.0
O 3:ASN18 2.5 39.6 1.0
CD 3:GLN163 3.1 44.4 1.0
C 3:VAL21 3.1 37.3 1.0
OE1 3:GLN163 3.3 49.1 1.0
CG 3:ASP193 3.3 31.1 1.0
C 3:ASN18 3.5 38.8 1.0
OD1 3:ASP193 3.6 33.1 1.0
C 3:ASP15 3.7 42.3 1.0
CA 3:VAL21 4.0 37.2 1.0
N 3:ASN18 4.0 38.4 1.0
N 3:THR22 4.0 36.7 1.0
OH 3:TYR161 4.0 29.6 1.0
CE2 3:TYR161 4.1 31.4 1.0
CB 3:VAL21 4.1 36.6 1.0
N 3:VAL21 4.1 36.7 1.0
CA 3:THR22 4.2 35.2 1.0
CA 3:ASN18 4.2 38.9 1.0
CA 3:TRP16 4.3 41.2 1.0
N 3:PRO19 4.3 38.4 1.0
CG 3:GLN163 4.4 42.7 1.0
CA 3:PRO19 4.5 38.9 1.0
N 3:TRP16 4.5 41.9 1.0
CG1 3:VAL21 4.5 36.5 1.0
C 3:TRP16 4.5 40.9 1.0
CZ 3:TYR161 4.6 30.6 1.0
CB 3:ASN18 4.6 38.2 1.0
N 3:GLU17 4.7 39.9 1.0
CB 3:ASP193 4.7 28.9 1.0
CA 3:ASP15 4.7 41.6 1.0
C 3:PRO19 4.8 38.4 1.0
CG2 3:THR22 4.9 37.5 1.0
O 3:TRP16 5.0 42.2 1.0

Magnesium binding site 9 out of 10 in 3e1f

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Magnesium binding site 9 out of 10 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Mg3004

b:1.7
occ:1.00
 OE1 4:GLU418 2.0 31.1 1.0
OE1 4:GLU461 2.0 30.3 1.0
O 4:HOH8044 2.1 39.0 1.0
O 4:HOH8107 2.3 11.7 1.0
OE2 4:GLU416 2.6 34.8 1.0
O 4:HOH8045 2.9 14.4 1.0
CD 4:GLU461 3.1 28.6 1.0
CD 4:GLU418 3.1 30.7 1.0
O4 4:GAL2001 3.3 31.3 1.0
OE2 4:GLU461 3.5 27.6 1.0
OD1 4:ASN102 3.6 42.8 1.0
CD 4:GLU416 3.6 35.4 1.0
CB 4:ASP201 3.7 32.3 1.0
OE2 4:GLU418 3.7 31.3 1.0
C2 4:GAL2001 3.8 28.9 1.0
OE1 4:GLU416 4.0 38.4 1.0
N 4:ASP201 4.0 32.0 1.0
O3 4:GAL2001 4.0 29.8 1.0
CG 4:GLU418 4.3 30.1 1.0
C3 4:GAL2001 4.3 28.9 1.0
CB 4:GLU418 4.4 32.2 1.0
CG 4:GLU461 4.4 27.1 1.0
O2 4:GAL2001 4.4 29.4 1.0
CA 4:ASP201 4.4 31.7 1.0
C4 4:GAL2001 4.5 29.1 1.0
O 4:ASN102 4.5 38.6 1.0
O 4:ASP199 4.6 26.7 1.0
CB 4:GLU461 4.7 27.5 1.0
ND2 4:ASN460 4.8 29.2 1.0
CG2 4:VAL103 4.8 39.9 1.0
CG 4:ASP201 4.8 33.2 1.0
CG 4:ASN102 4.8 42.9 1.0
C1 4:GAL2001 4.9 29.9 1.0
C 4:GLN200 4.9 32.0 1.0
C 4:ASN102 4.9 39.7 1.0
CG 4:GLU416 4.9 32.3 1.0
O5 4:GAL2001 5.0 30.1 1.0

Magnesium binding site 10 out of 10 in 3e1f

Go back to Magnesium Binding Sites List in 3e1f
Magnesium binding site 10 out of 10 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Mg3000

b:40.1
occ:1.00
 OD2 4:ASP193 2.0 34.4 1.0
NE2 4:GLN163 2.1 37.7 1.0
O 4:ASP15 2.2 43.9 1.0
O 4:VAL21 2.4 31.8 1.0
O 4:ASN18 2.6 32.1 1.0
CG 4:ASP193 3.0 34.8 1.0
CD 4:GLN163 3.1 39.4 1.0
OE1 4:GLN163 3.3 42.0 1.0
C 4:ASN18 3.4 33.4 1.0
OD1 4:ASP193 3.4 35.5 1.0
C 4:ASP15 3.4 43.3 1.0
C 4:VAL21 3.6 30.8 1.0
N 4:ASN18 3.7 36.2 1.0
CA 4:TRP16 3.8 41.9 1.0
OH 4:TYR161 3.9 40.4 1.0
C 4:TRP16 4.0 42.2 1.0
CA 4:ASN18 4.0 34.1 1.0
N 4:TRP16 4.1 42.5 1.0
N 4:GLU17 4.2 40.6 1.0
CE2 4:TYR161 4.2 38.0 1.0
N 4:PRO19 4.3 33.7 1.0
CB 4:ASP193 4.3 34.6 1.0
CA 4:VAL21 4.4 31.0 1.0
O 4:TRP16 4.4 43.3 1.0
CB 4:VAL21 4.5 28.8 1.0
CG 4:GLN163 4.5 38.3 1.0
CB 4:ASN18 4.5 33.2 1.0
N 4:VAL21 4.5 32.7 1.0
CZ 4:TYR161 4.5 38.2 1.0
CA 4:PRO19 4.5 33.9 1.0
CA 4:ASP15 4.6 43.4 1.0
N 4:THR22 4.6 30.1 1.0
CA 4:THR22 4.7 32.3 1.0
C 4:GLU17 4.8 37.7 1.0
CG1 4:VAL21 4.8 28.7 1.0
CA 4:GLU17 5.0 38.4 1.0
CB 4:ASP15 5.0 42.8 1.0

Reference:

D.H.Juers, B.Rob, M.L.Dugdale, N.Rahimzadeh, C.Giang, M.Lee, B.W.Matthews, R.E.Huber. Direct and Indirect Roles of His-418 in Metal Binding and in the Activity of Beta-Galactosidase (E. Coli). Protein Sci. V. 18 1281 2009.
ISSN: ISSN 0961-8368
PubMed: 19472413
DOI: 10.1002/PRO.140
Page generated: Wed Aug 14 12:49:23 2024

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