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Magnesium in PDB 1a49: Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase

Enzymatic activity of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase

All present enzymatic activity of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase:
2.7.1.40;

Protein crystallography data

The structure of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase, PDB code: 1a49 was solved by T.M.Larsen, M.M.Benning, I.Rayment, G.H.Reed, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.300, 216.500, 258.600, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1a49:

The structure of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase also contains other interesting chemical elements:

Potassium (K) 8 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase (pdb code 1a49). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase, PDB code: 1a49:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 1a49

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Magnesium binding site 1 out of 14 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg534

b:24.7
occ:1.00
O A:HOH6763 1.9 36.5 1.0
O4 A:OXL533 2.0 35.6 1.0
O1 A:OXL533 2.1 32.9 1.0
OD2 A:ASP295 2.1 35.5 1.0
OE1 A:GLU271 2.2 21.6 1.0
O2G A:ATP535 2.4 33.7 1.0
C2 A:OXL533 2.8 34.1 1.0
C1 A:OXL533 2.8 53.4 1.0
CG A:ASP295 3.0 60.7 1.0
CB A:ASP295 3.4 27.6 1.0
CD A:GLU271 3.4 44.2 1.0
PG A:ATP535 3.5 39.5 1.0
O A:HOH6003 3.7 11.5 1.0
O3G A:ATP535 3.8 21.0 1.0
O A:HOH6469 4.0 22.5 1.0
O2 A:OXL533 4.0 53.6 1.0
O3 A:OXL533 4.0 73.9 1.0
OE2 A:GLU271 4.1 30.1 1.0
O1G A:ATP535 4.1 27.7 1.0
NZ A:LYS269 4.2 32.2 1.0
N A:ASP295 4.2 22.6 1.0
OD1 A:ASP295 4.3 35.2 1.0
CA A:ASP295 4.4 36.5 1.0
CZ A:PHE243 4.6 45.8 1.0
CG A:GLU271 4.7 27.8 1.0
CB A:GLU271 4.7 30.5 1.0
CB A:ALA292 4.7 31.7 1.0
CE2 A:PHE243 4.7 36.8 1.0
O3B A:ATP535 4.7 20.5 1.0
CE A:LYS269 4.9 18.4 1.0
MG A:MG536 5.0 24.1 1.0
OD1 A:ASP177 5.0 29.8 1.0

Magnesium binding site 2 out of 14 in 1a49

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Magnesium binding site 2 out of 14 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg536

b:24.1
occ:1.00
O A:HOH6079 1.9 19.5 1.0
O1G A:ATP535 2.0 27.7 1.0
O1A A:ATP535 2.0 27.9 1.0
O A:HOH6469 2.2 22.5 1.0
O2B A:ATP535 2.3 28.4 1.0
PB A:ATP535 2.8 31.9 1.0
PG A:ATP535 2.9 39.5 1.0
O3B A:ATP535 3.1 20.5 1.0
PA A:ATP535 3.1 36.8 1.0
O2G A:ATP535 3.1 33.7 1.0
O3A A:ATP535 3.3 37.3 1.0
O2A A:ATP535 4.0 19.9 1.0
O A:HOH6612 4.0 35.3 1.0
C1 A:OXL533 4.2 53.4 1.0
O1B A:ATP535 4.2 32.0 1.0
O3G A:ATP535 4.2 21.0 1.0
O3 A:OXL533 4.2 73.9 1.0
OD2 A:ASP177 4.2 29.8 1.0
O5' A:ATP535 4.3 30.6 1.0
C2 A:OXL533 4.3 34.1 1.0
O A:HOH6366 4.3 38.5 1.0
C5' A:ATP535 4.4 41.6 1.0
O2 A:OXL533 4.4 53.6 1.0
OG A:SER361 4.4 21.9 1.0
NH2 A:ARG72 4.5 30.2 1.0
OG1 A:THR327 4.5 25.2 1.0
CB A:SER361 4.6 33.6 1.0
O1 A:OXL533 4.6 32.9 1.0
NH1 A:ARG72 4.7 43.8 1.0
O4 A:OXL533 4.8 35.6 1.0
O A:HOH6003 4.9 11.5 1.0
ND2 A:ASN74 4.9 26.0 1.0
MG A:MG534 5.0 24.7 1.0

Magnesium binding site 3 out of 14 in 1a49

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Magnesium binding site 3 out of 14 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1134

b:33.0
occ:1.00
O B:HOH7031 2.1 32.1 1.0
OD2 B:ASP895 2.1 24.9 1.0
OE1 B:GLU871 2.2 58.6 1.0
O1 B:OXL1133 2.3 39.2 1.0
O4 B:OXL1133 2.3 37.3 1.0
C1 B:OXL1133 3.1 29.3 1.0
C2 B:OXL1133 3.1 51.6 1.0
CG B:ASP895 3.2 89.9 1.0
CD B:GLU871 3.3 19.3 1.0
OE2 B:GLU871 3.7 28.8 1.0
O B:HOH6624 4.0 52.4 1.0
CB B:ASP895 4.0 25.8 1.0
O B:HOH6141 4.0 32.1 1.0
O B:HOH6426 4.1 45.3 1.0
NZ B:LYS869 4.2 15.6 1.0
O3 B:OXL1133 4.3 44.4 1.0
O2 B:OXL1133 4.3 24.3 1.0
OD1 B:ASP895 4.3 44.8 1.0
CE B:LYS869 4.6 20.1 1.0
CG B:GLU871 4.6 28.9 1.0
O B:HOH6868 4.7 42.6 1.0
N B:ASP895 4.8 21.5 1.0
CB B:ALA892 4.9 38.7 1.0

Magnesium binding site 4 out of 14 in 1a49

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Magnesium binding site 4 out of 14 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1734

b:31.0
occ:1.00
O1 C:OXL1733 2.1 50.0 1.0
OE1 C:GLU1471 2.1 34.1 1.0
O4 C:OXL1733 2.1 37.8 1.0
OD2 C:ASP1495 2.2 43.9 1.0
O2G C:ATP1735 2.4 27.0 1.0
C1 C:OXL1733 2.9 34.5 1.0
C2 C:OXL1733 2.9 29.4 1.0
CD C:GLU1471 3.0 23.9 1.0
OE2 C:GLU1471 3.3 44.7 1.0
O3G C:ATP1735 3.4 17.0 1.0
CG C:ASP1495 3.4 16.9 1.0
PG C:ATP1735 3.4 46.4 1.0
NZ C:LYS1469 3.6 36.5 1.0
O1G C:ATP1735 4.0 29.4 1.0
CB C:ASP1495 4.1 22.0 1.0
O3 C:OXL1733 4.1 43.8 1.0
CE1 C:PHE1443 4.2 25.1 1.0
O C:HOH7921 4.2 47.1 1.0
O2 C:OXL1733 4.2 37.8 1.0
CE C:LYS1469 4.3 32.0 1.0
O C:HOH6005 4.4 12.7 1.0
CG C:GLU1471 4.4 26.8 1.0
OD1 C:ASP1495 4.5 34.6 1.0
CB C:ALA1492 4.6 30.5 1.0
CZ C:PHE1443 4.7 32.6 1.0
O3B C:ATP1735 4.8 35.0 1.0
O C:HOH6006 4.8 25.4 1.0
CB C:GLU1471 4.8 20.1 1.0
CB C:SER1442 4.9 22.3 1.0
K C:K1732 4.9 43.0 1.0
CD1 C:PHE1443 4.9 40.0 1.0
N C:ASP1495 5.0 33.2 1.0

Magnesium binding site 5 out of 14 in 1a49

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Magnesium binding site 5 out of 14 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1736

b:31.8
occ:1.00
O1A C:ATP1735 1.9 19.6 1.0
O C:HOH6006 2.0 25.4 1.0
O C:HOH6663 2.0 24.2 1.0
O C:HOH6581 2.1 25.8 1.0
O1G C:ATP1735 2.1 29.4 1.0
O2B C:ATP1735 2.2 37.2 1.0
PB C:ATP1735 3.1 43.3 1.0
PA C:ATP1735 3.1 35.4 1.0
PG C:ATP1735 3.2 46.4 1.0
O3A C:ATP1735 3.3 42.2 1.0
O3B C:ATP1735 3.4 35.0 1.0
O2G C:ATP1735 3.6 27.0 1.0
OG C:SER1561 4.1 37.5 1.0
O2A C:ATP1735 4.1 21.6 1.0
O C:HOH6754 4.1 38.0 1.0
O C:HOH6879 4.1 59.5 1.0
CB C:SER1561 4.2 29.3 1.0
C1 C:OXL1733 4.2 34.5 1.0
O5' C:ATP1735 4.2 25.4 1.0
O3 C:OXL1733 4.3 43.8 1.0
OD2 C:ASP1377 4.3 41.6 1.0
O3G C:ATP1735 4.3 17.0 1.0
O C:HOH7436 4.4 36.0 1.0
C5' C:ATP1735 4.4 33.5 1.0
OG1 C:THR1527 4.4 27.2 1.0
NH1 C:ARG1272 4.4 41.7 1.0
O1B C:ATP1735 4.4 45.1 1.0
C2 C:OXL1733 4.5 29.4 1.0
CG2 C:THR1527 4.5 31.7 1.0
O1 C:OXL1733 4.6 50.0 1.0
O2 C:OXL1733 4.7 37.8 1.0
NH2 C:ARG1272 4.8 56.1 1.0
O4 C:OXL1733 4.9 37.8 1.0

Magnesium binding site 6 out of 14 in 1a49

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Magnesium binding site 6 out of 14 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2334

b:19.4
occ:1.00
O D:HOH6439 2.0 21.3 1.0
O1 D:OXL2333 2.1 22.1 1.0
OD2 D:ASP2095 2.1 10.7 1.0
O4 D:OXL2333 2.1 25.2 1.0
OE1 D:GLU2071 2.2 25.4 1.0
O2G D:ATP2335 2.3 15.4 1.0
C2 D:OXL2333 2.9 18.2 1.0
C1 D:OXL2333 2.9 41.2 1.0
CG D:ASP2095 3.2 33.7 1.0
PG D:ATP2335 3.3 26.7 1.0
CD D:GLU2071 3.3 57.0 1.0
O3G D:ATP2335 3.4 31.2 1.0
O1G D:ATP2335 3.8 17.4 1.0
CB D:ASP2095 3.8 29.7 1.0
OE2 D:GLU2071 3.8 34.0 1.0
NZ D:LYS2069 3.8 23.0 1.0
O D:HOH6045 3.9 11.8 1.0
O D:HOH6004 4.0 5.6 1.0
O2 D:OXL2333 4.1 23.7 1.0
O3 D:OXL2333 4.1 23.3 1.0
CE D:LYS2069 4.3 28.2 1.0
OD1 D:ASP2095 4.3 12.5 1.0
N D:ASP2095 4.5 29.5 1.0
CB D:ALA2092 4.6 17.1 1.0
CE1 D:PHE2043 4.6 33.4 1.0
O D:HOH7499 4.6 26.4 1.0
O3B D:ATP2335 4.6 26.7 1.0
CG D:GLU2071 4.7 28.8 1.0
CA D:ASP2095 4.8 28.7 1.0

Magnesium binding site 7 out of 14 in 1a49

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Magnesium binding site 7 out of 14 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2336

b:20.5
occ:1.00
O D:HOH6045 1.9 11.8 1.0
O D:HOH6387 2.0 20.0 1.0
O D:HOH7364 2.0 30.9 1.0
O2B D:ATP2335 2.0 28.9 1.0
O1A D:ATP2335 2.1 22.7 1.0
O1G D:ATP2335 2.2 17.4 1.0
PB D:ATP2335 3.0 31.0 1.0
PG D:ATP2335 3.0 26.7 1.0
PA D:ATP2335 3.1 25.7 1.0
O3B D:ATP2335 3.2 26.7 1.0
O3A D:ATP2335 3.3 13.4 1.0
O2G D:ATP2335 3.4 15.4 1.0
OD2 D:ASP1977 4.0 22.1 1.0
O2A D:ATP2335 4.1 17.4 1.0
O3G D:ATP2335 4.2 31.2 1.0
C1 D:OXL2333 4.2 41.2 1.0
OG D:SER2161 4.3 27.2 1.0
O1B D:ATP2335 4.3 13.2 1.0
O5' D:ATP2335 4.3 19.4 1.0
C2 D:OXL2333 4.3 18.2 1.0
C5' D:ATP2335 4.4 37.3 1.0
NH2 D:ARG1872 4.4 25.4 1.0
CB D:SER2161 4.5 20.2 1.0
O D:HOH6140 4.5 24.0 1.0
OG1 D:THR2127 4.5 17.1 1.0
O3 D:OXL2333 4.5 23.3 1.0
O1 D:OXL2333 4.5 22.1 1.0
O4 D:OXL2333 4.6 25.2 1.0
O D:HOH6621 4.6 39.5 1.0
O2 D:OXL2333 4.7 23.7 1.0
CG2 D:THR2127 4.7 14.3 1.0
O D:HOH6087 4.8 19.1 1.0
O D:HOH6004 4.8 5.6 1.0
NH1 D:ARG1872 4.9 38.5 1.0

Magnesium binding site 8 out of 14 in 1a49

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Magnesium binding site 8 out of 14 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg3534

b:18.2
occ:1.00
OD2 E:ASP3295 2.0 18.5 1.0
O1 E:OXL3533 2.1 35.9 1.0
O4 E:OXL3533 2.1 31.4 1.0
O E:HOH6988 2.1 27.4 1.0
OE1 E:GLU3271 2.2 27.2 1.0
O2G E:ATP3535 2.3 11.1 1.0
C2 E:OXL3533 2.8 26.0 1.0
C1 E:OXL3533 2.8 35.0 1.0
CG E:ASP3295 3.1 68.6 1.0
CD E:GLU3271 3.1 14.2 1.0
PG E:ATP3535 3.3 28.7 1.0
O3G E:ATP3535 3.5 23.0 1.0
OE2 E:GLU3271 3.5 47.1 1.0
CB E:ASP3295 3.7 32.8 1.0
O1G E:ATP3535 3.8 17.0 1.0
O E:HOH6348 3.8 31.4 1.0
O E:HOH6159 3.9 2.9 1.0
O2 E:OXL3533 4.0 24.8 1.0
O3 E:OXL3533 4.0 28.5 1.0
NZ E:LYS3269 4.2 11.1 1.0
OD1 E:ASP3295 4.2 31.8 1.0
N E:ASP3295 4.4 22.1 1.0
CE2 E:PHE3243 4.5 29.7 1.0
CE E:LYS3269 4.5 27.6 1.0
CG E:GLU3271 4.5 22.7 1.0
CZ E:PHE3243 4.6 34.2 1.0
CA E:ASP3295 4.6 17.4 1.0
CB E:ALA3292 4.7 23.7 1.0
O3B E:ATP3535 4.7 35.1 1.0
CB E:GLU3271 4.9 26.2 1.0
O E:HOH7785 5.0 34.9 1.0

Magnesium binding site 9 out of 14 in 1a49

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Magnesium binding site 9 out of 14 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg3536

b:25.1
occ:1.00
O1A E:ATP3535 2.0 18.5 1.0
O E:HOH6348 2.0 31.4 1.0
O E:HOH7443 2.0 26.6 1.0
O1G E:ATP3535 2.1 17.0 1.0
O2B E:ATP3535 2.2 21.1 1.0
O E:HOH6162 2.2 14.4 1.0
PG E:ATP3535 3.1 28.7 1.0
PB E:ATP3535 3.1 19.9 1.0
PA E:ATP3535 3.1 30.0 1.0
O3B E:ATP3535 3.3 35.1 1.0
O3A E:ATP3535 3.4 22.2 1.0
O2G E:ATP3535 3.5 11.1 1.0
OG E:SER3361 4.0 28.6 1.0
C1 E:OXL3533 4.0 35.0 1.0
OD2 E:ASP3177 4.1 24.2 1.0
O2A E:ATP3535 4.1 21.1 1.0
O E:HOH6317 4.1 23.4 1.0
O3 E:OXL3533 4.1 28.5 1.0
O E:HOH7793 4.2 49.7 1.0
O3G E:ATP3535 4.3 23.0 1.0
CB E:SER3361 4.3 29.3 1.0
O5' E:ATP3535 4.3 21.2 1.0
O1 E:OXL3533 4.3 35.9 1.0
C2 E:OXL3533 4.4 26.0 1.0
C5' E:ATP3535 4.4 7.5 1.0
O1B E:ATP3535 4.4 20.9 1.0
OG1 E:THR3327 4.5 30.1 1.0
NH2 E:ARG3072 4.6 25.5 1.0
CG2 E:THR3327 4.6 31.1 1.0
O2 E:OXL3533 4.7 24.8 1.0
O E:HOH6277 4.7 25.6 1.0
NH1 E:ARG3072 4.8 13.3 1.0
O4 E:OXL3533 4.8 31.4 1.0
O E:HOH6159 4.9 2.9 1.0

Magnesium binding site 10 out of 14 in 1a49

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Magnesium binding site 10 out of 14 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg4134

b:23.7
occ:1.00
OE1 F:GLU3871 2.1 38.3 1.0
O2G F:ATP4135 2.1 20.6 1.0
OD2 F:ASP3895 2.1 45.8 1.0
O1 F:OXL4133 2.1 39.8 1.0
O4 F:OXL4133 2.2 36.1 1.0
O F:HOH6460 2.2 24.1 1.0
C2 F:OXL4133 2.9 58.4 1.0
C1 F:OXL4133 2.9 52.2 1.0
CD F:GLU3871 3.0 17.7 1.0
CG F:ASP3895 3.1 19.3 1.0
PG F:ATP4135 3.3 58.4 1.0
OE2 F:GLU3871 3.4 31.9 1.0
O F:HOH6178 3.6 27.7 1.0
O3G F:ATP4135 3.6 27.2 1.0
CB F:ASP3895 3.8 33.5 1.0
O1G F:ATP4135 3.8 45.3 1.0
NZ F:LYS3869 3.8 32.9 1.0
O F:HOH7054 3.9 23.6 1.0
O2 F:OXL4133 4.1 41.0 1.0
CE F:LYS3869 4.1 20.1 1.0
O3 F:OXL4133 4.1 27.5 1.0
OD1 F:ASP3895 4.2 51.9 1.0
O F:HOH6491 4.3 34.2 1.0
CZ F:PHE3843 4.3 35.2 1.0
CG F:GLU3871 4.4 34.2 1.0
N F:ASP3895 4.5 32.4 1.0
CE2 F:PHE3843 4.6 15.0 1.0
CB F:ALA3892 4.6 32.4 1.0
O3B F:ATP4135 4.7 44.2 1.0
CB F:GLU3871 4.7 22.0 1.0
CA F:ASP3895 4.8 28.5 1.0

Reference:

T.M.Larsen, M.M.Benning, I.Rayment, G.H.Reed. Structure of the Bis(MG2+)-Atp-Oxalate Complex of the Rabbit Muscle Pyruvate Kinase at 2.1 A Resolution: Atp Binding Over A Barrel. Biochemistry V. 37 6247 1998.
ISSN: ISSN 0006-2960
PubMed: 9572839
DOI: 10.1021/BI980243S
Page generated: Mon Dec 14 03:26:38 2020

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