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Molybdenum in PDB 4bvp: Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate

Protein crystallography data

The structure of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate, PDB code: 4bvp was solved by M.Zebisch, P.Schaefer, N.Straeter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.34 / 1.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.564, 85.436, 71.779, 90.00, 103.94, 90.00
R / Rfree (%) 12.608 / 16.858

Other elements in 4bvp:

The structure of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Molybdenum Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 46;

Binding sites:

The binding sites of Molybdenum atom in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate (pdb code 4bvp). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 46 binding sites of Molybdenum where determined in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate, PDB code: 4bvp:
Jump to Molybdenum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Molybdenum binding site 1 out of 46 in 4bvp

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Molybdenum binding site 1 out of 46 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo1403

b:8.8
occ:1.00
MO A:MOO1403 0.0 8.8 1.0
O1 A:MOO1403 1.7 8.1 1.0
O2 A:MOO1403 1.7 8.7 1.0
O4 A:MOO1403 1.8 8.3 1.0
O3 A:MOO1403 1.8 9.3 1.0
O A:HOH2062 2.6 8.6 1.0
MG A:MG1404 3.7 10.0 1.0
O A:HOH2092 3.8 9.8 1.0
OG1 A:THR118 3.8 8.6 1.0
O A:HOH2227 3.8 11.1 1.0
N A:GLY189 3.8 7.7 1.0
N A:SER52 3.9 8.7 1.0
OG A:SER52 3.9 9.9 1.0
N A:ALA190 4.0 8.3 1.0
O A:HOH2003 4.0 9.4 1.0
CA A:GLY188 4.2 7.2 1.0
CB A:SER52 4.2 10.8 1.0
N A:ALA119 4.3 7.4 1.0
CB A:ALA119 4.3 8.3 1.0
C A:GLY188 4.4 6.9 1.0
OE2 A:GLU159 4.5 8.8 1.0
N A:SER191 4.5 6.5 1.0
O A:HOH2101 4.6 10.0 1.0
O A:HOH2093 4.6 8.3 1.0
CA A:GLY51 4.6 8.1 1.0
OG A:SER191 4.7 7.7 1.0
CA A:GLY189 4.7 9.3 1.0
CB A:THR118 4.7 7.3 1.0
CA A:SER52 4.7 9.2 1.0
C A:GLY51 4.8 6.9 1.0
CA A:ALA119 4.8 8.2 1.0
O A:SER191 4.8 7.4 1.0
CB A:ALA190 4.8 10.4 1.0
CA A:ALA190 4.9 8.3 1.0
N A:GLY120 4.9 8.4 1.0
C A:GLY189 4.9 6.7 1.0

Molybdenum binding site 2 out of 46 in 4bvp

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Molybdenum binding site 2 out of 46 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo1408

b:11.2
occ:0.90
MO1 A:M271408 0.0 11.2 0.9
O6 A:M271408 1.7 11.9 0.9
O9 A:M271408 1.7 11.3 0.9
O2 A:M271408 1.9 11.0 0.9
OD1 A:ASP344 2.0 12.9 1.0
O1 A:EDO1409 2.1 13.9 1.0
OD1 A:ASP343 2.2 12.0 1.0
CG A:ASP344 3.1 12.5 1.0
MO2 A:M271408 3.1 14.4 0.9
CG A:ASP343 3.2 13.3 1.0
C1 A:EDO1409 3.3 16.8 1.0
OD2 A:ASP343 3.5 12.5 1.0
OD2 A:ASP344 3.5 17.6 1.0
O A:HOH2231 3.7 37.0 1.0
O4 A:M271408 3.8 17.8 0.9
CG A:GLN307 4.2 14.3 1.0
CD1 A:TYR341 4.3 9.1 1.0
CB A:TYR341 4.4 10.1 1.0
CB A:ASP344 4.4 8.9 1.0
O2 A:EDO1409 4.4 17.1 1.0
N A:ASP344 4.4 9.5 1.0
O8 A:M271408 4.5 15.5 0.9
C2 A:EDO1409 4.5 19.6 1.0
N A:GLN307 4.5 10.6 1.0
CA A:TYR341 4.5 9.8 1.0
CB A:ASP343 4.6 12.4 1.0
C A:ASP343 4.6 8.8 1.0
CB A:GLN307 4.6 12.4 1.0
CA A:ASP344 4.7 9.9 1.0
N A:ASP343 4.7 11.7 1.0
C A:TYR341 4.8 8.6 1.0
CG A:TYR341 4.8 9.6 1.0
CA A:ASP343 4.9 9.2 1.0
O A:TYR341 5.0 10.9 1.0

Molybdenum binding site 3 out of 46 in 4bvp

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Molybdenum binding site 3 out of 46 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 3 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo1408

b:14.4
occ:0.90
MO2 A:M271408 0.0 14.4 0.9
O4 A:M271408 1.7 17.8 0.9
O8 A:M271408 1.7 15.5 0.9
O2 A:EDO1409 2.0 17.1 1.0
O2 A:M271408 2.0 11.0 0.9
O1 A:EDO1409 2.1 13.9 1.0
OD2 A:ASP343 2.4 12.5 1.0
C2 A:EDO1409 3.0 19.6 1.0
C1 A:EDO1409 3.0 16.8 1.0
MO1 A:M271408 3.1 11.2 0.9
CG A:ASP343 3.3 13.3 1.0
OD1 A:ASP343 3.5 12.0 1.0
O6 A:M271408 3.9 11.9 0.9
O A:HOH2231 4.3 37.0 1.0
NE2 A:GLN307 4.4 22.7 1.0
CG A:GLN307 4.4 14.3 1.0
O9 A:M271408 4.4 11.3 0.9
OD1 A:ASP344 4.6 12.9 1.0
CB A:ASP343 4.7 12.4 1.0
CD A:GLN307 5.0 15.9 1.0

Molybdenum binding site 4 out of 46 in 4bvp

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Molybdenum binding site 4 out of 46 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 4 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo1410

b:15.9
occ:0.90
MO1 A:M271410 0.0 15.9 0.9
O7 A:M271410 1.7 18.7 0.9
O1 A:M271410 1.7 15.6 0.9
O2 A:M271410 2.0 15.5 0.9
O2 A:EDO1411 2.0 18.6 1.0
O1 A:EDO1411 2.2 17.4 1.0
OE1 A:GLN143 2.8 16.7 1.0
C2 A:EDO1411 2.9 19.5 1.0
C1 A:EDO1411 3.1 19.7 1.0
MO2 A:M271410 3.2 16.4 0.9
CD A:GLN143 3.9 15.4 1.0
N A:SER144 4.0 15.2 1.0
N A:GLN145 4.0 14.3 1.0
ND1 A:HIS109 4.1 18.4 1.0
O8 A:M271410 4.1 18.1 0.9
CB A:GLN145 4.1 17.2 0.5
CB A:GLN143 4.2 15.6 1.0
CG A:GLN145 4.2 18.4 0.5
CB A:GLN145 4.2 16.9 0.5
CD1 A:TRP146 4.3 12.9 1.0
CA A:GLN143 4.3 16.1 1.0
O3 A:M271410 4.4 16.9 0.9
O4 A:M271410 4.4 19.9 0.9
CG A:GLN145 4.4 15.8 0.5
OG A:SER144 4.5 21.8 1.0
C A:GLN143 4.5 14.6 1.0
CD A:GLN145 4.6 21.6 0.5
CA A:GLN145 4.6 12.9 0.5
CA A:GLN145 4.6 12.4 0.5
CG A:GLN143 4.7 17.1 1.0
NE1 A:TRP146 4.7 13.4 1.0
N A:TRP146 4.7 12.7 1.0
NE2 A:GLN143 4.8 20.4 1.0
CB A:HIS109 4.8 15.0 1.0
NE2 A:GLN145 4.8 31.1 0.5
CG A:HIS109 4.9 14.2 1.0
CA A:SER144 5.0 19.6 1.0
CE1 A:HIS109 5.0 16.8 1.0
C A:SER144 5.0 16.2 1.0

Molybdenum binding site 5 out of 46 in 4bvp

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Molybdenum binding site 5 out of 46 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 5 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo1410

b:16.4
occ:0.90
MO2 A:M271410 0.0 16.4 0.9
O3 A:M271410 1.7 16.9 0.9
O4 A:M271410 1.7 19.9 0.9
O8 A:M271410 1.8 18.1 0.9
O2 A:M271410 2.1 15.5 0.9
O1 A:EDO1411 2.2 17.4 1.0
OE1 A:GLN143 2.3 16.7 1.0
MO1 A:M271410 3.2 15.9 0.9
CD A:GLN143 3.2 15.4 1.0
C1 A:EDO1411 3.4 19.7 1.0
NE2 A:GLN143 3.5 20.4 1.0
ND1 A:HIS109 3.9 18.4 1.0
NE1 A:TRP146 4.0 13.4 1.0
CE1 A:HIS109 4.0 16.8 1.0
CA A:ALA104 4.3 14.9 1.0
CD1 A:TRP146 4.3 12.9 1.0
O1 A:M271410 4.3 15.6 0.9
O7 A:M271410 4.4 18.7 0.9
O2 A:EDO1411 4.4 18.6 1.0
CB A:ALA104 4.4 17.3 1.0
C2 A:EDO1411 4.5 19.5 1.0
CG A:GLN143 4.6 17.1 1.0
CH2 A:TRP139 4.6 17.4 1.0
CZ2 A:TRP139 4.8 17.1 1.0

Molybdenum binding site 6 out of 46 in 4bvp

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Molybdenum binding site 6 out of 46 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 6 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo1412

b:14.3
occ:0.70
MO3 A:6LL1412 0.0 14.3 0.7
O12 A:6LL1412 1.7 15.0 0.7
O11 A:6LL1412 1.8 16.4 0.7
O3 A:6LL1412 1.9 15.5 0.7
O1 A:EDO1414 2.0 20.0 1.0
OD2 A:ASP158 2.2 18.9 1.0
O2 A:EDO1414 2.3 20.9 1.0
C1 A:EDO1414 3.1 25.3 1.0
C2 A:EDO1414 3.2 26.4 1.0
CG A:ASP158 3.3 17.5 1.0
MO2 A:6LL1412 3.7 14.5 0.7
OD1 A:ASP158 3.7 14.8 1.0
NZ A:LYS152 3.8 35.0 1.0
O2 A:6LL1412 3.8 17.2 0.7
CE A:LYS152 4.1 28.5 1.0
O4 A:6LL1412 4.4 12.4 0.7
N A:THR155 4.4 8.5 1.0
CB A:ASP158 4.5 11.7 1.0
CG2 A:THR155 4.5 11.5 1.0
O A:HOH2086 4.6 29.6 1.0
O8 A:6LL1412 4.6 17.4 0.7
OG1 A:THR155 4.6 10.9 1.0
CA A:ILE154 4.7 8.0 1.0
CB A:ILE154 4.8 9.4 1.0
CG2 A:ILE154 4.9 11.1 1.0

Molybdenum binding site 7 out of 46 in 4bvp

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Molybdenum binding site 7 out of 46 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 7 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo1412

b:14.5
occ:0.70
MO2 A:6LL1412 0.0 14.5 0.7
O8 A:6LL1412 1.7 17.4 0.7
O4 A:6LL1412 1.8 12.4 0.7
O3 A:6LL1412 2.0 15.5 0.7
O2 A:6LL1412 2.1 17.2 0.7
O2 A:GOL1413 2.1 20.5 1.0
OD1 A:ASP158 2.3 14.8 1.0
MO1 A:6LL1412 3.2 17.4 0.7
C2 A:GOL1413 3.2 21.2 1.0
CG A:ASP158 3.2 17.5 1.0
OD2 A:ASP158 3.5 18.9 1.0
MO3 A:6LL1412 3.7 14.3 0.7
O2 A:EDO1414 3.7 20.9 1.0
O3 A:GOL1413 3.9 22.1 1.0
O A:HOH2232 4.0 35.4 1.0
OG1 A:THR155 4.0 10.9 1.0
C3 A:GOL1413 4.1 20.6 1.0
O1 A:GOL1413 4.2 20.7 1.0
O1 A:6LL1412 4.3 18.6 0.7
O7 A:6LL1412 4.3 21.5 0.7
C1 A:GOL1413 4.4 22.9 1.0
O11 A:6LL1412 4.4 16.4 0.7
O12 A:6LL1412 4.5 15.0 0.7
CB A:ASP158 4.6 11.7 1.0
O A:HOH2090 4.6 21.5 1.0
CG2 A:THR155 4.8 11.5 1.0
C2 A:EDO1414 4.9 26.4 1.0
N A:ASP158 4.9 9.2 1.0
CA A:ASP158 5.0 9.3 1.0

Molybdenum binding site 8 out of 46 in 4bvp

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Molybdenum binding site 8 out of 46 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 8 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo1412

b:17.4
occ:0.70
MO1 A:6LL1412 0.0 17.4 0.7
O7 A:6LL1412 1.7 21.5 0.7
O1 A:6LL1412 1.7 18.6 0.7
O1 A:GOL1413 1.9 20.7 1.0
O2 A:6LL1412 2.1 17.2 0.7
O2 A:GOL1413 2.2 20.5 1.0
OD1 A:ASP158 2.5 14.8 1.0
C1 A:GOL1413 3.0 22.9 1.0
C2 A:GOL1413 3.1 21.2 1.0
MO2 A:6LL1412 3.2 14.5 0.7
CG A:ASP158 3.5 17.5 1.0
O2 A:EDO1414 3.9 20.9 1.0
CA A:ASP158 4.1 9.3 1.0
CD2 A:LEU161 4.1 13.9 1.0
CB A:ASP158 4.2 11.7 1.0
O8 A:6LL1412 4.2 17.4 0.7
C2 A:EDO1414 4.4 26.4 1.0
C3 A:GOL1413 4.4 20.6 1.0
O4 A:6LL1412 4.4 12.4 0.7
OD2 A:ASP158 4.4 18.9 1.0
CE1 A:HIS391 4.4 23.2 1.0
NE2 A:HIS391 4.5 21.6 1.0
O3 A:6LL1412 4.5 15.5 0.7
O A:HOH2221 4.6 40.4 1.0
N A:ASP158 4.9 9.2 1.0

Molybdenum binding site 9 out of 46 in 4bvp

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Molybdenum binding site 9 out of 46 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 9 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo1415

b:16.1
occ:0.90
MO7 A:XBO1415 0.0 16.1 0.9
O24 A:XBO1415 1.7 16.2 0.9
O23 A:XBO1415 1.7 15.8 0.9
O20 A:XBO1415 1.9 14.1 0.9
O19 A:XBO1415 2.0 15.9 0.9
O5 A:XBO1415 2.2 16.7 0.9
O17 A:XBO1415 2.2 14.2 0.9
MO5 A:XBO1415 3.2 18.2 0.9
MO6 A:XBO1415 3.3 16.7 0.9
MO1 A:XBO1415 3.4 16.0 0.9
O22 A:XBO1415 3.6 17.9 0.9
O16 A:XBO1415 3.7 22.2 0.9
O1 A:XBO1415 3.8 17.4 0.9
O2 A:XBO1415 3.9 18.1 0.9
O A:HOH2206 4.0 18.7 1.0
NZ A:LYS82 4.0 20.3 1.0
MO4 A:XBO1415 4.2 23.0 0.9
CE A:LYS82 4.2 19.0 1.0
O3 A:XBO1415 4.4 20.1 0.9
O9 A:XBO1415 4.4 19.3 0.9
O13 A:XBO1415 4.4 25.1 0.9
O12 A:XBO1415 4.4 20.5 0.9
O21 A:XBO1415 4.6 18.6 0.9
O7 B:WSQ1403 4.6 14.9 0.9
O15 A:XBO1415 4.7 21.2 0.9
O18 A:XBO1415 4.7 16.9 0.9
O4 A:XBO1415 4.8 18.5 0.9

Molybdenum binding site 10 out of 46 in 4bvp

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Molybdenum binding site 10 out of 46 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 10 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with Heptamolybdate and Octamolybdate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo1415

b:16.0
occ:0.90
MO1 A:XBO1415 0.0 16.0 0.9
O4 A:XBO1415 1.8 18.5 0.9
O1 A:XBO1415 1.8 17.4 0.9
O3 A:XBO1415 1.9 20.1 0.9
O17 A:XBO1415 1.9 14.2 0.9
O5 A:XBO1415 2.2 16.7 0.9
O2 A:XBO1415 2.3 18.1 0.9
MO7 A:XBO1415 3.4 16.1 0.9
MO6 A:XBO1415 3.4 16.7 0.9
MO2 A:XBO1415 3.4 19.6 0.9
MO4 A:XBO1415 3.4 23.0 0.9
MO3 A:XBO1415 3.4 20.4 0.9
MO5 A:XBO1415 3.4 18.2 0.9
O7 A:XBO1415 3.4 18.1 0.9
O18 A:XBO1415 3.4 16.9 0.9
O19 A:XBO1415 3.5 15.9 0.9
O12 A:XBO1415 3.5 20.5 0.9
O9 A:XBO1415 3.6 19.3 0.9
O20 A:XBO1415 3.6 14.1 0.9
O8 A:XBO1415 4.3 23.3 0.9
O15 A:XBO1415 4.4 21.2 0.9
O11 A:XBO1415 4.4 26.2 0.9
O23 A:XBO1415 4.5 15.8 0.9
O22 A:XBO1415 4.5 17.9 0.9
O14 A:XBO1415 4.5 26.8 0.9
O A:HOH2206 4.5 18.7 1.0
O24 A:XBO1415 4.7 16.2 0.9
O10 A:XBO1415 4.8 22.2 0.9
O21 A:XBO1415 4.8 18.6 0.9
O13 A:XBO1415 4.8 25.1 0.9
O16 A:XBO1415 4.9 22.2 0.9
O6 A:XBO1415 4.9 23.1 0.9
OE1 A:GLU345 4.9 20.3 1.0

Reference:

M.Zebisch, M.Krauss, P.Schafer, N.Strater. Structures of Legionella Pneumophila NTPDASE1 in Complex with Polyoxometallates. Acta Crystallogr.,Sect.D V. 70 1147 2014.
ISSN: ISSN 0907-4449
PubMed: 24699658
DOI: 10.1107/S1399004714001916
Page generated: Tue Dec 15 05:18:48 2020

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