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Zinc in PDB 6cty: Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution

Enzymatic activity of Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution

All present enzymatic activity of Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution:
3.5.2.3;

Protein crystallography data

The structure of Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution, PDB code: 6cty was solved by J.Lipowska, I.G.Shabalin, J.Winsor, M.Woinska, D.R.Cooper, K.Kwon, L.Shuvalova, W.F.Anderson, W.Minor, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.838, 112.202, 208.264, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.8

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution (pdb code 6cty). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution, PDB code: 6cty:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 6cty

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Zinc binding site 1 out of 12 in the Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:45.8
occ:1.00
 O4 A:MLT403 2.0 48.5 1.0
OQ2 A:KCX103 2.0 40.6 1.0
ND1 A:HIS140 2.2 38.0 1.0
NE2 A:HIS178 2.2 29.1 1.0
C4 A:MLT403 2.8 39.3 1.0
O5 A:MLT403 2.9 45.7 1.0
CX A:KCX103 3.0 34.8 1.0
CE1 A:HIS178 3.1 29.9 1.0
CE1 A:HIS140 3.1 40.5 1.0
OQ1 A:KCX103 3.2 36.6 1.0
CG A:HIS140 3.3 35.6 1.0
CD2 A:HIS178 3.3 30.7 1.0
ZN A:ZN402 3.4 46.9 1.0
CB A:HIS140 3.7 34.5 1.0
NE2 A:HIS140 4.2 40.6 1.0
NZ A:KCX103 4.2 37.2 1.0
ND1 A:HIS178 4.2 29.3 1.0
CE1 A:HIS17 4.3 35.9 1.0
C3 A:MLT403 4.3 40.5 1.0
CD2 A:HIS140 4.3 38.6 1.0
NE2 A:HIS17 4.4 32.6 1.0
CG A:HIS178 4.4 31.0 1.0
O A:LEU223 4.4 52.5 1.0
CE1 A:TYR105 4.5 37.1 1.0
CA A:HIS140 4.5 31.4 1.0
OD1 A:ASP251 4.5 37.6 1.0
CE A:KCX103 4.8 33.0 1.0
CG2 A:THR110 4.8 50.8 1.0
OD2 A:ASP251 4.9 33.6 1.0
CG A:ASP251 5.0 33.0 1.0

Zinc binding site 2 out of 12 in 6cty

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Zinc binding site 2 out of 12 in the Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:46.9
occ:1.00
 OD1 A:ASP251 2.0 37.6 1.0
O4 A:MLT403 2.0 48.5 1.0
OQ1 A:KCX103 2.0 36.6 1.0
NE2 A:HIS19 2.2 32.0 1.0
NE2 A:HIS17 2.2 32.6 1.0
C4 A:MLT403 3.0 39.3 1.0
CX A:KCX103 3.1 34.8 1.0
CE1 A:HIS19 3.1 34.2 1.0
CG A:ASP251 3.1 33.0 1.0
CD2 A:HIS19 3.1 33.1 1.0
CD2 A:HIS17 3.1 32.0 1.0
CE1 A:HIS17 3.2 35.9 1.0
C3 A:MLT403 3.3 40.5 1.0
OQ2 A:KCX103 3.4 40.6 1.0
ZN A:ZN401 3.4 45.8 1.0
OD2 A:ASP251 3.8 33.6 1.0
O5 A:MLT403 4.1 45.7 1.0
CD2 A:HIS178 4.2 30.7 1.0
CB A:ASP251 4.2 32.5 1.0
NE2 A:HIS178 4.2 29.1 1.0
ND1 A:HIS19 4.2 38.2 1.0
NZ A:KCX103 4.2 37.2 1.0
CG A:HIS19 4.3 33.4 1.0
ND1 A:HIS17 4.3 39.7 1.0
CG A:MET43 4.3 32.8 1.0
CG A:HIS17 4.3 34.7 1.0
CA A:ASP251 4.6 31.2 1.0
C2 A:MLT403 4.8 43.3 1.0
OH A:TYR105 4.8 36.4 1.0

Zinc binding site 3 out of 12 in 6cty

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Zinc binding site 3 out of 12 in the Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:72.0
occ:1.00
 O5 B:MLT403 2.0 0.7 1.0
OQ1 B:KCX103 2.0 68.3 1.0
ND1 B:HIS140 2.2 47.0 1.0
NE2 B:HIS178 2.2 44.8 1.0
C4 B:MLT403 2.8 75.9 1.0
O4 B:MLT403 2.9 88.0 1.0
CX B:KCX103 3.0 57.3 1.0
CE1 B:HIS140 3.0 46.7 1.0
CE1 B:HIS178 3.1 35.5 1.0
OQ2 B:KCX103 3.2 62.9 1.0
CG B:HIS140 3.3 40.7 1.0
CD2 B:HIS178 3.3 34.2 1.0
ZN B:ZN402 3.4 56.0 1.0
CB B:HIS140 3.7 36.9 1.0
NE2 B:HIS140 4.2 50.3 1.0
NZ B:KCX103 4.2 59.2 1.0
ND1 B:HIS178 4.3 36.6 1.0
C3 B:MLT403 4.3 66.5 1.0
CE1 B:HIS17 4.3 43.0 1.0
CD2 B:HIS140 4.3 46.2 1.0
CG B:HIS178 4.4 30.9 1.0
CE1 B:TYR105 4.4 46.0 1.0
O B:LEU223 4.4 49.0 1.0
NE2 B:HIS17 4.4 44.0 1.0
CA B:HIS140 4.5 36.2 1.0
OD1 B:ASP251 4.6 42.1 1.0
CG2 B:THR110 4.8 0.8 1.0
CE B:KCX103 4.8 57.7 1.0
OD2 B:ASP251 4.9 36.2 1.0
CD1 B:TYR105 5.0 44.7 1.0

Zinc binding site 4 out of 12 in 6cty

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Zinc binding site 4 out of 12 in the Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:56.0
occ:1.00
 OD1 B:ASP251 2.0 42.1 1.0
O5 B:MLT403 2.0 0.7 1.0
OQ2 B:KCX103 2.0 62.9 1.0
NE2 B:HIS19 2.2 39.1 1.0
NE2 B:HIS17 2.2 44.0 1.0
C4 B:MLT403 3.0 75.9 1.0
CG B:ASP251 3.1 32.5 1.0
CE1 B:HIS19 3.1 38.1 1.0
CX B:KCX103 3.2 57.3 1.0
CD2 B:HIS19 3.2 37.9 1.0
CE1 B:HIS17 3.2 43.0 1.0
CD2 B:HIS17 3.2 45.6 1.0
C3 B:MLT403 3.3 66.5 1.0
ZN B:ZN401 3.4 72.0 1.0
OQ1 B:KCX103 3.5 68.3 1.0
OD2 B:ASP251 3.8 36.2 1.0
CD2 B:HIS178 4.1 34.2 1.0
O4 B:MLT403 4.1 88.0 1.0
NE2 B:HIS178 4.2 44.8 1.0
CB B:ASP251 4.2 32.4 1.0
ND1 B:HIS19 4.3 37.7 1.0
CG B:HIS19 4.3 35.3 1.0
ND1 B:HIS17 4.3 49.8 1.0
NZ B:KCX103 4.3 59.2 1.0
CG B:MET43 4.3 39.3 1.0
CG B:HIS17 4.3 43.8 1.0
CA B:ASP251 4.7 33.9 1.0
OH B:TYR105 4.8 41.2 1.0
C2 B:MLT403 4.8 64.7 1.0

Zinc binding site 5 out of 12 in 6cty

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Zinc binding site 5 out of 12 in the Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:49.5
occ:1.00
 OQ1 C:KCX103 2.0 43.8 1.0
O5 C:MLT403 2.0 57.1 1.0
NE2 C:HIS178 2.2 38.0 1.0
ND1 C:HIS140 2.3 41.8 1.0
C4 C:MLT403 2.9 59.0 1.0
CX C:KCX103 3.0 47.7 1.0
CE1 C:HIS178 3.0 36.5 1.0
O4 C:MLT403 3.1 59.7 1.0
CE1 C:HIS140 3.2 41.1 1.0
OQ2 C:KCX103 3.2 45.3 1.0
CD2 C:HIS178 3.3 38.1 1.0
CG C:HIS140 3.3 43.2 1.0
ZN C:ZN402 3.4 60.3 1.0
CB C:HIS140 3.6 41.6 1.0
CE1 C:HIS17 4.2 50.0 1.0
NZ C:KCX103 4.2 46.7 1.0
ND1 C:HIS178 4.2 34.9 1.0
NE2 C:HIS17 4.3 51.6 1.0
NE2 C:HIS140 4.3 40.1 1.0
C3 C:MLT403 4.3 50.3 1.0
CG C:HIS178 4.3 34.0 1.0
CD2 C:HIS140 4.4 44.2 1.0
CE1 C:TYR105 4.4 43.0 1.0
O C:LEU223 4.4 61.4 1.0
CA C:HIS140 4.5 40.6 1.0
OD1 C:ASP251 4.5 52.8 1.0
CE C:KCX103 4.7 42.5 1.0
OD2 C:ASP251 4.9 47.6 1.0
CG2 C:THR110 4.9 46.3 1.0
CG C:ASP251 4.9 47.4 1.0
CD1 C:TYR105 5.0 43.6 1.0

Zinc binding site 6 out of 12 in 6cty

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Zinc binding site 6 out of 12 in the Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:60.3
occ:1.00
 OD1 C:ASP251 2.0 52.8 1.0
O5 C:MLT403 2.0 57.1 1.0
OQ2 C:KCX103 2.0 45.3 1.0
NE2 C:HIS19 2.2 35.0 1.0
NE2 C:HIS17 2.2 51.6 1.0
C4 C:MLT403 3.0 59.0 1.0
CX C:KCX103 3.1 47.7 1.0
CE1 C:HIS19 3.1 35.2 1.0
CD2 C:HIS17 3.1 49.4 1.0
CG C:ASP251 3.2 47.4 1.0
CD2 C:HIS19 3.2 34.1 1.0
CE1 C:HIS17 3.2 50.0 1.0
C3 C:MLT403 3.3 50.3 1.0
ZN C:ZN401 3.4 49.5 1.0
OQ1 C:KCX103 3.4 43.8 1.0
OD2 C:ASP251 3.9 47.6 1.0
O4 C:MLT403 4.2 59.7 1.0
CD2 C:HIS178 4.2 38.1 1.0
NE2 C:HIS178 4.2 38.0 1.0
NZ C:KCX103 4.2 46.7 1.0
ND1 C:HIS19 4.2 38.1 1.0
CB C:ASP251 4.2 43.6 1.0
CG C:MET43 4.3 47.7 1.0
ND1 C:HIS17 4.3 53.6 1.0
CG C:HIS19 4.3 37.0 1.0
CG C:HIS17 4.3 47.5 1.0
CA C:ASP251 4.7 40.6 1.0
OH C:TYR105 4.7 45.8 1.0
C2 C:MLT403 4.8 48.3 1.0

Zinc binding site 7 out of 12 in 6cty

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Zinc binding site 7 out of 12 in the Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:48.4
occ:1.00
 OD1 D:ASP251 2.0 34.1 1.0
O4 D:MLT403 2.0 60.0 1.0
OQ2 D:KCX103 2.0 43.1 1.0
NE2 D:HIS19 2.2 33.7 1.0
NE2 D:HIS17 2.3 30.7 1.0
C4 D:MLT403 2.9 50.4 1.0
CG D:ASP251 3.1 33.8 1.0
CE1 D:HIS19 3.1 33.9 1.0
C3 D:MLT403 3.1 47.3 1.0
CX D:KCX103 3.2 41.0 1.0
CD2 D:HIS19 3.2 30.7 1.0
CE1 D:HIS17 3.2 32.9 1.0
CD2 D:HIS17 3.2 32.7 1.0
ZN D:ZN402 3.4 42.5 1.0
OQ1 D:KCX103 3.4 42.9 1.0
OD2 D:ASP251 3.7 35.3 1.0
O5 D:MLT403 4.1 50.8 1.0
CD2 D:HIS178 4.1 35.2 1.0
NE2 D:HIS178 4.1 31.9 1.0
CB D:ASP251 4.2 33.6 1.0
ND1 D:HIS19 4.3 34.6 1.0
NZ D:KCX103 4.3 38.2 1.0
CG D:HIS19 4.3 31.3 1.0
ND1 D:HIS17 4.3 37.1 1.0
CG D:HIS17 4.4 32.6 1.0
CG D:MET43 4.4 30.2 1.0
C2 D:MLT403 4.7 41.6 1.0
CA D:ASP251 4.7 33.0 1.0
OH D:TYR105 4.7 34.9 1.0

Zinc binding site 8 out of 12 in 6cty

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Zinc binding site 8 out of 12 in the Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:42.5
occ:1.00
 OQ1 D:KCX103 2.0 42.9 1.0
O4 D:MLT403 2.0 60.0 1.0
NE2 D:HIS178 2.1 31.9 1.0
ND1 D:HIS140 2.2 30.6 1.0
CE1 D:HIS178 2.9 31.5 1.0
C4 D:MLT403 2.9 50.4 1.0
CX D:KCX103 3.0 41.0 1.0
CE1 D:HIS140 3.1 33.6 1.0
O5 D:MLT403 3.2 50.8 1.0
OQ2 D:KCX103 3.2 43.1 1.0
CG D:HIS140 3.2 27.7 1.0
CD2 D:HIS178 3.3 35.2 1.0
ZN D:ZN401 3.4 48.4 1.0
CB D:HIS140 3.6 24.6 1.0
ND1 D:HIS178 4.1 31.4 1.0
NZ D:KCX103 4.2 38.2 1.0
CE1 D:HIS17 4.2 32.9 1.0
NE2 D:HIS140 4.2 32.0 1.0
CG D:HIS178 4.3 29.6 1.0
CD2 D:HIS140 4.3 34.0 1.0
NE2 D:HIS17 4.3 30.7 1.0
C3 D:MLT403 4.4 47.3 1.0
CA D:HIS140 4.4 25.4 1.0
CE1 D:TYR105 4.4 34.8 1.0
O D:LEU223 4.5 46.2 1.0
OD1 D:ASP251 4.6 34.1 1.0
CE D:KCX103 4.7 32.8 1.0
CG2 D:THR110 4.9 46.5 1.0
OD2 D:ASP251 5.0 35.3 1.0

Zinc binding site 9 out of 12 in 6cty

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Zinc binding site 9 out of 12 in the Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:74.1
occ:1.00
 O E:HOH605 2.0 0.1 1.0
OD1 E:ASP251 2.0 51.0 1.0
OQ1 E:KCX103 2.1 95.7 1.0
NE2 E:HIS19 2.3 42.0 1.0
NE2 E:HIS17 2.3 39.1 1.0
CG E:ASP251 3.1 41.2 1.0
CE1 E:HIS19 3.2 44.8 1.0
CX E:KCX103 3.2 80.3 1.0
CE1 E:HIS17 3.2 40.1 1.0
ZN E:ZN402 3.3 0.9 1.0
CD2 E:HIS17 3.3 40.1 1.0
CD2 E:HIS19 3.3 42.4 1.0
OQ2 E:KCX103 3.5 81.1 1.0
OD2 E:ASP251 3.7 39.9 1.0
CD2 E:HIS178 4.0 46.4 1.0
NE2 E:HIS178 4.1 49.5 1.0
CB E:ASP251 4.3 37.7 1.0
ND1 E:HIS19 4.4 45.1 1.0
NZ E:KCX103 4.4 66.5 1.0
ND1 E:HIS17 4.4 45.3 1.0
CG E:MET43 4.4 39.6 1.0
CG E:HIS17 4.4 39.7 1.0
CG E:HIS19 4.4 43.0 1.0
OH E:TYR105 4.8 36.4 1.0
CA E:ASP251 4.8 34.1 1.0

Zinc binding site 10 out of 12 in 6cty

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Zinc binding site 10 out of 12 in the Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Dihydroorotase Pyrc From Yersinia Pestis in Complex with Zinc and Malate at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:0.9
occ:1.00
 OQ2 E:KCX103 2.0 81.1 1.0
O E:HOH605 2.0 0.1 1.0
ND1 E:HIS140 2.2 49.9 1.0
NE2 E:HIS178 2.3 49.5 1.0
CX E:KCX103 2.9 80.3 1.0
OQ1 E:KCX103 3.0 95.7 1.0
CE1 E:HIS140 3.1 50.3 1.0
CE1 E:HIS178 3.2 42.1 1.0
ZN E:ZN401 3.3 74.1 1.0
CG E:HIS140 3.3 44.2 1.0
CD2 E:HIS178 3.4 46.4 1.0
CB E:HIS140 3.7 39.6 1.0
NZ E:KCX103 4.1 66.5 1.0
NE2 E:HIS140 4.2 45.8 1.0
CE1 E:HIS17 4.3 40.1 1.0
CE1 E:TYR105 4.3 39.6 1.0
ND1 E:HIS178 4.3 40.6 1.0
NE2 E:HIS17 4.3 39.1 1.0
CD2 E:HIS140 4.4 50.1 1.0
CG E:HIS178 4.5 41.8 1.0
CA E:HIS140 4.6 38.8 1.0
O E:LEU223 4.6 46.6 1.0
OD1 E:ASP251 4.6 51.0 1.0
CE E:KCX103 4.7 55.2 1.0
CD1 E:TYR105 4.9 42.9 1.0

Reference:

J.Lipowska, C.D.Miks, K.Kwon, L.Shuvalova, H.Zheng, K.Lewinski, D.R.Cooper, I.G.Shabalin, W.Minor. Pyrimidine Biosynthesis in Pathogens - Structures and Analysis of Dihydroorotases From Yersinia Pestis and Vibrio Cholerae. Int.J.Biol.Macromol. V. 136 1176 2019.
ISSN: ISSN 0141-8130
PubMed: 31207330
DOI: 10.1016/J.IJBIOMAC.2019.05.149
Page generated: Mon Oct 28 19:09:50 2024

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