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Magnesium in PDB 6hxh: Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp

Enzymatic activity of Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp

All present enzymatic activity of Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp:
2.3.3.8;

Protein crystallography data

The structure of Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp, PDB code: 6hxh was solved by K.Verstraete, K.Verschueren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.46 / 3.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 150.364, 154.011, 154.087, 91.53, 110.04, 107.46
R / Rfree (%) 15.6 / 18.7

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp (pdb code 6hxh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp, PDB code: 6hxh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 6hxh

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Magnesium binding site 1 out of 16 in the Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1201

b:0.9
occ:1.00
 OG1 A:FLC1203 2.3 0.9 1.0
O1 A:PO41202 2.4 0.4 1.0
OG A:SER308 2.4 0.5 1.0
OE2 A:GLU599 2.7 0.5 1.0
CGC A:FLC1203 3.3 0.2 1.0
CB A:SER308 3.4 0.2 1.0
P A:PO41202 3.6 0.1 1.0
OG2 A:FLC1203 3.6 0.8 1.0
CD A:GLU599 3.7 0.4 1.0
O2 A:PO41202 3.8 0.1 1.0
OE1 A:GLU306 3.9 0.4 1.0
OE1 A:GLU599 4.0 0.6 1.0
OE2 A:GLU306 4.0 0.5 1.0
O4 A:PO41202 4.2 0.5 1.0
CB A:SER263 4.3 0.5 1.0
N A:GLY282 4.3 0.7 1.0
CD A:GLU306 4.4 0.0 1.0
O5P A:COA1204 4.5 0.8 1.0
OG A:SER263 4.6 0.6 1.0
CA A:SER308 4.6 0.5 1.0
HA1 A:FLC1203 4.6 0.8 1.0
CG A:FLC1203 4.7 0.1 1.0
N A:GLY309 4.7 0.4 1.0
C A:SER308 4.7 1.0 1.0
HG2 A:FLC1203 4.8 0.3 1.0
O3 A:PO41202 4.8 0.4 1.0
CA A:GLY281 4.9 0.7 1.0

Magnesium binding site 2 out of 16 in 6hxh

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Magnesium binding site 2 out of 16 in the Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1206

b:89.7
occ:1.00
 HOA2 A:ADP1205 1.6 0.7 1.0
O1B A:ADP1205 2.0 0.0 1.0
O2A A:ADP1205 2.2 0.2 1.0
O A:ASN203 2.2 0.6 1.0
O A:HOH1302 2.3 90.8 1.0
OD2 A:ASP216 2.5 0.4 1.0
PB A:ADP1205 3.2 0.3 1.0
PA A:ADP1205 3.3 0.6 1.0
C A:ASN203 3.4 0.7 1.0
O3A A:ADP1205 3.4 0.2 1.0
CG A:ASP216 3.6 0.9 1.0
O A:HOH1301 3.6 0.8 1.0
HO3' A:ADP1205 3.6 0.5 1.0
CB A:ASP216 3.9 0.1 1.0
O3B A:ADP1205 4.0 0.1 1.0
O1A A:ADP1205 4.1 0.2 1.0
CD A:PRO204 4.1 0.6 1.0
ND2 A:ASN203 4.1 0.4 1.0
H5'2 A:ADP1205 4.2 1.0 1.0
CB A:ASN203 4.2 0.9 1.0
N A:PRO204 4.2 0.7 1.0
CG A:ASN203 4.2 0.8 1.0
CA A:ASN203 4.3 0.9 1.0
O2B A:ADP1205 4.4 0.2 1.0
HOB3 A:ADP1205 4.5 0.9 1.0
H3' A:ADP1205 4.5 0.4 1.0
HOB2 A:ADP1205 4.6 0.8 1.0
O5' A:ADP1205 4.6 1.0 1.0
O3' A:ADP1205 4.6 0.1 1.0
OD1 A:ASP216 4.7 0.0 1.0
OD1 A:ASN203 4.8 0.2 1.0
O A:GLY139 4.9 0.7 1.0
C5' A:ADP1205 4.9 0.5 1.0

Magnesium binding site 3 out of 16 in 6hxh

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Magnesium binding site 3 out of 16 in the Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1201

b:80.3
occ:1.00
 OG2 B:FLC1203 2.4 0.1 1.0
O1 B:PO41202 2.4 0.3 1.0
OG B:SER308 2.6 92.5 1.0
OE1 B:GLU599 2.7 0.2 1.0
CGC B:FLC1203 3.2 0.9 1.0
OG1 B:FLC1203 3.4 0.4 1.0
P B:PO41202 3.5 0.2 1.0
O2 B:PO41202 3.5 0.6 1.0
CB B:SER308 3.6 94.1 1.0
CD B:GLU599 3.8 0.3 1.0
O5P A:COA1207 4.1 0.5 1.0
OE2 B:GLU599 4.2 0.9 1.0
O4 B:PO41202 4.3 0.9 1.0
OE2 B:GLU306 4.3 0.4 1.0
CB B:SER263 4.4 0.0 1.0
OE1 B:GLU306 4.6 0.3 1.0
CG B:FLC1203 4.7 0.0 1.0
OG B:SER263 4.7 0.3 1.0
O3 B:PO41202 4.7 0.7 1.0
N B:GLY282 4.8 0.2 1.0
N B:GLY309 4.8 95.4 1.0
HG2 B:FLC1203 4.8 0.2 1.0
NE2 B:HIS760 4.8 0.3 1.0
CA B:SER308 4.8 95.1 1.0
CD B:GLU306 4.9 0.9 1.0
S1P A:COA1207 4.9 0.6 1.0
C3P A:COA1207 5.0 0.5 1.0
HA1 B:FLC1203 5.0 0.4 1.0
CD2 B:HIS760 5.0 0.2 1.0

Magnesium binding site 4 out of 16 in 6hxh

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Magnesium binding site 4 out of 16 in the Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1205

b:0.6
occ:1.00
 HOA2 B:ADP1204 1.5 0.9 1.0
O2A B:ADP1204 1.9 0.4 1.0
O B:HOH1301 1.9 99.7 1.0
O B:ASN203 2.0 0.9 1.0
O1B B:ADP1204 2.4 0.2 1.0
O B:HOH1302 2.5 0.9 1.0
OD2 B:ASP216 2.8 0.2 1.0
CG B:ASP216 3.0 0.8 1.0
C B:ASN203 3.2 0.7 1.0
CB B:ASP216 3.2 0.7 1.0
PA B:ADP1204 3.2 0.1 1.0
PB B:ADP1204 3.5 0.3 1.0
HO3' B:ADP1204 3.6 0.5 1.0
O3A B:ADP1204 3.6 0.6 1.0
OD1 B:ASP216 3.8 0.1 1.0
ND2 B:ASN203 3.8 1.0 1.0
O1A B:ADP1204 3.9 0.5 1.0
N B:PRO204 4.1 0.4 1.0
CB B:ASN203 4.1 0.1 1.0
CD B:PRO204 4.1 0.8 1.0
CA B:ASN203 4.1 1.0 1.0
H5'2 B:ADP1204 4.2 0.6 1.0
CG B:ASN203 4.3 0.7 1.0
H3' B:ADP1204 4.3 0.2 1.0
O5' B:ADP1204 4.4 0.8 1.0
O3' B:ADP1204 4.5 0.7 1.0
O2B B:ADP1204 4.5 0.9 1.0
O3B B:ADP1204 4.5 0.6 1.0
HOB2 B:ADP1204 4.6 0.2 1.0
N B:ASN203 4.7 0.5 1.0
CA B:ASP216 4.7 0.8 1.0
C5' B:ADP1204 4.9 0.1 1.0
C3' B:ADP1204 4.9 0.2 1.0
NH2 B:ARG66 4.9 0.7 1.0

Magnesium binding site 5 out of 16 in 6hxh

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Magnesium binding site 5 out of 16 in the Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1201

b:94.6
occ:1.00
 OG C:SER308 2.1 0.1 1.0
OG1 C:FLC1203 2.3 1.0 1.0
O2 C:PO41202 2.4 0.3 1.0
OE1 C:GLU599 2.9 0.1 1.0
OE2 C:GLU599 3.0 0.1 1.0
CB C:SER308 3.2 0.8 1.0
CGC C:FLC1203 3.3 0.2 1.0
CD C:GLU599 3.3 0.0 1.0
P C:PO41202 3.5 0.4 1.0
O1 C:PO41202 3.5 0.6 1.0
OG2 C:FLC1203 3.6 0.1 1.0
O5P C:COA1204 4.1 0.5 1.0
O4 C:PO41202 4.3 0.2 1.0
OE1 C:GLU306 4.3 0.2 1.0
OE2 C:GLU306 4.3 0.4 1.0
CB C:SER263 4.4 0.5 1.0
N C:GLY309 4.4 0.4 1.0
CA C:SER308 4.5 0.8 1.0
N C:GLY282 4.6 0.2 1.0
CG C:FLC1203 4.6 0.6 1.0
O3 C:PO41202 4.6 0.8 1.0
HA1 C:FLC1203 4.7 0.7 1.0
OG C:SER263 4.7 0.8 1.0
C C:SER308 4.7 0.2 1.0
HG2 C:FLC1203 4.7 0.7 1.0
CD C:GLU306 4.8 0.5 1.0
CG C:GLU599 4.8 0.5 1.0
S1P C:COA1204 4.9 0.1 1.0
NE2 C:HIS760 4.9 0.7 1.0

Magnesium binding site 6 out of 16 in 6hxh

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Magnesium binding site 6 out of 16 in the Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1206

b:0.3
occ:1.00
 HOA2 C:ADP1205 1.9 0.0 1.0
O C:ASN203 2.0 0.6 1.0
O C:HOH1301 2.2 86.4 1.0
O1B C:ADP1205 2.3 0.7 1.0
OD2 C:ASP216 2.4 0.2 1.0
O2A C:ADP1205 2.6 0.5 1.0
O C:HOH1302 2.9 0.9 1.0
CG C:ASP216 2.9 0.9 1.0
C C:ASN203 3.1 0.7 1.0
CB C:ASP216 3.3 0.4 1.0
CB C:ASN203 3.4 0.9 1.0
ND2 C:ASN203 3.4 0.3 1.0
PB C:ADP1205 3.6 0.3 1.0
CG C:ASN203 3.7 0.5 1.0
CA C:ASN203 3.7 0.7 1.0
OD1 C:ASP216 3.8 0.5 1.0
PA C:ADP1205 3.8 0.3 1.0
O3A C:ADP1205 4.0 0.2 1.0
HO3' C:ADP1205 4.1 0.9 1.0
N C:PRO204 4.2 0.7 1.0
N C:ASN203 4.3 0.0 1.0
H5'2 C:ADP1205 4.3 0.2 1.0
CD C:PRO204 4.5 0.8 1.0
O3B C:ADP1205 4.6 1.0 1.0
HOB2 C:ADP1205 4.6 0.0 1.0
OD1 C:ASN203 4.6 0.8 1.0
O2B C:ADP1205 4.6 0.2 1.0
O1A C:ADP1205 4.6 0.0 1.0
H3' C:ADP1205 4.7 0.6 1.0
CA C:ASP216 4.8 0.2 1.0
OE1 C:GLU201 4.9 0.2 1.0
O5' C:ADP1205 5.0 0.3 1.0

Magnesium binding site 7 out of 16 in 6hxh

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Magnesium binding site 7 out of 16 in the Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1201

b:76.8
occ:1.00
 O4 D:PO41202 2.4 0.1 1.0
OE1 D:GLU599 2.4 0.3 1.0
OG D:SER308 2.5 0.3 1.0
OG2 D:FLC1203 2.6 0.9 1.0
OE2 D:GLU599 3.0 0.1 1.0
CD D:GLU599 3.1 0.7 1.0
OG1 D:FLC1203 3.4 97.4 1.0
CGC D:FLC1203 3.4 0.8 1.0
P D:PO41202 3.5 0.8 1.0
O2 D:PO41202 3.5 0.1 1.0
CB D:SER308 3.8 0.2 1.0
OE1 D:GLU306 4.2 0.0 1.0
OE2 D:GLU306 4.2 0.3 1.0
O5P D:COA1204 4.2 0.7 1.0
O1 D:PO41202 4.3 0.0 1.0
CB D:SER263 4.3 0.3 1.0
CG D:GLU599 4.6 0.0 1.0
CD D:GLU306 4.6 0.8 1.0
N D:GLY282 4.7 0.4 1.0
OG D:SER263 4.7 0.7 1.0
O3 D:PO41202 4.7 0.1 1.0
C D:SER308 4.8 0.8 1.0
CG D:FLC1203 4.8 0.7 1.0
HA1 D:FLC1203 4.9 0.2 1.0
CA D:SER308 4.9 0.7 1.0
N D:GLY309 5.0 0.4 1.0
NE2 D:HIS760 5.0 0.1 1.0
CD2 D:HIS760 5.0 0.3 1.0

Magnesium binding site 8 out of 16 in 6hxh

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Magnesium binding site 8 out of 16 in the Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1206

b:0.6
occ:1.00
 HOA2 D:ADP1205 1.9 0.6 1.0
O1B D:ADP1205 2.2 0.6 1.0
O D:HOH1301 2.3 79.4 1.0
OD2 D:ASP216 2.3 0.6 1.0
O D:ASN203 2.4 0.9 1.0
O2A D:ADP1205 2.9 0.5 1.0
CG D:ASP216 3.0 0.1 1.0
PB D:ADP1205 3.4 0.2 1.0
C D:ASN203 3.6 1.0 1.0
CB D:ASP216 3.6 0.5 1.0
O D:HOH1302 3.7 90.5 1.0
OD1 D:ASP216 3.7 0.3 1.0
O3A D:ADP1205 3.7 0.3 1.0
PA D:ADP1205 3.8 0.0 1.0
CB D:ASN203 3.9 0.5 1.0
OD1 D:ASN203 3.9 0.2 1.0
CA D:ASN203 4.2 0.9 1.0
CG D:ASN203 4.3 0.7 1.0
O2B D:ADP1205 4.3 0.6 1.0
HOB2 D:ADP1205 4.4 0.6 1.0
O1A D:ADP1205 4.5 0.3 1.0
O3B D:ADP1205 4.6 0.1 1.0
N D:ASN203 4.6 0.7 1.0
OE1 D:GLU201 4.6 0.2 1.0
N D:PRO204 4.7 0.8 1.0
H5'2 D:ADP1205 4.8 0.4 1.0
HO3' D:ADP1205 4.9 0.6 1.0
CD D:PRO204 5.0 0.8 1.0

Magnesium binding site 9 out of 16 in 6hxh

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Magnesium binding site 9 out of 16 in the Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1201

b:71.5
occ:1.00
 OG E:SER308 2.2 0.5 1.0
O1 E:PO41202 2.2 0.8 1.0
OG1 E:FLC1203 2.3 0.8 1.0
OE1 E:GLU599 3.1 0.2 1.0
OE2 E:GLU599 3.1 0.1 1.0
CGC E:FLC1203 3.3 0.9 1.0
P E:PO41202 3.5 0.5 1.0
CB E:SER308 3.5 0.1 1.0
CD E:GLU599 3.5 1.0 1.0
OG2 E:FLC1203 3.7 0.4 1.0
O2 E:PO41202 3.9 0.3 1.0
OE1 E:GLU306 3.9 97.6 1.0
O4 E:PO41202 4.1 0.5 1.0
CB E:SER263 4.2 99.0 1.0
N E:GLY282 4.2 0.9 1.0
OE2 E:GLU306 4.2 96.0 1.0
O5P E:COA1204 4.3 0.9 1.0
CD E:GLU306 4.5 0.6 1.0
C E:SER308 4.5 0.7 1.0
CA E:SER308 4.5 98.0 1.0
OG E:SER263 4.6 0.8 1.0
O3 E:PO41202 4.7 0.8 1.0
N E:GLY309 4.7 0.3 1.0
CG E:FLC1203 4.7 0.1 1.0
CA E:GLY282 4.8 0.6 1.0
HA1 E:FLC1203 4.8 0.8 1.0
O E:SER308 4.8 0.9 1.0
HG2 E:FLC1203 4.9 0.7 1.0

Magnesium binding site 10 out of 16 in 6hxh

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Magnesium binding site 10 out of 16 in the Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Human Atp Citrate Lyase Holoenzyme in Complex with Citrate, Coenzyme A and Mg.Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1206

b:0.0
occ:1.00
 HOA2 E:ADP1205 1.6 0.6 1.0
O1B E:ADP1205 2.0 0.7 1.0
O E:ASN203 2.3 0.9 1.0
O E:HOH1301 2.3 79.5 1.0
O2A E:ADP1205 2.5 1.0 1.0
OD2 E:ASP216 2.7 0.3 1.0
CG E:ASP216 2.9 0.3 1.0
PB E:ADP1205 3.3 0.8 1.0
CB E:ASP216 3.4 0.1 1.0
PA E:ADP1205 3.5 0.3 1.0
C E:ASN203 3.5 0.8 1.0
OD1 E:ASP216 3.5 0.6 1.0
O3A E:ADP1205 3.6 1.0 1.0
O E:HOH1302 3.9 0.9 1.0
CB E:ASN203 4.1 0.1 1.0
O1A E:ADP1205 4.1 0.3 1.0
O3B E:ADP1205 4.2 0.6 1.0
ND2 E:ASN203 4.2 0.1 1.0
CA E:ASN203 4.2 0.6 1.0
O2B E:ADP1205 4.4 0.5 1.0
H5'2 E:ADP1205 4.4 0.7 1.0
HOB2 E:ADP1205 4.4 0.6 1.0
N E:PRO204 4.6 0.9 1.0
CG E:ASN203 4.6 0.6 1.0
N E:ASN203 4.7 0.6 1.0
CD E:PRO204 4.8 0.6 1.0
HO3' E:ADP1205 4.8 0.5 1.0
NH2 E:ARG66 4.8 0.2 1.0
HOB3 E:ADP1205 4.8 0.6 1.0
O5' E:ADP1205 4.8 0.3 1.0
OE1 E:GLU201 4.9 0.2 1.0
CA E:ASP216 4.9 0.4 1.0

Reference:

K.H.G.Verschueren, C.Blanchet, J.Felix, A.Dansercoer, D.De Vos, Y.Bloch, J.Van Beeumen, D.Svergun, I.Gutsche, S.N.Savvides, K.Verstraete. Structure of Atp Citrate Lyase and the Origin of Citrate Synthase in the Krebs Cycle. Nature V. 568 571 2019.
ISSN: ESSN 1476-4687
PubMed: 30944476
DOI: 10.1038/S41586-019-1095-5
Page generated: Tue Oct 1 02:47:57 2024

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