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Magnesium in PDB 6qfb: 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: 6qfb 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) 47.83 / 3.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 214.277, 215.398, 158.421, 90.00, 117.27, 90.00
R / Rfree (%) 16.2 / 19.3

Magnesium 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 6qfb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 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: 6qfb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6qfb

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Magnesium binding site 1 out of 5 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:Mg1204

b:89.3
occ:1.00
 O2B A:ADP1203 1.8 0.8 1.0
O1A A:ADP1203 2.2 0.9 1.0
O A:ASN203 2.3 0.5 1.0
OD2 A:ASP216 2.5 0.8 1.0
PB A:ADP1203 3.1 0.4 1.0
PA A:ADP1203 3.3 0.3 1.0
C A:ASN203 3.5 0.1 1.0
O3A A:ADP1203 3.5 0.1 1.0
CG A:ASP216 3.5 1.0 1.0
ND2 A:ASN203 3.9 0.2 1.0
O3B A:ADP1203 4.0 1.0 1.0
CB A:ASP216 4.0 0.8 1.0
O2A A:ADP1203 4.1 0.2 1.0
CG A:ASN203 4.2 0.9 1.0
O1B A:ADP1203 4.2 0.4 1.0
CB A:ASN203 4.2 0.8 1.0
CD A:PRO204 4.3 0.8 1.0
N A:PRO204 4.3 0.4 1.0
CA A:ASN203 4.4 0.6 1.0
OD1 A:ASP216 4.6 1.0 1.0
O5' A:ADP1203 4.6 0.2 1.0
O A:GLY139 4.7 1.0 1.0
O3' A:ADP1203 4.8 0.1 1.0
OD1 A:ASN203 4.9 0.3 1.0
C5' A:ADP1203 5.0 0.0 1.0

Magnesium binding site 2 out of 5 in 6qfb

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Magnesium binding site 2 out of 5 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
B:Mg1205

b:85.0
occ:1.00
 O2A B:ADP1204 2.0 0.0 1.0
O1B B:ADP1204 2.0 0.6 1.0
O B:ASN203 2.2 0.6 1.0
OD2 B:ASP216 2.6 1.0 1.0
PA B:ADP1204 3.2 0.6 1.0
C B:ASN203 3.3 0.9 1.0
PB B:ADP1204 3.4 0.2 1.0
ND2 B:ASN203 3.5 0.8 1.0
O3A B:ADP1204 3.6 0.9 1.0
CG B:ASP216 3.6 0.2 1.0
O1A B:ADP1204 4.0 0.1 1.0
CD B:PRO204 4.0 0.6 1.0
N B:PRO204 4.1 98.7 1.0
CB B:ASP216 4.1 0.2 1.0
CG B:ASN203 4.2 0.5 1.0
O2B B:ADP1204 4.3 0.7 1.0
CB B:ASN203 4.3 96.5 1.0
O3B B:ADP1204 4.3 0.7 1.0
CA B:ASN203 4.4 97.7 1.0
O3' B:ADP1204 4.5 0.3 1.0
O5' B:ADP1204 4.5 0.1 1.0
NE2 B:HIS760 4.6 0.2 1.0
OD1 B:ASP216 4.6 0.1 1.0
C5' B:ADP1204 4.8 0.3 1.0
C3' B:ADP1204 4.9 0.5 1.0
O B:GLY139 4.9 0.6 1.0

Magnesium binding site 3 out of 5 in 6qfb

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Magnesium binding site 3 out of 5 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:Mg1206

b:91.3
occ:1.00
 O2 B:2HP1201 2.5 0.0 1.0
OG B:SER308 2.5 0.3 1.0
OG2 B:FLC1202 2.6 0.1 1.0
OE1 B:GLU599 3.3 0.2 1.0
OG1 B:FLC1202 3.3 0.5 1.0
CGC B:FLC1202 3.3 0.2 1.0
CB B:SER308 3.4 0.3 1.0
P B:2HP1201 3.6 0.5 1.0
O1 B:2HP1201 3.6 1.0 1.0
O5P A:COA1202 4.0 0.3 1.0
CD B:GLU599 4.2 0.6 1.0
CB B:SER263 4.3 0.7 1.0
OE2 B:GLU599 4.3 0.1 1.0
OE2 B:GLU306 4.3 0.9 1.0
O4 B:2HP1201 4.5 0.6 1.0
S1P A:COA1202 4.5 0.4 1.0
OE1 B:GLU306 4.5 0.9 1.0
OG B:SER263 4.6 0.0 1.0
N B:GLY309 4.6 0.5 1.0
CA B:SER308 4.7 0.9 1.0
O3 B:2HP1201 4.7 0.2 1.0
C B:SER308 4.8 0.7 1.0
CG B:FLC1202 4.8 0.1 1.0
N B:GLY282 4.8 0.9 1.0
CD B:GLU306 4.8 0.6 1.0

Magnesium binding site 4 out of 5 in 6qfb

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Magnesium binding site 4 out of 5 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
C:Mg1203

b:0.4
occ:1.00
 O2B C:ADP1202 1.9 0.1 1.0
O2A C:ADP1202 2.1 0.4 1.0
O C:ASN203 2.2 0.8 1.0
OD2 C:ASP216 2.9 0.6 1.0
PA C:ADP1202 3.3 0.3 1.0
PB C:ADP1202 3.3 0.5 1.0
C C:ASN203 3.3 0.4 1.0
O3A C:ADP1202 3.5 0.5 1.0
CG C:ASP216 3.9 0.2 1.0
ND2 C:ASN203 3.9 0.1 1.0
CD C:PRO204 3.9 0.5 1.0
N C:PRO204 4.1 1.0 1.0
O1A C:ADP1202 4.1 0.3 1.0
CG C:ASN203 4.1 0.8 1.0
O3B C:ADP1202 4.2 0.2 1.0
CB C:ASP216 4.2 0.0 1.0
O1B C:ADP1202 4.2 0.2 1.0
O C:GLY139 4.2 0.7 1.0
CB C:ASN203 4.4 0.5 1.0
CA C:ASN203 4.4 0.9 1.0
O5' C:ADP1202 4.5 0.2 1.0
O3' C:ADP1202 4.6 0.5 1.0
OD1 C:ASN203 4.7 0.7 1.0
C C:GLY139 4.8 0.8 1.0
C5' C:ADP1202 4.8 0.0 1.0
OD1 C:ASP216 4.9 0.9 1.0
C3' C:ADP1202 5.0 0.9 1.0

Magnesium binding site 5 out of 5 in 6qfb

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Magnesium binding site 5 out of 5 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
D:Mg1204

b:93.5
occ:1.00
 O1B D:ADP1203 1.8 0.3 1.0
O2A D:ADP1203 2.3 0.6 1.0
O D:ASN203 2.3 0.5 1.0
OD2 D:ASP216 2.8 0.7 1.0
PB D:ADP1203 3.2 0.8 1.0
PA D:ADP1203 3.5 0.7 1.0
C D:ASN203 3.5 0.7 1.0
O3A D:ADP1203 3.6 0.3 1.0
ND2 D:ASN203 3.6 0.2 1.0
O D:GLY139 3.7 0.2 1.0
CG D:ASP216 3.8 0.1 1.0
O3B D:ADP1203 4.1 0.2 1.0
CG D:ASN203 4.2 0.6 1.0
CB D:ASN203 4.2 0.7 1.0
O2B D:ADP1203 4.2 0.9 1.0
CB D:ASP216 4.3 0.5 1.0
CD D:PRO204 4.3 0.5 1.0
N D:PRO204 4.4 0.6 1.0
O1A D:ADP1203 4.4 0.3 1.0
CA D:ASN203 4.5 0.6 1.0
O3' D:ADP1203 4.5 1.0 1.0
C D:GLY139 4.6 0.4 1.0
O5' D:ADP1203 4.7 0.8 1.0
C5' D:ADP1203 4.8 0.2 1.0
OD1 D:ASP216 4.9 0.9 1.0
CA D:VAL140 4.9 0.5 1.0
CG2 D:VAL140 5.0 0.5 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 15:28:17 2024

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