Atomistry » Magnesium » PDB 6q5a-6qin » 6qfb
Atomistry »
  Magnesium »
    PDB 6q5a-6qin »
      6qfb »

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

Go back to Magnesium Binding Sites List in 6qfb
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

Go back to Magnesium Binding Sites List in 6qfb
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

Go back to Magnesium Binding Sites List in 6qfb
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

Go back to Magnesium Binding Sites List in 6qfb
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

Go back to Magnesium Binding Sites List in 6qfb
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy