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Calcium in PDB 6qcl: Citryl-Coa Lyase Core Module of Chlorobium Limicola Atp Citrate Lyase in Complex with Acetyl-Coa and L-Malate

Protein crystallography data

The structure of Citryl-Coa Lyase Core Module of Chlorobium Limicola Atp Citrate Lyase in Complex with Acetyl-Coa and L-Malate, PDB code: 6qcl 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) 45.62 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.730, 100.817, 105.012, 90.00, 102.99, 90.00
R / Rfree (%) 15.7 / 17.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Citryl-Coa Lyase Core Module of Chlorobium Limicola Atp Citrate Lyase in Complex with Acetyl-Coa and L-Malate (pdb code 6qcl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Citryl-Coa Lyase Core Module of Chlorobium Limicola Atp Citrate Lyase in Complex with Acetyl-Coa and L-Malate, PDB code: 6qcl:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6qcl

Go back to Calcium Binding Sites List in 6qcl
Calcium binding site 1 out of 2 in the Citryl-Coa Lyase Core Module of Chlorobium Limicola Atp Citrate Lyase in Complex with Acetyl-Coa and L-Malate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Citryl-Coa Lyase Core Module of Chlorobium Limicola Atp Citrate Lyase in Complex with Acetyl-Coa and L-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:14.4
occ:1.00
OE1 A:GLN602 2.3 20.4 1.0
OE2 A:GLU603 2.3 19.2 1.0
O A:HOH877 2.4 19.6 1.0
CD A:GLN602 3.4 35.7 1.0
H A:GLU603 3.4 14.5 1.0
CD A:GLU603 3.5 35.6 1.0
HE22 A:GLN602 3.5 27.2 1.0
NE2 A:GLN602 3.9 28.6 1.0
HB2 A:GLU603 3.9 15.2 1.0
OE1 A:GLU603 4.0 30.0 1.0
O A:HOH890 4.1 28.3 1.0
O A:HOH807 4.2 24.6 1.0
HA A:GLN602 4.2 15.4 1.0
N A:GLU603 4.4 14.1 1.0
HG3 A:GLN602 4.6 24.6 1.0
CG A:GLN602 4.6 25.5 1.0
CG A:GLU603 4.6 17.5 1.0
O A:HOH851 4.7 29.1 1.0
CB A:GLU603 4.7 14.9 1.0
HE21 A:GLN602 4.9 29.5 1.0

Calcium binding site 2 out of 2 in 6qcl

Go back to Calcium Binding Sites List in 6qcl
Calcium binding site 2 out of 2 in the Citryl-Coa Lyase Core Module of Chlorobium Limicola Atp Citrate Lyase in Complex with Acetyl-Coa and L-Malate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Citryl-Coa Lyase Core Module of Chlorobium Limicola Atp Citrate Lyase in Complex with Acetyl-Coa and L-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:15.0
occ:1.00
OE1 B:GLN602 2.2 23.9 1.0
O B:HOH859 2.3 21.7 1.0
OE2 B:GLU603 2.4 19.1 1.0
CD B:GLN602 3.2 40.4 1.0
HE22 B:GLN602 3.3 28.9 1.0
H B:GLU603 3.4 11.3 1.0
CD B:GLU603 3.5 28.2 1.0
NE2 B:GLN602 3.7 31.8 1.0
OE1 B:GLU603 4.0 32.6 1.0
HB2 B:GLU603 4.1 15.1 1.0
HA B:GLN602 4.1 11.5 1.0
O B:HOH898 4.1 25.6 1.0
O B:HOH813 4.2 22.7 1.0
O B:HOH856 4.4 35.7 1.0
N B:GLU603 4.5 13.4 1.0
HG3 B:GLN602 4.5 33.1 1.0
CG B:GLN602 4.5 33.0 1.0
O B:HOH803 4.6 32.9 1.0
HE21 B:GLN602 4.7 33.0 1.0
CG B:GLU603 4.7 15.3 1.0
CB B:GLU603 4.8 14.1 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: Wed Jul 9 17:09:18 2025

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