Fluorine in PDB 9euq: Cryoem Structure of LMCA1 in E2P State

All present enzymatic activity of Cryoem Structure of LMCA1 in E2P State:
7.2.2.10;

The structure of Cryoem Structure of LMCA1 in E2P State also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Cryoem Structure of LMCA1 in E2P State (pdb code 9euq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Cryoem Structure of LMCA1 in E2P State, PDB code: 9euq:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Cryoem Structure of LMCA1 in E2P State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryoem Structure of LMCA1 in E2P State within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:75.3 occ:1.00 F1 A:BEF902 0.0 75.3 1.0 BE A:BEF902 1.5 70.0 1.0 MG A:MG901 2.3 69.2 1.0 F2 A:BEF902 2.5 66.0 1.0 F3 A:BEF902 2.5 73.1 1.0 OD2 A:ASP334 2.7 66.0 1.0 O A:GLY166 2.9 83.3 1.0 O A:THR336 2.9 67.6 1.0 OD1 A:ASP334 3.1 73.0 1.0 CA A:GLY166 3.1 79.8 1.0 C A:GLY166 3.2 84.0 1.0 CG A:ASP334 3.3 67.0 1.0 CB A:THR336 3.4 70.5 1.0 O A:THR165 3.5 85.1 1.0 C A:THR336 3.8 62.6 1.0 CA A:THR336 3.9 64.0 1.0 N A:THR336 3.9 64.9 1.0 ND2 A:ASN626 4.0 66.6 1.0 N A:GLY166 4.1 79.2 1.0 OG1 A:THR336 4.1 72.9 1.0 C A:THR165 4.2 81.1 1.0 CG2 A:THR336 4.3 75.8 1.0 OD1 A:ASP623 4.3 69.5 1.0 N A:GLU167 4.3 83.5 1.0 OD1 A:ASN626 4.4 68.1 1.0 CG A:ASN626 4.7 66.3 1.0 OG1 A:THR549 4.7 73.9 1.0 CB A:ASP334 4.8 58.6 1.0 OE2 A:GLU167 4.8 83.4 1.0 OD2 A:ASP627 4.8 73.2 1.0 N A:GLY550 4.9 63.6 1.0 CG A:GLU167 4.9 83.1 1.0 NZ A:LYS604 4.9 63.3 1.0

Fluorine binding site 2 out of 3 in the Cryoem Structure of LMCA1 in E2P State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryoem Structure of LMCA1 in E2P State within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:66.0 occ:1.00 F2 A:BEF902 0.0 66.0 1.0 BE A:BEF902 1.5 70.0 1.0 OD1 A:ASP334 2.1 73.0 1.0 N A:THR336 2.5 64.9 1.0 OG1 A:THR549 2.5 73.9 1.0 F3 A:BEF902 2.5 73.1 1.0 F1 A:BEF902 2.5 75.3 1.0 CG A:ASP334 2.9 67.0 1.0 N A:LYS335 3.0 49.5 1.0 OD2 A:ASP334 3.2 66.0 1.0 CB A:THR336 3.3 70.5 1.0 CB A:THR549 3.3 62.8 1.0 OG1 A:THR336 3.3 72.9 1.0 CA A:THR336 3.3 64.0 1.0 C A:LYS335 3.4 61.6 1.0 CA A:LYS335 3.5 50.1 1.0 CB A:LYS335 3.7 55.0 1.0 O A:THR336 3.7 67.6 1.0 CA A:THR549 3.8 53.9 1.0 N A:GLY550 3.9 63.6 1.0 C A:THR336 4.0 62.6 1.0 C A:ASP334 4.0 57.1 1.0 MG A:MG901 4.1 69.2 1.0 CB A:ASP334 4.2 58.6 1.0 CA A:ASP334 4.3 55.7 1.0 C A:THR549 4.4 62.7 1.0 OE2 A:GLU167 4.4 83.4 1.0 O A:LYS335 4.5 70.5 1.0 O A:THR165 4.6 85.1 1.0 NZ A:LYS604 4.6 63.3 1.0 CG2 A:THR549 4.7 59.7 1.0 O A:ILE548 4.7 68.5 1.0 CG2 A:THR336 4.8 75.8 1.0 CE A:LYS335 4.8 61.0 1.0 CG A:LYS335 4.9 60.7 1.0 N A:ASP551 5.0 67.0 1.0 N A:THR549 5.0 51.9 1.0

Fluorine binding site 3 out of 3 in the Cryoem Structure of LMCA1 in E2P State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryoem Structure of LMCA1 in E2P State within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:73.1 occ:1.00 F3 A:BEF902 0.0 73.1 1.0 BE A:BEF902 1.5 70.0 1.0 OD1 A:ASP334 2.0 73.0 1.0 F2 A:BEF902 2.5 66.0 1.0 F1 A:BEF902 2.5 75.3 1.0 NZ A:LYS604 2.7 63.3 1.0 ND2 A:ASN626 2.8 66.6 1.0 CG A:ASP334 2.8 67.0 1.0 N A:GLY550 3.1 63.6 1.0 OD2 A:ASP334 3.2 66.0 1.0 CA A:THR549 3.4 53.9 1.0 CE A:LYS604 3.6 51.9 1.0 OG1 A:THR549 3.7 73.9 1.0 C A:THR549 3.8 62.7 1.0 O A:THR165 3.8 85.1 1.0 CG A:ASN626 3.9 66.3 1.0 OD1 A:ASP627 4.0 70.9 1.0 O A:ILE548 4.0 68.5 1.0 CB A:THR549 4.1 62.8 1.0 CB A:ASP334 4.1 58.6 1.0 MG A:MG901 4.1 69.2 1.0 CA A:GLY550 4.2 63.1 1.0 OD1 A:ASN626 4.2 68.1 1.0 CA A:GLY166 4.5 79.8 1.0 N A:THR549 4.5 51.9 1.0 C A:THR165 4.6 81.1 1.0 N A:LYS335 4.6 49.5 1.0 CA A:ASP334 4.7 55.7 1.0 OD2 A:ASP627 4.7 73.2 1.0 C A:ILE548 4.7 59.2 1.0 CG A:ASP627 4.8 68.3 1.0 N A:GLY166 4.9 79.2 1.0 N A:THR336 4.9 64.9 1.0 O A:THR549 4.9 68.0 1.0 CD A:LYS604 5.0 48.4 1.0

I.Prabudiansyah, F.Oradd, K.Magkakis, K.Pounot, M.Levantino, M.Andersson. Dephosphorylation and Ion Binding in Prokaryotic Calcium Transport Sci Adv 2024.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ADP2916