Fluorine in PDB 7yam: Cryoem Structure of SPCA1A in E2P State

All present enzymatic activity of Cryoem Structure of SPCA1A in E2P State:
7.2.2.10;

The structure of Cryoem Structure of SPCA1A in E2P State also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Cryoem Structure of SPCA1A in E2P State (pdb code 7yam). 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 SPCA1A in E2P State, PDB code: 7yam:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Cryoem Structure of SPCA1A 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 SPCA1A in E2P State within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:3.7 occ:1.00 F1 A:BEF1001 0.0 3.7 1.0 BE A:BEF1001 1.5 3.7 1.0 MG A:MG1002 1.8 3.0 1.0 OD1 A:ASP350 2.3 2.5 1.0 OD2 A:ASP350 2.3 2.5 1.0 F3 A:BEF1001 2.5 3.7 1.0 F2 A:BEF1001 2.6 3.7 1.0 CG A:ASP350 2.6 2.5 1.0 O A:THR352 2.8 3.0 1.0 CB A:THR352 3.7 3.0 1.0 O A:SER186 3.7 10.1 1.0 C A:THR352 3.7 3.0 1.0 OD1 A:ASP644 3.9 4.4 1.0 CA A:GLY190 3.9 8.3 1.0 N A:THR352 4.0 3.0 1.0 CA A:THR352 4.0 3.0 1.0 CB A:ASP350 4.1 2.5 1.0 OD2 A:ASP648 4.2 4.6 1.0 ND2 A:ASN647 4.3 4.8 1.0 OD1 A:ASN647 4.4 4.8 1.0 CG2 A:THR352 4.5 3.0 1.0 N A:GLY190 4.6 8.3 1.0 OG1 A:THR352 4.6 3.0 1.0 OG1 A:THR570 4.8 2.9 1.0 CG A:ASN647 4.8 4.8 1.0 NZ A:LYS625 4.9 3.2 1.0 C A:SER186 4.9 10.1 1.0 C A:ASP350 4.9 2.5 1.0 N A:GLY353 5.0 2.9 1.0 CA A:ASP350 5.0 2.5 1.0 N A:LYS351 5.0 2.2 1.0 CG A:ASP644 5.0 4.4 1.0

Fluorine binding site 2 out of 3 in the Cryoem Structure of SPCA1A 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 SPCA1A in E2P State within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:3.7 occ:1.00 F2 A:BEF1001 0.0 3.7 1.0 BE A:BEF1001 1.6 3.7 1.0 OG1 A:THR570 2.2 2.9 1.0 OD1 A:ASP350 2.3 2.5 1.0 F3 A:BEF1001 2.5 3.7 1.0 F1 A:BEF1001 2.6 3.7 1.0 N A:THR352 2.9 3.0 1.0 CB A:THR352 3.2 3.0 1.0 OG1 A:THR352 3.3 3.0 1.0 CB A:THR570 3.4 2.9 1.0 CG A:ASP350 3.4 2.5 1.0 CA A:THR352 3.6 3.0 1.0 N A:LYS351 3.7 2.2 1.0 CA A:GLY190 3.7 8.3 1.0 O A:GLY190 3.9 8.3 1.0 OD2 A:ASP350 4.0 2.5 1.0 C A:LYS351 4.0 2.2 1.0 O A:THR352 4.0 3.0 1.0 CA A:THR570 4.0 2.9 1.0 MG A:MG1002 4.1 3.0 1.0 CA A:LYS351 4.2 2.2 1.0 N A:GLY571 4.2 3.6 1.0 CB A:LYS351 4.2 2.2 1.0 C A:THR352 4.3 3.0 1.0 C A:ASP350 4.3 2.5 1.0 C A:GLY190 4.3 8.3 1.0 CG2 A:THR570 4.6 2.9 1.0 CG2 A:THR352 4.6 3.0 1.0 CB A:ASP350 4.6 2.5 1.0 CA A:ASP350 4.6 2.5 1.0 C A:THR570 4.7 2.9 1.0 NZ A:LYS625 4.7 3.2 1.0 CE A:LYS351 4.9 2.2 1.0 N A:GLY190 4.9 8.3 1.0 O A:ILE569 4.9 2.2 1.0

Fluorine binding site 3 out of 3 in the Cryoem Structure of SPCA1A 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 SPCA1A in E2P State within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:3.7 occ:1.00 F3 A:BEF1001 0.0 3.7 1.0 BE A:BEF1001 1.5 3.7 1.0 OD1 A:ASP350 2.3 2.5 1.0 F2 A:BEF1001 2.5 3.7 1.0 F1 A:BEF1001 2.5 3.7 1.0 NZ A:LYS625 2.8 3.2 1.0 ND2 A:ASN647 2.9 4.8 1.0 CG A:ASP350 3.2 2.5 1.0 CG A:ASN647 3.7 4.8 1.0 OG1 A:THR570 3.7 2.9 1.0 OD2 A:ASP350 3.7 2.5 1.0 OD1 A:ASN647 3.8 4.8 1.0 CE A:LYS625 3.9 3.2 1.0 CA A:GLY190 3.9 8.3 1.0 N A:GLY571 3.9 3.6 1.0 MG A:MG1002 4.1 3.0 1.0 CA A:THR570 4.1 2.9 1.0 OD1 A:ASP648 4.2 4.6 1.0 OD2 A:ASP648 4.2 4.6 1.0 CB A:ASP350 4.3 2.5 1.0 CB A:THR570 4.4 2.9 1.0 N A:GLY190 4.4 8.3 1.0 C A:THR570 4.6 2.9 1.0 CG A:ASP648 4.6 4.6 1.0 O A:THR189 4.6 10.3 1.0 C A:THR189 4.7 10.3 1.0 O A:ILE569 4.7 2.2 1.0 CA A:ASP350 4.9 2.5 1.0 CA A:GLY571 4.9 3.6 1.0 CB A:ASN647 5.0 4.8 1.0

Z.Chen, S.Watanabe, H.Hashida, M.Inoue, Y.Daigaku, M.Kikkawa, K.Inaba. Cryo-Em Structures of Human SPCA1A Reveal the Mechanism of Ca 2+ /Mn 2+ Transport Into the Golgi Apparatus. Sci Adv V. 9 D9742 2023.
ISSN: ESSN 2375-2548
PubMed: 36867705
DOI: 10.1126/SCIADV.ADD9742