Calcium in PDB 9kqi: Cryo-Em Structure of PSS1 with Calcium

All present enzymatic activity of Cryo-Em Structure of PSS1 with Calcium:
2.7.8.29;

The binding sites of Calcium atom in the Cryo-Em Structure of PSS1 with Calcium (pdb code 9kqi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryo-Em Structure of PSS1 with Calcium, PDB code: 9kqi:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of PSS1 with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of PSS1 with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca509 b:68.9 occ:1.00 OE1 A:GLU200 2.4 73.7 1.0 O A:SER511 2.5 79.9 1.0 OE1 A:GLN217 2.8 90.3 1.0 OE1 A:GLU197 3.0 64.9 1.0 NE2 A:GLN217 3.1 94.2 1.0 CD A:GLN217 3.2 94.2 1.0 CD A:GLU200 3.5 72.1 1.0 C A:SER511 3.5 80.5 1.0 OXT A:SER511 3.8 78.4 1.0 CD A:GLU197 3.9 60.6 1.0 OE2 A:GLU200 4.0 70.6 1.0 OD1 A:ASP221 4.0 87.3 1.0 OE2 A:GLU197 4.0 60.0 1.0 OD2 A:ASP221 4.1 88.0 1.0 CG A:ASP221 4.1 87.6 1.0 NE2 A:HIS172 4.3 86.2 1.0 NE1 A:TRP196 4.3 54.0 1.0 CG A:GLN217 4.4 94.7 1.0 CG A:GLU200 4.8 66.9 1.0 CA A:SER511 4.9 77.8 1.0 CD1 A:TRP196 4.9 53.2 1.0 CB A:GLU200 4.9 60.6 1.0 CD2 A:HIS172 4.9 83.0 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of PSS1 with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of PSS1 with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca510 b:68.2 occ:1.00 O B:SER512 2.4 78.4 1.0 OE1 B:GLU200 2.5 73.4 1.0 OE1 B:GLU197 2.8 68.8 1.0 OE1 B:GLN217 2.8 89.3 1.0 NE2 B:GLN217 3.0 92.5 1.0 CD B:GLN217 3.1 92.7 1.0 C B:SER512 3.5 78.8 1.0 CD B:GLU200 3.6 71.8 1.0 CD B:GLU197 3.7 64.8 1.0 OE2 B:GLU197 3.8 63.5 1.0 OXT B:SER512 3.8 76.3 1.0 OE2 B:GLU200 4.1 70.1 1.0 OD2 B:ASP221 4.1 87.0 1.0 CG B:GLN217 4.2 93.4 1.0 CG B:ASP221 4.3 86.3 1.0 NE2 B:HIS172 4.3 86.0 1.0 OD1 B:ASP221 4.3 86.0 1.0 NE1 B:TRP196 4.4 53.2 1.0 CE1 B:HIS172 4.7 83.5 1.0 CB B:GLN217 4.8 92.1 1.0 CG B:GLU200 4.8 67.8 1.0 CD1 B:TRP196 4.8 51.4 1.0 CA B:SER512 4.8 77.4 1.0 CB B:GLU200 4.9 60.4 1.0

Y.Ning, R.Xu, J.Yu, J.Ge. Structural Basis For Catalytic Mechanism of Human Phosphatidylserine Synthase 1. Cell Discov V. 11 20 2025.
ISSN: ESSN 2056-5968
PubMed: 40044636
DOI: 10.1038/S41421-025-00775-3