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

Enzymatic activity of Cryo-Em Structure of PSS1 with Calcium

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of PSS1 with Calcium (pdb code 9kqj). 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: 9kqj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 9kqj

Go back to Calcium Binding Sites List in 9kqj
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:69.6
occ:1.00
OE1 A:GLU200 2.3 67.7 1.0
OE2 A:GLU197 2.4 63.4 1.0
OE1 A:GLN217 2.8 81.1 1.0
CD A:GLU197 3.1 59.0 1.0
OE1 A:GLU197 3.1 56.9 1.0
CD A:GLU200 3.4 68.0 1.0
OD2 A:ASP221 3.6 78.2 1.0
OE2 A:GLU200 3.8 69.4 1.0
CD A:GLN217 3.8 84.8 1.0
NE2 A:GLN217 4.1 83.7 1.0
CG A:ASP221 4.2 81.4 1.0
CB A:ASP221 4.3 79.0 1.0
NE1 A:TRP196 4.4 54.9 1.0
CG A:GLU197 4.6 53.6 1.0
CG A:GLU200 4.7 61.6 1.0
CD1 A:TRP196 4.8 49.7 1.0
CB A:GLU200 4.8 55.5 1.0
CE1 A:HIS172 5.0 71.8 1.0

Calcium binding site 2 out of 2 in 9kqj

Go back to Calcium Binding Sites List in 9kqj
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:Ca511

b:64.1
occ:1.00
OE1 B:GLU197 2.3 65.8 1.0
OE1 B:GLU200 2.4 68.5 1.0
OE2 B:GLU197 2.8 60.8 1.0
CD B:GLU197 2.9 63.3 1.0
OE1 B:GLN217 3.2 85.1 1.0
OD2 B:ASP221 3.2 77.4 1.0
CD B:GLU200 3.3 68.2 1.0
OE2 B:GLU200 3.7 69.5 1.0
CG B:ASP221 4.2 79.9 1.0
CD B:GLN217 4.3 88.1 1.0
CG B:GLU197 4.4 57.1 1.0
NE1 B:TRP196 4.5 55.1 1.0
CG B:GLU200 4.6 60.3 1.0
NE2 B:GLN217 4.6 87.5 1.0
CB B:ASP221 4.7 76.8 1.0
CE1 B:HIS172 4.7 71.8 1.0
CB B:GLU200 4.8 56.0 1.0
CD1 B:TRP196 4.9 50.2 1.0

Reference:

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
Page generated: Thu Jul 10 10:12:42 2025

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