Calcium in PDB 9i24: Coagulation Factor Xa Complex with A2-Loop Peptide

The structure of Coagulation Factor Xa Complex with A2-Loop Peptide, PDB code: 9i24 was solved by J.A.Huntington, F.I.Ustok, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.38 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.473, 72.419, 82.335, 90, 90, 90
R / Rfree (%)	14.1 / 17.2

The structure of Coagulation Factor Xa Complex with A2-Loop Peptide also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Coagulation Factor Xa Complex with A2-Loop Peptide (pdb code 9i24). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Coagulation Factor Xa Complex with A2-Loop Peptide, PDB code: 9i24:

Calcium binding site 1 out of 1 in the Coagulation Factor Xa Complex with A2-Loop Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Coagulation Factor Xa Complex with A2-Loop Peptide within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca301 b:21.6 occ:0.60 O H:GLN75 2.2 31.1 1.0 O H:ASN72 2.3 20.0 1.0 OD1 H:ASP70 2.3 17.1 1.0 OE2 H:GLU80 2.3 25.3 1.0 O H:HOH485 2.4 21.9 1.0 O H:HOH416 2.6 26.0 1.0 CG H:ASP70 3.3 14.7 1.0 C H:ASN72 3.3 18.4 1.0 C H:GLN75 3.4 30.5 1.0 CD H:GLU80 3.4 25.2 1.0 OD2 H:ASP70 3.7 17.1 1.0 CG H:GLU80 3.8 22.5 1.0 N H:ASN72 3.8 18.9 1.0 CA H:ASN72 4.0 20.2 1.0 N H:GLU77 4.1 32.8 1.0 CA H:GLU76 4.1 32.4 1.0 N H:GLU76 4.2 32.7 1.0 O H:HOH590 4.2 40.5 1.0 CB H:ASN72 4.2 23.6 1.0 N H:THR73 4.3 17.1 1.0 N H:GLN75 4.3 27.5 1.0 CA H:GLN75 4.4 32.8 1.0 CA H:THR73 4.4 16.9 1.0 OE1 H:GLU80 4.5 27.1 1.0 N H:ARG71 4.5 17.2 1.0 CB H:ASP70 4.6 14.6 1.0 C H:GLU76 4.6 33.7 1.0 CG H:GLU77 4.6 41.3 1.0 OE1 H:GLU77 4.6 39.8 1.0 O H:HOH490 4.6 30.2 1.0 CB H:GLU77 4.7 39.5 1.0 C H:THR73 4.7 20.2 1.0 CA H:ASP70 4.8 14.4 1.0 CG H:GLN75 4.8 39.6 1.0 CD H:GLU77 4.8 43.6 1.0 C H:ARG71 4.9 20.1 1.0 CG H:ASN72 5.0 24.2 1.0

F.I.Ustok, A.Faille, J.A.Huntington. A 3.3- Angstrom Cryo-Em Structure of An Engineered High-Affinity Human Prothrombinase Complex. Blood 2025.
ISSN: ESSN 1528-0020
PubMed: 41144779
DOI: 10.1182/BLOOD.2025031527