Calcium in PDB 8eph: Crystal Structure of Human Coagulation Factor Ixa (S195A), Apo-Form, Des-Gla

The structure of Crystal Structure of Human Coagulation Factor Ixa (S195A), Apo-Form, Des-Gla, PDB code: 8eph was solved by V.N.Kolyadko, S.Krishnaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	78.16 / 1.88
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.247, 90.247, 156.347, 90, 90, 90
R / Rfree (%)	18.4 / 21.1

The binding sites of Calcium atom in the Crystal Structure of Human Coagulation Factor Ixa (S195A), Apo-Form, Des-Gla (pdb code 8eph). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Coagulation Factor Ixa (S195A), Apo-Form, Des-Gla, PDB code: 8eph:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human Coagulation Factor Ixa (S195A), Apo-Form, Des-Gla


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Coagulation Factor Ixa (S195A), Apo-Form, Des-Gla within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:51.9 occ:1.00 O A:HOH353 2.2 38.8 1.0 O A:ASP65 2.3 26.1 1.0 OE1 A:GLN50 2.5 42.7 1.0 OD2 A:ASP64 2.6 50.0 1.0 O A:GLY48 2.7 50.1 1.0 OD1 A:ASP64 2.7 51.6 1.0 CG A:ASP64 3.0 40.3 1.0 OD2 A:ASP47 3.2 74.3 1.0 OD1 A:ASP47 3.2 82.7 1.0 C A:ASP65 3.5 29.0 1.0 CD A:GLN50 3.5 46.6 1.0 CG A:ASP47 3.5 83.8 1.0 N A:ASN67 3.8 38.2 1.0 NE2 A:GLN50 3.9 45.8 1.0 C A:GLY48 3.9 57.1 1.0 CA A:ILE66 4.1 38.8 1.0 N A:ILE66 4.2 31.6 1.0 N A:ASP65 4.3 26.3 1.0 C A:ILE66 4.4 41.8 1.0 CB A:ASP64 4.4 33.2 1.0 CA A:ASP65 4.5 26.4 1.0 N A:GLN50 4.5 38.2 1.0 O A:SER68 4.5 25.5 1.0 C A:ASP64 4.6 28.1 1.0 CA A:ASP49 4.6 48.5 1.0 N A:GLY48 4.7 69.9 1.0 N A:ASP49 4.7 51.0 1.0 CA A:ASN67 4.7 40.5 1.0 CG A:GLN50 4.9 44.2 1.0 CA A:ASP64 4.9 27.0 1.0 N A:SER68 4.9 34.5 1.0 CA A:GLY48 4.9 61.5 1.0 CB A:ASP47 5.0 83.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human Coagulation Factor Ixa (S195A), Apo-Form, Des-Gla


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Coagulation Factor Ixa (S195A), Apo-Form, Des-Gla within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:29.8 occ:1.00 O B:HOH447 2.2 26.2 1.0 OE1 B:GLU70 2.3 24.2 1.0 OE1 B:GLU77 2.3 37.1 1.0 O B:ASN72 2.3 29.0 1.0 O B:GLU75 2.3 40.9 1.0 OE2 B:GLU80 2.3 29.6 1.0 CD B:GLU70 3.3 24.2 1.0 C B:ASN72 3.4 28.1 1.0 CD B:GLU80 3.4 28.0 1.0 CD B:GLU77 3.5 38.3 1.0 C B:GLU75 3.5 42.9 1.0 OE2 B:GLU70 3.6 28.0 1.0 CG B:GLU80 3.9 26.5 1.0 N B:ASN72 4.0 26.8 1.0 N B:GLU77 4.1 29.9 1.0 CA B:ASN72 4.2 28.5 1.0 N B:GLU75 4.3 42.9 1.0 CG B:GLU77 4.3 33.6 1.0 N B:THR76 4.3 40.6 1.0 CA B:THR76 4.3 38.0 1.0 OE2 B:GLU77 4.3 38.3 1.0 N B:ILE73 4.4 30.6 1.0 CA B:GLU75 4.4 44.0 1.0 CB B:GLU77 4.4 33.5 1.0 N B:HIS71 4.4 25.8 1.0 CA B:ILE73 4.5 35.8 1.0 OE1 B:GLU80 4.6 28.1 1.0 CG B:GLU70 4.6 24.6 1.0 CB B:ASN72 4.7 28.4 1.0 C B:THR76 4.7 34.2 1.0 C B:ILE73 4.7 38.3 1.0 C B:HIS71 4.9 27.2 1.0 N B:GLU74 5.0 40.6 1.0 CA B:GLU77 5.0 31.2 1.0 CB B:GLU75 5.0 48.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human Coagulation Factor Ixa (S195A), Apo-Form, Des-Gla


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Coagulation Factor Ixa (S195A), Apo-Form, Des-Gla within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:53.2 occ:1.00 O C:ASP65 2.4 29.3 1.0 OE1 C:GLN50 2.5 43.3 1.0 OD2 C:ASP64 2.5 46.2 1.0 O C:HOH369 2.6 42.7 1.0 O C:GLY48 2.6 48.9 1.0 OD1 C:ASP64 2.6 43.2 1.0 CG C:ASP64 2.9 37.2 1.0 OD2 C:ASP47 3.2 77.0 1.0 OD1 C:ASP47 3.3 77.3 1.0 CD C:GLN50 3.5 45.3 1.0 C C:ASP65 3.6 29.5 1.0 CG C:ASP47 3.6 82.1 1.0 C C:GLY48 3.8 59.1 1.0 NE2 C:GLN50 3.8 47.5 1.0 N C:ASN67 3.9 36.8 1.0 CA C:ILE66 4.2 40.0 1.0 N C:ASP65 4.3 25.4 1.0 N C:ILE66 4.3 34.8 1.0 CB C:ASP64 4.3 31.3 1.0 N C:GLN50 4.4 37.1 1.0 CA C:ASP49 4.5 46.4 1.0 C C:ILE66 4.5 39.8 1.0 C C:ASP64 4.6 26.8 1.0 CA C:ASP65 4.6 27.0 1.0 O C:SER68 4.6 25.1 1.0 N C:ASP49 4.6 48.1 1.0 N C:GLY48 4.7 71.3 1.0 CA C:ASN67 4.8 40.5 1.0 CG C:GLN50 4.8 42.1 1.0 CA C:ASP64 4.9 26.5 1.0 CA C:GLY48 4.9 63.8 1.0 N C:SER68 5.0 31.7 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human Coagulation Factor Ixa (S195A), Apo-Form, Des-Gla


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Coagulation Factor Ixa (S195A), Apo-Form, Des-Gla within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:25.6 occ:1.00 OE1 D:GLU77 2.3 32.7 1.0 O D:GLU75 2.3 31.4 1.0 OE1 D:GLU70 2.3 20.8 1.0 O D:ASN72 2.3 24.6 1.0 O D:HOH417 2.3 24.8 1.0 OE2 D:GLU80 2.3 23.3 1.0 CD D:GLU77 2.9 36.7 1.0 OE2 D:GLU77 3.1 46.2 1.0 CD D:GLU70 3.3 23.6 1.0 C D:ASN72 3.4 25.8 1.0 C D:GLU75 3.4 33.9 1.0 CD D:GLU80 3.4 23.1 1.0 OE2 D:GLU70 3.6 24.4 1.0 CG D:GLU80 3.9 21.3 1.0 N D:ASN72 4.0 25.2 1.0 N D:GLU77 4.1 27.2 1.0 CA D:ASN72 4.2 25.3 1.0 CG D:GLU77 4.3 34.9 1.0 N D:THR76 4.3 33.3 1.0 CA D:THR76 4.3 34.3 1.0 N D:GLU75 4.3 34.7 1.0 N D:ILE73 4.4 26.7 1.0 O D:HOH520 4.4 35.6 1.0 CA D:GLU75 4.4 36.9 1.0 CA D:ILE73 4.4 30.4 1.0 N D:HIS71 4.5 22.2 1.0 CB D:GLU77 4.5 32.3 1.0 OE1 D:GLU80 4.5 22.7 1.0 CG D:GLU70 4.6 22.7 1.0 C D:THR76 4.6 31.1 1.0 CB D:ASN72 4.7 27.3 1.0 C D:ILE73 4.7 32.1 1.0 CA D:GLU77 5.0 28.7 1.0 C D:HIS71 5.0 23.8 1.0 N D:GLU74 5.0 33.0 1.0

V.N.Kolyadko, J.M.Layzer, K.Perry, B.A.Sullenger, S.Krishnaswamy. Allosteric Control of Coagulation Factor Ixa Via Its Exosite II Regulates Blood Clotting Proc.Natl.Acad.Sci.Usa 2024.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.2401136121