Calcium in PDB 8epk: Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A)

The structure of Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A), PDB code: 8epk 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)	60.24 / 2.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.496, 79.579, 84.317, 90, 101.78, 90
R / Rfree (%)	23.1 / 26.1

The structure of Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A) also contains other interesting chemical elements:

Fluorine	(F)	22 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Calcium atom in the Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A) (pdb code 8epk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A), PDB code: 8epk:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:128.0 occ:1.00 OE2 B:GLU70 2.3 105.0 1.0 O B:GLU75 2.4 122.8 1.0 O B:ASN72 2.5 113.9 1.0 OE2 B:GLU80 2.6 111.5 1.0 OE1 B:GLU77 3.0 115.8 1.0 CD B:GLU70 3.2 101.6 1.0 OE1 B:GLU70 3.4 101.8 1.0 CD B:GLU80 3.5 110.5 1.0 C B:GLU75 3.5 126.5 1.0 C B:ASN72 3.6 112.6 1.0 CD B:GLU77 3.8 116.7 1.0 OE2 B:GLU77 3.8 116.0 1.0 CA B:ILE73 3.9 110.9 1.0 CG B:GLU80 4.1 105.6 1.0 C B:ILE73 4.2 115.8 1.0 CA B:THR76 4.2 126.5 1.0 N B:ILE73 4.2 111.2 1.0 O B:ILE73 4.3 116.3 1.0 N B:THR76 4.3 128.6 1.0 OE1 B:GLU80 4.3 113.7 1.0 N B:GLU75 4.4 126.9 1.0 CG B:GLU70 4.6 98.0 1.0 CA B:GLU75 4.6 129.7 1.0 N B:ASN72 4.8 110.0 1.0 N B:GLU77 4.8 123.0 1.0 CA B:ASN72 4.8 112.9 1.0 N B:GLU74 4.8 119.9 1.0

Calcium binding site 2 out of 2 in the Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:124.1 occ:1.00 O D:GLU75 2.3 123.0 1.0 OE2 D:GLU70 2.3 111.9 1.0 O D:ASN72 2.4 116.4 1.0 OE2 D:GLU80 2.7 109.6 1.0 OE1 D:GLU77 2.8 119.4 1.0 CD D:GLU70 3.3 107.7 1.0 C D:GLU75 3.4 126.8 1.0 CD D:GLU80 3.5 109.3 1.0 C D:ASN72 3.5 115.5 1.0 CD D:GLU77 3.5 121.2 1.0 OE2 D:GLU77 3.6 120.8 1.0 OE1 D:GLU70 3.6 107.0 1.0 CA D:ILE73 4.0 111.6 1.0 CA D:THR76 4.1 127.8 1.0 CG D:GLU80 4.1 104.8 1.0 N D:THR76 4.1 129.6 1.0 N D:ILE73 4.2 113.2 1.0 C D:ILE73 4.2 115.1 1.0 OE1 D:GLU80 4.3 113.0 1.0 N D:GLU75 4.3 126.5 1.0 O D:ILE73 4.3 114.3 1.0 CA D:GLU75 4.5 129.7 1.0 N D:GLU77 4.6 126.0 1.0 N D:ASN72 4.6 115.6 1.0 CA D:ASN72 4.6 117.4 1.0 CG D:GLU70 4.7 104.6 1.0 N D:GLU74 4.8 119.2 1.0 C D:THR76 4.8 129.5 1.0 CG D:GLU77 4.9 124.7 1.0 N D:HIS71 5.0 109.2 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