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Calcium in PDB 2pr3: Factor Xa Inhibitor

Enzymatic activity of Factor Xa Inhibitor

All present enzymatic activity of Factor Xa Inhibitor:
3.4.21.6;

Protein crystallography data

The structure of Factor Xa Inhibitor, PDB code: 2pr3 was solved by E.Zhang, J.T.Kohrt, C.F.Bigge, B.C.Finzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.485, 72.354, 77.880, 90.00, 90.00, 90.00
R / Rfree (%) 25.5 / 26.7

Other elements in 2pr3:

The structure of Factor Xa Inhibitor also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Factor Xa Inhibitor (pdb code 2pr3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Factor Xa Inhibitor, PDB code: 2pr3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2pr3

Go back to Calcium Binding Sites List in 2pr3
Calcium binding site 1 out of 2 in the Factor Xa Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Factor Xa Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:26.1
occ:1.00
O A:ASN72 2.2 28.6 1.0
OE1 A:GLU80 2.4 30.1 1.0
OD1 A:ASP70 2.4 22.7 1.0
O A:GLN75 2.6 57.8 1.0
C A:ASN72 3.3 27.6 1.0
CG A:ASP70 3.4 23.4 1.0
CD A:GLU80 3.4 28.2 1.0
OD2 A:ASP70 3.8 22.2 1.0
CG A:GLU80 3.8 26.3 1.0
C A:GLN75 3.8 57.4 1.0
N A:GLU77 3.9 53.4 1.0
OE1 A:GLU76 4.0 64.5 1.0
N A:ASN72 4.0 25.1 1.0
O A:HOH1115 4.0 48.8 1.0
CA A:ASN72 4.1 27.8 1.0
CA A:GLU76 4.2 57.0 1.0
CB A:ASN72 4.2 29.2 1.0
N A:THR73 4.3 29.4 1.0
OE2 A:GLU80 4.5 29.6 1.0
N A:GLU76 4.5 57.5 1.0
CB A:GLU77 4.5 52.5 1.0
CA A:THR73 4.5 32.6 1.0
C A:GLU76 4.6 55.1 1.0
N A:ARG71 4.6 20.3 1.0
CB A:ASP70 4.7 18.6 1.0
C A:THR73 4.8 36.5 1.0
N A:GLU74 4.8 41.5 1.0
CA A:ASP70 4.9 19.3 1.0
CA A:GLU77 4.9 51.0 1.0
O A:HOH1080 4.9 86.1 1.0
N A:GLN75 5.0 53.6 1.0

Calcium binding site 2 out of 2 in 2pr3

Go back to Calcium Binding Sites List in 2pr3
Calcium binding site 2 out of 2 in the Factor Xa Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Factor Xa Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:34.0
occ:1.00
O A:LYS224 2.3 21.5 1.0
O A:ARG222 2.4 26.3 1.0
O A:TYR185 2.5 20.9 1.0
O A:ASP185A 2.7 24.6 1.0
O A:HOH1036 3.0 25.1 1.0
C A:ASP185A 3.4 25.4 1.0
C A:ARG222 3.4 26.2 1.0
C A:LYS224 3.4 20.6 1.0
C A:TYR185 3.6 22.7 1.0
N A:LYS224 3.7 24.3 1.0
CA A:ASP185A 3.8 27.4 1.0
N A:ARG222 4.0 22.1 1.0
CA A:LYS224 4.1 20.8 1.0
C A:ALA221 4.1 21.9 1.0
N A:LYS223 4.1 25.9 1.0
CA A:LYS223 4.1 26.7 1.0
N A:GLY223A 4.2 25.2 1.0
N A:ASP185A 4.2 23.8 1.0
O A:ALA221 4.3 24.1 1.0
N A:THR185B 4.3 28.2 1.0
CA A:ARG222 4.3 24.8 1.0
O A:HOH1029 4.4 22.3 1.0
C A:LYS223 4.4 25.6 1.0
N A:TYR225 4.5 19.4 1.0
CA A:ALA221 4.5 20.7 1.0
CB A:LYS224 4.6 22.0 1.0
O A:LYS186 4.6 25.9 1.0
C A:GLY223A 4.7 26.4 1.0
CA A:THR185B 4.8 30.2 1.0
CA A:TYR185 4.8 23.0 1.0
CA A:TYR225 4.8 19.4 1.0
CA A:GLY223A 5.0 25.4 1.0

Reference:

C.A.Van Huis, C.F.Bigge, A.Casimiro-Garcia, W.L.Cody, D.A.Dudley, K.J.Filipski, R.J.Heemstra, J.T.Kohrt, L.S.Narasimhan, R.P.Schaum, E.Zhang, J.W.Bryant, S.Haarer, N.Janiczek, R.J.Leadley, T.Mcclanahan, J.Thomas Peterson, K.M.Welch, J.J.Edmunds. Structure-Based Drug Design of Pyrrolidine-1, 2-Dicarboxamides As A Novel Series of Orally Bioavailable Factor Xa Inhibitors Chem.Biol.Drug Des. V. 69 444 2007.
ISSN: ISSN 1747-0277
PubMed: 17581239
DOI: 10.1111/J.1747-0285.2007.00520.X
Page generated: Sat Dec 12 03:50:15 2020

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