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Calcium in PDB 1xkb: Factor Xa Complexed with A Synthetic Inhibitor Fx-2212A,(2S)-(3'- Amidino-3-Biphenylyl)-5-(4-Pyridylamino)Pentanoic Acid

Enzymatic activity of Factor Xa Complexed with A Synthetic Inhibitor Fx-2212A,(2S)-(3'- Amidino-3-Biphenylyl)-5-(4-Pyridylamino)Pentanoic Acid

All present enzymatic activity of Factor Xa Complexed with A Synthetic Inhibitor Fx-2212A,(2S)-(3'- Amidino-3-Biphenylyl)-5-(4-Pyridylamino)Pentanoic Acid:
3.4.21.6;

Protein crystallography data

The structure of Factor Xa Complexed with A Synthetic Inhibitor Fx-2212A,(2S)-(3'- Amidino-3-Biphenylyl)-5-(4-Pyridylamino)Pentanoic Acid, PDB code: 1xkb was solved by K.Kamata, S.H.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.270, 105.220, 63.240, 90.00, 103.40, 90.00
R / Rfree (%) 20.6 / 29.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Factor Xa Complexed with A Synthetic Inhibitor Fx-2212A,(2S)-(3'- Amidino-3-Biphenylyl)-5-(4-Pyridylamino)Pentanoic Acid (pdb code 1xkb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Factor Xa Complexed with A Synthetic Inhibitor Fx-2212A,(2S)-(3'- Amidino-3-Biphenylyl)-5-(4-Pyridylamino)Pentanoic Acid, PDB code: 1xkb:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1xkb

Go back to Calcium Binding Sites List in 1xkb
Calcium binding site 1 out of 3 in the Factor Xa Complexed with A Synthetic Inhibitor Fx-2212A,(2S)-(3'- Amidino-3-Biphenylyl)-5-(4-Pyridylamino)Pentanoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Factor Xa Complexed with A Synthetic Inhibitor Fx-2212A,(2S)-(3'- Amidino-3-Biphenylyl)-5-(4-Pyridylamino)Pentanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:66.4
occ:1.00
 O A:LEU65 2.8 52.7 1.0
OE1 A:GLN49 2.9 54.4 1.0
OD1 A:BHD63 3.0 48.6 1.0
O A:GLY64 3.3 49.6 1.0
OD2 A:BHD63 3.3 50.8 1.0
CA A:GLY66 3.3 47.5 1.0
CG A:BHD63 3.5 49.7 1.0
C A:LEU65 3.5 51.9 1.0
N A:GLY66 3.8 49.7 1.0
C A:GLY66 3.8 46.5 1.0
CD A:GLN49 3.8 54.3 1.0
N A:GLU67 3.9 44.0 1.0
CG A:GLN49 4.1 52.6 1.0
C A:GLY64 4.4 51.3 1.0
O A:GLY66 4.6 46.1 1.0
CA A:LEU65 4.8 52.3 1.0

Calcium binding site 2 out of 3 in 1xkb

Go back to Calcium Binding Sites List in 1xkb
Calcium binding site 2 out of 3 in the Factor Xa Complexed with A Synthetic Inhibitor Fx-2212A,(2S)-(3'- Amidino-3-Biphenylyl)-5-(4-Pyridylamino)Pentanoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Factor Xa Complexed with A Synthetic Inhibitor Fx-2212A,(2S)-(3'- Amidino-3-Biphenylyl)-5-(4-Pyridylamino)Pentanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:44.3
occ:1.00
 OD1 C:ASP70 2.5 31.8 1.0
O C:ASN72 2.6 37.4 1.0
OE2 C:GLU80 2.8 49.5 1.0
OE2 C:GLU77 2.9 49.1 1.0
O C:GLN75 2.9 53.5 1.0
CD C:GLU77 3.1 49.0 1.0
OE1 C:GLU76 3.1 63.4 1.0
OE1 C:GLU80 3.2 48.7 1.0
OE1 C:GLU77 3.2 50.6 1.0
CD C:GLU80 3.4 47.2 1.0
C C:ASN72 3.6 36.6 1.0
CG C:ASP70 3.7 33.0 1.0
C C:GLN75 3.8 52.6 1.0
CA C:GLU76 3.8 54.4 1.0
N C:GLU77 4.1 52.4 1.0
CG C:GLU77 4.1 49.5 1.0
CD C:GLU76 4.2 61.7 1.0
N C:GLU76 4.2 53.3 1.0
N C:ASN72 4.3 33.8 1.0
C C:GLU76 4.4 54.0 1.0
OD2 C:ASP70 4.4 35.2 1.0
N C:THR73 4.4 38.3 1.0
CA C:ASN72 4.4 35.3 1.0
CA C:THR73 4.5 40.8 1.0
C C:THR73 4.7 42.9 1.0
CB C:ASN72 4.8 35.4 1.0
O C:THR73 4.8 43.3 1.0
N C:ARG71 4.8 33.4 1.0
CB C:ASP70 4.8 33.7 1.0
OE2 C:GLU76 4.8 63.5 1.0
CB C:GLU76 4.8 56.1 1.0
CG C:GLU80 4.9 45.4 1.0
CA C:ASP70 4.9 33.0 1.0
N C:GLN75 5.0 49.0 1.0

Calcium binding site 3 out of 3 in 1xkb

Go back to Calcium Binding Sites List in 1xkb
Calcium binding site 3 out of 3 in the Factor Xa Complexed with A Synthetic Inhibitor Fx-2212A,(2S)-(3'- Amidino-3-Biphenylyl)-5-(4-Pyridylamino)Pentanoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Factor Xa Complexed with A Synthetic Inhibitor Fx-2212A,(2S)-(3'- Amidino-3-Biphenylyl)-5-(4-Pyridylamino)Pentanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:51.0
occ:1.00
 O D:GLN75 2.6 53.7 1.0
OD1 D:ASP70 2.6 28.5 1.0
OE1 D:GLU80 2.6 60.2 1.0
O D:ASN72 2.9 33.9 1.0
OE2 D:GLU77 3.0 47.9 1.0
CG D:GLU77 3.1 48.8 1.0
CD D:GLU77 3.4 48.1 1.0
CG D:ASP70 3.7 28.4 1.0
N D:GLU77 3.7 53.7 1.0
C D:GLN75 3.7 53.2 1.0
CD D:GLU80 3.8 58.0 1.0
C D:ASN72 3.8 33.6 1.0
CA D:GLU76 4.0 54.9 1.0
N D:ASN72 4.1 32.2 1.0
OD2 D:ASP70 4.3 28.4 1.0
C D:GLU76 4.3 54.8 1.0
N D:GLU76 4.3 53.5 1.0
CB D:GLU77 4.4 51.2 1.0
OE2 D:GLU80 4.4 62.1 1.0
CA D:ASN72 4.5 33.0 1.0
N D:ARG71 4.5 30.7 1.0
OE1 D:GLU77 4.6 48.4 1.0
CA D:ASP70 4.6 27.6 1.0
CA D:GLU77 4.6 51.8 1.0
CB D:ASN72 4.7 32.6 1.0
CB D:ASP70 4.7 26.4 1.0
N D:THR73 4.8 35.7 1.0
N D:GLN75 4.8 50.9 1.0
CB D:GLU80 4.8 47.4 1.0
N D:GLY78 4.9 49.9 1.0
CA D:GLN75 4.9 52.7 1.0
CG D:GLU80 4.9 53.7 1.0

Reference:

K.Kamata, H.Kawamoto, T.Honma, T.Iwama, S.H.Kim. Structural Basis For Chemical Inhibition of Human Blood Coagulation Factor Xa. Proc.Natl.Acad.Sci.Usa V. 95 6630 1998.
ISSN: ISSN 0027-8424
PubMed: 9618463
DOI: 10.1073/PNAS.95.12.6630
Page generated: Sat Dec 12 03:27:22 2020

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