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Calcium in PDB 8qod: Crystal Structure of Fviia in Complex with A Benzamidine-Based Inhibitor

Enzymatic activity of Crystal Structure of Fviia in Complex with A Benzamidine-Based Inhibitor

All present enzymatic activity of Crystal Structure of Fviia in Complex with A Benzamidine-Based Inhibitor:
3.4.21.21;

Protein crystallography data

The structure of Crystal Structure of Fviia in Complex with A Benzamidine-Based Inhibitor, PDB code: 8qod was solved by H.A.Schreuder, A.Liesum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.88 / 1.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.811, 81.51, 125.498, 90, 90, 90
R / Rfree (%) 18.2 / 21.4

Other elements in 8qod:

The structure of Crystal Structure of Fviia in Complex with A Benzamidine-Based Inhibitor also contains other interesting chemical elements:

Bromine (Br) 1 atom
Chlorine (Cl) 2 atoms
Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Fviia in Complex with A Benzamidine-Based Inhibitor (pdb code 8qod). 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 Fviia in Complex with A Benzamidine-Based Inhibitor, PDB code: 8qod:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8qod

Go back to Calcium Binding Sites List in 8qod
Calcium binding site 1 out of 4 in the Crystal Structure of Fviia in Complex with A Benzamidine-Based Inhibitor


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 Fviia in Complex with A Benzamidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:23.1
occ:0.31
 O A:HOH342 2.2 44.8 1.0
OD2 A:ASP63 2.3 47.6 1.0
OD1 A:ASP63 2.5 45.1 1.0
O A:GLY47 2.5 47.6 1.0
OD1 A:ASP46 2.5 56.1 1.0
O A:HOH336 2.5 52.8 1.0
O A:GLN64 2.6 35.8 1.0
CG A:ASP63 2.6 43.3 1.0
O C:HOH604 2.9 76.4 1.0
CG A:ASP46 3.7 55.4 1.0
C A:GLN64 3.7 34.6 1.0
C A:GLY47 3.7 47.2 1.0
CB A:ASP63 4.1 33.7 1.0
N A:GLN64 4.1 29.3 1.0
CB A:ASP46 4.2 49.9 1.0
CA A:ASP48 4.3 45.4 1.0
O A:HOH304 4.3 53.4 1.0
N A:GLN49 4.4 42.2 1.0
O A:SER67 4.4 25.7 1.0
N A:GLN66 4.4 36.9 1.0
O A:ASP46 4.5 48.2 1.0
N A:ASP48 4.5 46.1 1.0
C A:ASP46 4.5 47.9 1.0
CA A:GLN64 4.5 30.6 1.0
N A:LEU65 4.6 36.3 1.0
CA A:LEU65 4.6 38.1 1.0
O A:HOH463 4.6 76.5 1.0
C A:ASP63 4.7 29.2 1.0
N A:GLY47 4.7 47.3 1.0
OD2 A:ASP46 4.7 57.7 1.0
CA A:ASP63 4.8 29.2 1.0
CA A:GLY47 4.8 47.4 1.0
C A:ASP48 4.9 43.9 1.0
C A:LEU65 5.0 38.2 1.0

Calcium binding site 2 out of 4 in 8qod

Go back to Calcium Binding Sites List in 8qod
Calcium binding site 2 out of 4 in the Crystal Structure of Fviia in Complex with A Benzamidine-Based Inhibitor


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 Fviia in Complex with A Benzamidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:23.6
occ:0.30
 OE11 A:CGU29 2.1 32.2 1.0
OE12 A:CGU25 2.1 35.4 1.0
OE22 A:CGU25 2.1 37.7 1.0
O A:HOH420 2.1 38.4 1.0
OE21 A:CGU29 2.2 34.9 1.0
CD1 A:CGU29 3.0 32.5 1.0
CD2 A:CGU29 3.0 34.8 1.0
CD1 A:CGU25 3.0 35.6 1.0
CD2 A:CGU25 3.1 37.4 1.0
CG A:CGU29 3.2 33.1 1.0
CG A:CGU25 3.3 36.2 1.0
O A:HOH353 4.0 32.4 1.0
NH2 A:ARG28 4.0 39.0 1.0
O A:HOH481 4.1 70.7 1.0
O A:HOH448 4.1 38.5 1.0
OE12 A:CGU29 4.2 32.0 1.0
OE11 A:CGU25 4.2 35.3 1.0
OE21 A:CGU25 4.2 38.0 1.0
OE22 A:CGU29 4.3 35.7 1.0
O A:HOH357 4.7 36.9 1.0
CB A:CGU29 4.8 32.0 1.0
O A:CGU25 4.8 33.1 1.0
CB A:CGU25 4.8 35.7 1.0

Calcium binding site 3 out of 4 in 8qod

Go back to Calcium Binding Sites List in 8qod
Calcium binding site 3 out of 4 in the Crystal Structure of Fviia in Complex with A Benzamidine-Based Inhibitor


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 Fviia in Complex with A Benzamidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:95.0
occ:1.00
 OE21 A:CGU14 2.2 56.1 1.0
OE12 A:CGU19 2.2 59.7 1.0
OE21 A:CGU19 2.5 59.7 1.0
OE12 A:CGU14 2.9 56.0 1.0
CD1 A:CGU19 3.1 59.7 1.0
CD2 A:CGU14 3.1 55.9 1.0
CD2 A:CGU19 3.2 59.6 1.0
CG A:CGU14 3.4 55.4 1.0
CD1 A:CGU14 3.5 55.8 1.0
CG A:CGU19 3.5 59.2 1.0
OE22 A:CGU19 4.2 59.7 1.0
OE11 A:CGU19 4.2 60.0 1.0
OE22 A:CGU14 4.4 55.9 1.0
OE11 A:CGU14 4.6 56.1 1.0
CB A:CGU14 5.0 54.4 1.0

Calcium binding site 4 out of 4 in 8qod

Go back to Calcium Binding Sites List in 8qod
Calcium binding site 4 out of 4 in the Crystal Structure of Fviia in Complex with A Benzamidine-Based Inhibitor


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 Fviia in Complex with A Benzamidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:21.0
occ:0.60
 OE2 B:GLU80 2.1 24.0 1.0
O B:GLU75 2.1 20.9 1.0
O B:HOH622 2.1 16.3 1.0
O B:ASP72 2.2 16.8 1.0
OE1 B:GLU70 2.2 16.7 1.0
O B:HOH428 2.3 21.1 1.0
CD B:GLU70 3.1 18.0 1.0
CD B:GLU80 3.1 24.6 1.0
C B:GLU75 3.2 21.5 1.0
C B:ASP72 3.3 16.2 1.0
OE2 B:GLU70 3.4 20.9 1.0
N B:ASP72 3.7 15.8 1.0
OE1 B:GLU80 3.8 25.1 1.0
CA B:HIS76 3.9 22.2 1.0
N B:HIS76 4.0 21.0 1.0
CA B:ASP72 4.0 15.8 1.0
O B:HOH504 4.1 19.3 1.0
N B:LEU73 4.2 15.5 1.0
N B:GLU75 4.2 20.7 1.0
CG B:GLU80 4.2 19.8 1.0
O B:HOH581 4.3 27.4 1.0
CA B:GLU75 4.3 21.0 1.0
N B:HIS71 4.4 15.2 1.0
CA B:LEU73 4.4 16.6 1.0
CB B:ASP72 4.4 16.9 1.0
CG B:GLU70 4.5 14.8 1.0
ND1 B:HIS76 4.6 29.0 1.0
O B:HOH411 4.6 42.2 1.0
C B:HIS76 4.7 22.9 1.0
C B:LEU73 4.7 18.5 1.0
N B:ASP77 4.7 21.5 1.0
C B:HIS71 4.8 15.7 1.0
CB B:GLU75 4.9 23.2 1.0

Reference:

L.Tesmer, H.Hans Matter, O.Klingler, M.Schudok, G.Hessler, A.R.Mehdipour, S.Guessregen, G.Hummer, H.A.Schreuder. Crystallography and Molecular Simulations Capture S1 Pocket Collapse in Allosteric Regulation of Factor Viia and Other Serine Proteases. To Be Published.
Page generated: Thu Jul 10 06:38:09 2025

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