Atomistry » Calcium » PDB 8q5n-8r1b » 8qod
Atomistry »
  Calcium »
    PDB 8q5n-8r1b »
      8qod »

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 Oct 31 17:11:19 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy