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Calcium in PDB 5mhm: Fxiiia in Complex with the Inhibitor ZED1630

Enzymatic activity of Fxiiia in Complex with the Inhibitor ZED1630

All present enzymatic activity of Fxiiia in Complex with the Inhibitor ZED1630:
2.3.2.13;

Protein crystallography data

The structure of Fxiiia in Complex with the Inhibitor ZED1630, PDB code: 5mhm was solved by M.Stieler, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.88 / 2.12
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.912, 80.715, 103.190, 88.44, 76.60, 81.79
R / Rfree (%) 17 / 21.3

Other elements in 5mhm:

The structure of Fxiiia in Complex with the Inhibitor ZED1630 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Fxiiia in Complex with the Inhibitor ZED1630 (pdb code 5mhm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Fxiiia in Complex with the Inhibitor ZED1630, PDB code: 5mhm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5mhm

Go back to Calcium Binding Sites List in 5mhm
Calcium binding site 1 out of 6 in the Fxiiia in Complex with the Inhibitor ZED1630


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Fxiiia in Complex with the Inhibitor ZED1630 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:17.8
occ:1.00
O A:ALA264 2.3 14.2 1.0
OD1 A:ASN267 2.3 15.6 1.0
O A:LYS269 2.3 19.1 1.0
O A:ASN267 2.4 17.2 1.0
OD1 A:ASP271 2.5 29.5 1.0
O A:HOH982 2.5 17.4 1.0
OD2 A:ASP271 2.5 23.3 1.0
CG A:ASP271 2.8 27.4 1.0
CG A:ASN267 3.2 16.7 1.0
C A:ALA264 3.3 15.5 1.0
C A:ASN267 3.3 15.9 1.0
C A:LYS269 3.5 21.4 1.0
N A:LYS269 3.7 20.1 1.0
C A:ALA268 3.9 21.5 1.0
ND2 A:ASN267 3.9 18.3 1.0
CA A:LYS269 4.1 23.7 1.0
CA A:ALA264 4.1 15.1 1.0
CA A:ASN267 4.1 14.3 1.0
N A:ALA268 4.2 14.8 1.0
N A:MET265 4.2 15.4 1.0
CB A:ASP271 4.2 22.8 1.0
CB A:ASN267 4.2 15.4 1.0
CA A:MET265 4.3 15.4 1.0
N A:ASP271 4.3 21.6 1.0
N A:ASN267 4.3 17.4 1.0
O A:ALA268 4.3 21.7 1.0
O A:TYR407 4.4 17.5 1.0
CA A:ALA268 4.4 18.8 1.0
CB A:LYS269 4.5 33.1 1.0
CB A:ALA264 4.5 11.8 1.0
OD2 A:ASP270 4.5 23.3 1.0
CB A:ASP270 4.6 22.2 1.0
N A:ASP270 4.6 16.3 1.0
C A:MET265 4.6 12.5 1.0
N A:GLY273 4.7 16.9 1.0
CA A:GLY273 4.8 14.8 1.0
CA A:ASP271 4.8 23.0 1.0
O A:MET265 4.8 14.7 1.0
CA A:ASP270 5.0 19.6 1.0

Calcium binding site 2 out of 6 in 5mhm

Go back to Calcium Binding Sites List in 5mhm
Calcium binding site 2 out of 6 in the Fxiiia in Complex with the Inhibitor ZED1630


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Fxiiia in Complex with the Inhibitor ZED1630 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:39.5
occ:1.00
OD2 A:ASP367 2.3 31.7 1.0
OD1 A:ASN347 2.3 43.3 1.0
O A:GLN349 2.3 35.2 1.0
OD1 A:ASP345 2.3 34.8 1.0
OD1 A:ASP343 2.4 28.1 1.0
OD2 A:ASP351 2.4 37.2 1.0
CG A:ASP367 3.2 36.6 1.0
CG A:ASN347 3.2 39.9 1.0
CG A:ASP345 3.4 40.3 1.0
OD1 A:ASP367 3.4 40.2 1.0
CG A:ASP343 3.4 35.5 1.0
C A:GLN349 3.5 31.6 1.0
ND2 A:ASN347 3.6 43.4 1.0
CG A:ASP351 3.7 46.6 1.0
OD2 A:ASP345 3.8 47.7 1.0
N A:ASP351 4.0 44.0 1.0
OD2 A:ASP343 4.0 32.4 1.0
N A:GLN349 4.2 36.5 1.0
CA A:MET350 4.4 36.8 1.0
N A:MET350 4.4 31.3 1.0
CB A:ASP351 4.4 45.3 1.0
N A:ASP345 4.4 36.6 1.0
CA A:GLN349 4.5 31.0 1.0
O A:HOH1214 4.5 44.7 1.0
CB A:ASP343 4.5 35.5 1.0
CB A:ASP367 4.5 37.5 1.0
CG A:GLN349 4.6 40.5 1.0
N A:ASN344 4.6 40.1 1.0
CB A:ASN347 4.6 35.9 1.0
C A:MET350 4.6 41.3 1.0
N A:ASN347 4.6 35.5 1.0
OD1 A:ASP351 4.6 53.2 1.0
CA A:ASP343 4.6 35.6 1.0
CB A:ASP345 4.7 37.2 1.0
CE A:MET350 4.8 33.6 1.0
CA A:ASP351 4.8 45.2 1.0
N A:LEU348 4.9 35.2 1.0
CA A:ASP345 4.9 38.7 1.0
CA A:ASN347 5.0 35.7 1.0
N A:ALA346 5.0 40.9 1.0
C A:ASP345 5.0 41.0 1.0

Calcium binding site 3 out of 6 in 5mhm

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Calcium binding site 3 out of 6 in the Fxiiia in Complex with the Inhibitor ZED1630


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Fxiiia in Complex with the Inhibitor ZED1630 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:27.8
occ:1.00
O A:HOH933 2.2 18.9 1.0
OE2 A:GLU485 2.3 28.6 1.0
OE2 A:GLU490 2.3 39.8 1.0
O A:ALA457 2.4 31.8 1.0
O A:HOH1094 2.4 30.7 1.0
OD1 A:ASN436 2.5 31.7 1.0
OE1 A:GLU485 2.5 35.4 1.0
CD A:GLU485 2.8 31.8 1.0
CG A:ASN436 3.4 38.7 1.0
CD A:GLU490 3.5 38.5 1.0
C A:ALA457 3.5 35.4 1.0
ND2 A:ASN436 3.8 26.9 1.0
O A:HOH934 4.1 38.4 1.0
CA A:THR458 4.1 32.2 1.0
OE1 A:GLU490 4.2 40.3 1.0
N A:THR458 4.2 32.9 1.0
NZ A:LYS482 4.3 33.1 1.0
CG A:GLU485 4.3 35.3 1.0
NH2 A:ARG491 4.3 42.7 1.0
OD1 A:ASP438 4.4 35.4 1.0
O A:ASN436 4.5 28.9 1.0
CG A:GLU490 4.5 32.6 1.0
O A:HOH993 4.5 28.0 1.0
CA A:ALA457 4.6 37.6 1.0
CB A:ASN436 4.7 27.6 1.0
O A:ILE460 4.7 26.5 1.0
C A:THR458 4.7 39.9 1.0
CA A:ASN436 4.8 26.6 1.0
C A:ASN436 4.9 30.8 1.0
O A:HOH1005 4.9 33.8 1.0
CB A:ALA457 5.0 34.9 1.0

Calcium binding site 4 out of 6 in 5mhm

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Calcium binding site 4 out of 6 in the Fxiiia in Complex with the Inhibitor ZED1630


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Fxiiia in Complex with the Inhibitor ZED1630 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca801

b:18.3
occ:1.00
O B:LYS269 2.3 17.7 1.0
OD1 B:ASN267 2.3 16.8 1.0
O B:ASN267 2.4 15.6 1.0
O B:ALA264 2.4 18.1 1.0
OD1 B:ASP271 2.4 23.4 1.0
O B:HOH1061 2.4 10.6 1.0
OD2 B:ASP271 2.5 15.6 1.0
CG B:ASP271 2.8 21.6 1.0
CG B:ASN267 3.3 18.7 1.0
C B:ASN267 3.3 23.4 1.0
C B:ALA264 3.4 20.1 1.0
C B:LYS269 3.4 21.7 1.0
N B:LYS269 3.7 17.2 1.0
C B:ALA268 3.8 23.5 1.0
ND2 B:ASN267 4.0 17.5 1.0
CA B:LYS269 4.0 24.7 1.0
CA B:ASN267 4.1 17.0 1.0
N B:ALA268 4.1 17.2 1.0
CA B:ALA264 4.2 22.2 1.0
O B:ALA268 4.2 20.6 1.0
CB B:ASP271 4.2 17.5 1.0
N B:MET265 4.2 18.5 1.0
CB B:ASN267 4.2 18.7 1.0
N B:ASN267 4.3 16.6 1.0
CA B:MET265 4.3 20.6 1.0
N B:ASP271 4.3 17.2 1.0
CA B:ALA268 4.4 18.0 1.0
O B:TYR407 4.4 16.5 1.0
CB B:LYS269 4.5 24.2 1.0
OD2 B:ASP270 4.6 18.7 1.0
N B:ASP270 4.6 18.9 1.0
CB B:ALA264 4.6 14.2 1.0
CB B:ASP270 4.6 18.3 1.0
C B:MET265 4.6 21.0 1.0
CA B:ASP271 4.8 22.3 1.0
N B:GLY273 4.8 17.9 1.0
O B:MET265 4.9 14.5 1.0
CA B:GLY273 4.9 15.7 1.0
CA B:ASP270 5.0 21.6 1.0

Calcium binding site 5 out of 6 in 5mhm

Go back to Calcium Binding Sites List in 5mhm
Calcium binding site 5 out of 6 in the Fxiiia in Complex with the Inhibitor ZED1630


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Fxiiia in Complex with the Inhibitor ZED1630 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:29.9
occ:1.00
OD1 B:ASP345 2.3 35.1 1.0
OD2 B:ASP367 2.3 35.5 1.0
OD1 B:ASN347 2.3 34.4 1.0
O B:GLN349 2.4 27.6 1.0
OD1 B:ASP343 2.4 22.8 1.0
OD2 B:ASP351 2.4 36.1 1.0
CG B:ASP367 3.2 37.1 1.0
CG B:ASP345 3.3 37.9 1.0
CG B:ASN347 3.3 31.2 1.0
OD1 B:ASP367 3.4 37.5 1.0
C B:GLN349 3.6 29.2 1.0
CG B:ASP343 3.6 26.1 1.0
CG B:ASP351 3.6 39.2 1.0
OD2 B:ASP345 3.7 40.4 1.0
ND2 B:ASN347 3.8 37.2 1.0
N B:ASP351 4.0 33.5 1.0
OD2 B:ASP343 4.2 27.9 1.0
N B:GLN349 4.3 33.5 1.0
CB B:ASP351 4.4 35.2 1.0
CG B:GLN349 4.4 33.0 1.0
CA B:MET350 4.4 29.9 1.0
N B:MET350 4.4 28.3 1.0
N B:ASP345 4.4 32.7 1.0
CA B:GLN349 4.5 32.1 1.0
O B:HOH1152 4.5 36.7 1.0
CB B:ASP367 4.6 32.8 1.0
OD1 B:ASP351 4.6 41.0 1.0
N B:ASN347 4.6 30.8 1.0
N B:ASN344 4.6 32.8 1.0
C B:MET350 4.6 33.5 1.0
CE B:MET350 4.6 23.1 1.0
CB B:ASP345 4.7 24.9 1.0
CB B:ASP343 4.7 22.0 1.0
CB B:ASN347 4.7 32.0 1.0
CA B:ASP343 4.7 25.3 1.0
O B:HOH919 4.7 48.9 1.0
CA B:ASP351 4.9 34.4 1.0
N B:LEU348 4.9 22.6 1.0
CA B:ASP345 4.9 30.6 1.0
CA B:ASN347 5.0 30.2 1.0

Calcium binding site 6 out of 6 in 5mhm

Go back to Calcium Binding Sites List in 5mhm
Calcium binding site 6 out of 6 in the Fxiiia in Complex with the Inhibitor ZED1630


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Fxiiia in Complex with the Inhibitor ZED1630 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca805

b:22.4
occ:1.00
O B:HOH1015 2.3 23.3 1.0
OE2 B:GLU490 2.3 35.2 1.0
O B:ALA457 2.3 27.7 1.0
OE1 B:GLU485 2.4 30.6 1.0
OE2 B:GLU485 2.4 26.0 1.0
OD1 B:ASN436 2.4 26.3 1.0
O B:HOH996 2.4 25.8 1.0
CD B:GLU485 2.7 30.7 1.0
CG B:ASN436 3.4 27.1 1.0
CD B:GLU490 3.5 33.2 1.0
C B:ALA457 3.5 28.6 1.0
ND2 B:ASN436 3.7 23.4 1.0
OE1 B:GLU490 4.1 27.2 1.0
CA B:THR458 4.1 29.9 1.0
O B:HOH982 4.2 26.4 1.0
NZ B:LYS482 4.2 23.4 1.0
CG B:GLU485 4.2 29.6 1.0
NH1 B:ARG491 4.3 27.6 1.0
N B:THR458 4.3 30.8 1.0
O B:ASN436 4.4 23.2 1.0
O B:HOH1168 4.4 24.9 1.0
CG B:GLU490 4.5 30.9 1.0
OD1 B:ASP438 4.5 33.2 1.0
CA B:ALA457 4.6 34.5 1.0
CB B:ASN436 4.6 30.9 1.0
O B:ILE460 4.7 27.5 1.0
CA B:ASN436 4.8 22.1 1.0
C B:THR458 4.8 31.2 1.0
C B:ASN436 4.9 24.5 1.0
CB B:ALA457 5.0 33.6 1.0

Reference:

M.Stieler, A.Heine, G.Klebe. Fxiiia in Complex with the Inhibitor MI0621 To Be Published.
Page generated: Sat Dec 12 05:37:44 2020

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