Atomistry » Calcium » PDB 4niv-4o4h » 4niy
Atomistry »
  Calcium »
    PDB 4niv-4o4h »
      4niy »

Calcium in PDB 4niy: Crystal Structure of Trypsiligase (K60E/N143H/Y151H/D189K Trypsin) Complexed to Yrh-Ecotin (M84Y/M85R/A86H Ecotin)

Enzymatic activity of Crystal Structure of Trypsiligase (K60E/N143H/Y151H/D189K Trypsin) Complexed to Yrh-Ecotin (M84Y/M85R/A86H Ecotin)

All present enzymatic activity of Crystal Structure of Trypsiligase (K60E/N143H/Y151H/D189K Trypsin) Complexed to Yrh-Ecotin (M84Y/M85R/A86H Ecotin):
3.4.21.4;

Protein crystallography data

The structure of Crystal Structure of Trypsiligase (K60E/N143H/Y151H/D189K Trypsin) Complexed to Yrh-Ecotin (M84Y/M85R/A86H Ecotin), PDB code: 4niy was solved by M.Schoepfel, C.Parthier, M.T.Stubbs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.60 / 2.84
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.241, 78.615, 98.084, 90.00, 96.62, 90.00
R / Rfree (%) 19.2 / 25.2

Other elements in 4niy:

The structure of Crystal Structure of Trypsiligase (K60E/N143H/Y151H/D189K Trypsin) Complexed to Yrh-Ecotin (M84Y/M85R/A86H Ecotin) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Trypsiligase (K60E/N143H/Y151H/D189K Trypsin) Complexed to Yrh-Ecotin (M84Y/M85R/A86H Ecotin) (pdb code 4niy). 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 Trypsiligase (K60E/N143H/Y151H/D189K Trypsin) Complexed to Yrh-Ecotin (M84Y/M85R/A86H Ecotin), PDB code: 4niy:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4niy

Go back to Calcium Binding Sites List in 4niy
Calcium binding site 1 out of 4 in the Crystal Structure of Trypsiligase (K60E/N143H/Y151H/D189K Trypsin) Complexed to Yrh-Ecotin (M84Y/M85R/A86H Ecotin)


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 Trypsiligase (K60E/N143H/Y151H/D189K Trypsin) Complexed to Yrh-Ecotin (M84Y/M85R/A86H Ecotin) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:43.1
occ:1.00
 OE2 A:GLU80 2.3 52.4 1.0
O A:ASN72 2.4 38.8 1.0
OE1 A:GLU70 2.5 50.6 1.0
O A:VAL75 2.6 56.8 1.0
OE1 A:GLU77 2.9 64.9 1.0
C A:ASN72 3.3 41.1 1.0
CD A:GLU80 3.4 54.9 1.0
CD A:GLU70 3.5 40.5 1.0
CG A:GLU80 3.7 46.5 1.0
N A:ASN72 3.8 43.1 1.0
C A:VAL75 3.8 54.9 1.0
CD A:GLU77 3.9 63.5 1.0
OE2 A:GLU70 4.0 44.5 1.0
CA A:ASN72 4.0 43.5 1.0
CG A:GLU77 4.1 51.4 1.0
N A:ASP71 4.1 50.2 1.0
N A:GLU77 4.2 51.2 1.0
N A:ILE73 4.3 37.7 1.0
CA A:VAL76 4.3 55.9 1.0
CB A:ASN72 4.4 45.8 1.0
OE1 A:GLU80 4.5 54.3 1.0
CA A:ILE73 4.5 45.4 1.0
CA A:GLU70 4.5 31.7 1.0
N A:VAL76 4.6 55.7 1.0
CG A:GLU70 4.6 38.3 1.0
CB A:GLU70 4.7 36.6 1.0
CB A:GLU77 4.7 43.4 1.0
C A:VAL76 4.7 49.1 1.0
C A:ASP71 4.8 36.9 1.0
N A:VAL75 4.8 51.6 1.0
C A:GLU70 4.9 36.2 1.0
CA A:VAL75 4.9 48.6 1.0

Calcium binding site 2 out of 4 in 4niy

Go back to Calcium Binding Sites List in 4niy
Calcium binding site 2 out of 4 in the Crystal Structure of Trypsiligase (K60E/N143H/Y151H/D189K Trypsin) Complexed to Yrh-Ecotin (M84Y/M85R/A86H Ecotin)


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 Trypsiligase (K60E/N143H/Y151H/D189K Trypsin) Complexed to Yrh-Ecotin (M84Y/M85R/A86H Ecotin) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:20.4
occ:1.00
 OE2 B:GLU80 2.3 20.4 1.0
O B:ASN72 2.4 26.0 1.0
O B:VAL75 2.4 22.7 1.0
OE1 B:GLU70 2.4 18.0 1.0
OE1 B:GLU77 3.2 31.6 1.0
CD B:GLU80 3.4 19.7 1.0
CD B:GLU70 3.4 18.0 1.0
C B:ASN72 3.4 17.7 1.0
C B:VAL75 3.6 24.6 1.0
CG B:GLU80 3.7 17.4 1.0
OE2 B:GLU70 3.8 22.6 1.0
CA B:VAL76 4.1 24.6 1.0
N B:ASN72 4.1 25.7 1.0
CD B:GLU77 4.1 36.0 1.0
CG B:GLU77 4.2 28.8 1.0
CA B:ASN72 4.2 20.9 1.0
N B:VAL76 4.3 27.1 1.0
N B:GLU77 4.3 33.6 1.0
N B:ILE73 4.3 16.9 1.0
CA B:ILE73 4.3 16.8 1.0
N B:ASP71 4.5 21.6 1.0
OE1 B:GLU80 4.5 27.8 1.0
CG B:GLU70 4.6 13.4 1.0
N B:VAL75 4.6 21.3 1.0
C B:VAL76 4.7 31.1 1.0
CB B:ASN72 4.7 18.9 1.0
CA B:VAL75 4.7 19.2 1.0
CA B:GLU70 4.7 16.1 1.0
C B:ILE73 4.8 16.3 1.0
CB B:GLU70 4.8 14.4 1.0
CB B:GLU77 4.9 35.0 1.0

Calcium binding site 3 out of 4 in 4niy

Go back to Calcium Binding Sites List in 4niy
Calcium binding site 3 out of 4 in the Crystal Structure of Trypsiligase (K60E/N143H/Y151H/D189K Trypsin) Complexed to Yrh-Ecotin (M84Y/M85R/A86H Ecotin)


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 Trypsiligase (K60E/N143H/Y151H/D189K Trypsin) Complexed to Yrh-Ecotin (M84Y/M85R/A86H Ecotin) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:32.7
occ:1.00
 OE2 C:GLU80 2.1 31.1 1.0
O C:VAL75 2.4 44.1 1.0
OE1 C:GLU70 2.5 33.7 1.0
O C:ASN72 2.6 30.9 1.0
CD C:GLU80 3.1 34.0 1.0
OE1 C:GLU77 3.2 38.7 1.0
CD C:GLU70 3.4 27.6 1.0
CG C:GLU80 3.5 29.7 1.0
C C:VAL75 3.6 42.2 1.0
C C:ASN72 3.6 34.2 1.0
OE2 C:GLU70 3.7 29.8 1.0
CA C:VAL76 3.9 39.8 1.0
N C:GLU77 4.1 43.5 1.0
CD C:GLU77 4.1 36.0 1.0
CG C:GLU77 4.2 28.8 1.0
N C:VAL76 4.2 41.1 1.0
OE1 C:GLU80 4.2 33.7 1.0
N C:ASN72 4.3 37.4 1.0
CA C:ASN72 4.4 36.7 1.0
C C:VAL76 4.5 41.3 1.0
N C:ASP71 4.5 29.2 1.0
N C:ILE73 4.5 34.3 1.0
CA C:ILE73 4.6 38.5 1.0
CG C:GLU70 4.6 25.0 1.0
CA C:GLU70 4.7 19.2 1.0
N C:VAL75 4.7 34.6 1.0
CA C:VAL75 4.8 37.0 1.0
CB C:ASN72 4.8 32.9 1.0
CB C:GLU77 4.8 27.8 1.0
CB C:GLU70 4.9 25.8 1.0
CB C:GLU80 5.0 24.8 1.0
C C:ILE73 5.0 35.1 1.0

Calcium binding site 4 out of 4 in 4niy

Go back to Calcium Binding Sites List in 4niy
Calcium binding site 4 out of 4 in the Crystal Structure of Trypsiligase (K60E/N143H/Y151H/D189K Trypsin) Complexed to Yrh-Ecotin (M84Y/M85R/A86H Ecotin)


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 Trypsiligase (K60E/N143H/Y151H/D189K Trypsin) Complexed to Yrh-Ecotin (M84Y/M85R/A86H Ecotin) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:56.8
occ:1.00
 OE2 D:GLU80 2.2 58.0 1.0
O D:VAL75 2.3 72.8 1.0
O D:ASN72 2.4 62.0 1.0
OE1 D:GLU70 2.6 77.8 1.0
OE1 D:GLU77 3.2 70.7 1.0
CD D:GLU80 3.3 52.5 1.0
C D:ASN72 3.5 64.1 1.0
CD D:GLU70 3.5 68.8 1.0
C D:VAL75 3.5 68.6 1.0
CG D:GLU80 3.7 47.0 1.0
OE2 D:GLU70 3.9 65.9 1.0
CA D:VAL76 4.0 61.1 1.0
CD D:GLU77 4.1 68.6 1.0
CG D:GLU77 4.1 64.2 1.0
N D:GLU77 4.1 57.8 1.0
N D:ASN72 4.1 62.4 1.0
N D:VAL76 4.2 53.5 1.0
CA D:ASN72 4.3 65.5 1.0
OE1 D:GLU80 4.4 51.0 1.0
N D:ILE73 4.4 61.7 1.0
C D:VAL76 4.5 65.1 1.0
CA D:ILE73 4.5 67.7 1.0
N D:ASP71 4.5 56.2 1.0
N D:VAL75 4.6 61.6 1.0
CA D:VAL75 4.7 64.8 1.0
CB D:ASN72 4.7 62.1 1.0
CG D:GLU70 4.7 56.3 1.0
CB D:GLU77 4.8 66.6 1.0
CA D:GLU70 4.8 45.5 1.0
C D:ILE73 4.9 68.7 1.0
CB D:GLU70 4.9 50.6 1.0

Reference:

S.Liebscher, M.Schopfel, T.Aumuller, A.Sharkhuukhen, A.Pech, E.Hoss, C.Parthier, G.Jahreis, M.T.Stubbs, F.Bordusa. N-Terminal Protein Modification By Substrate-Activated Reverse Proteolysis. Angew.Chem.Int.Ed.Engl. V. 53 3024 2014.
ISSN: ISSN 1433-7851
PubMed: 24520050
DOI: 10.1002/ANIE.201307736
Page generated: Sun Jul 14 11:07:33 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy