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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: Sat Dec 12 05:01:10 2020

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