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Calcium in PDB 3aav: Bovine Beta-Trypsin Bound to Meta-Diamidino Schiff Base Copper (II) Chelate

Enzymatic activity of Bovine Beta-Trypsin Bound to Meta-Diamidino Schiff Base Copper (II) Chelate

All present enzymatic activity of Bovine Beta-Trypsin Bound to Meta-Diamidino Schiff Base Copper (II) Chelate:
3.4.21.4;

Protein crystallography data

The structure of Bovine Beta-Trypsin Bound to Meta-Diamidino Schiff Base Copper (II) Chelate, PDB code: 3aav was solved by D.Iyaguchi, S.Kawano, E.Toyota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 54.568, 54.568, 107.235, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 20.9

Other elements in 3aav:

The structure of Bovine Beta-Trypsin Bound to Meta-Diamidino Schiff Base Copper (II) Chelate also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Bovine Beta-Trypsin Bound to Meta-Diamidino Schiff Base Copper (II) Chelate (pdb code 3aav). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Bovine Beta-Trypsin Bound to Meta-Diamidino Schiff Base Copper (II) Chelate, PDB code: 3aav:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3aav

Go back to Calcium Binding Sites List in 3aav
Calcium binding site 1 out of 2 in the Bovine Beta-Trypsin Bound to Meta-Diamidino Schiff Base Copper (II) Chelate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bovine Beta-Trypsin Bound to Meta-Diamidino Schiff Base Copper (II) Chelate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:14.2
occ:1.00
OE1 A:GLU52 2.2 15.4 1.0
O A:VAL57 2.3 13.1 1.0
OE2 A:GLU62 2.3 15.0 1.0
O A:HOH227 2.4 14.9 1.0
O A:ASN54 2.4 16.4 1.0
O A:HOH291 2.4 17.6 1.0
CD A:GLU52 3.3 15.1 1.0
CD A:GLU62 3.4 13.7 1.0
C A:VAL57 3.4 14.5 1.0
C A:ASN54 3.5 14.8 1.0
CG A:GLU62 3.7 15.6 1.0
OE2 A:GLU52 3.7 15.2 1.0
N A:GLU59 4.1 16.4 1.0
CA A:VAL58 4.1 15.8 1.0
N A:VAL58 4.1 14.7 1.0
OE1 A:GLU59 4.2 18.8 1.0
N A:VAL57 4.2 13.5 1.0
CA A:ILE55 4.3 14.7 1.0
N A:ILE55 4.3 15.2 1.0
N A:ASN54 4.3 15.8 1.0
CA A:VAL57 4.4 14.7 1.0
O A:HOH294 4.5 17.9 1.0
N A:ASP53 4.5 17.0 1.0
OE1 A:GLU62 4.5 14.0 1.0
CG A:GLU59 4.5 17.9 1.0
CA A:ASN54 4.5 15.4 1.0
C A:ILE55 4.5 14.2 1.0
CG A:GLU52 4.6 14.2 1.0
C A:VAL58 4.6 16.4 1.0
CA A:GLU52 4.7 15.7 1.0
CD A:GLU59 4.8 20.8 1.0
CB A:GLU59 4.8 17.2 1.0
CB A:GLU52 4.8 14.3 1.0
CB A:ASN54 4.8 15.4 1.0
O A:HOH293 4.9 19.2 1.0
N A:ASN56 4.9 13.6 1.0
O A:ILE55 5.0 14.9 1.0
C A:ASP53 5.0 16.1 1.0

Calcium binding site 2 out of 2 in 3aav

Go back to Calcium Binding Sites List in 3aav
Calcium binding site 2 out of 2 in the Bovine Beta-Trypsin Bound to Meta-Diamidino Schiff Base Copper (II) Chelate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bovine Beta-Trypsin Bound to Meta-Diamidino Schiff Base Copper (II) Chelate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2002

b:14.8
occ:1.00
OE1 B:GLU52 2.2 15.2 1.0
O B:VAL57 2.2 13.8 1.0
OE2 B:GLU62 2.3 15.5 1.0
O B:ASN54 2.3 17.1 1.0
O B:HOH229 2.4 15.0 1.0
O B:HOH224 2.4 16.6 1.0
CD B:GLU52 3.3 15.8 1.0
CD B:GLU62 3.3 15.6 1.0
C B:VAL57 3.4 14.3 1.0
C B:ASN54 3.5 16.2 1.0
CG B:GLU62 3.7 17.6 1.0
OE2 B:GLU52 3.8 16.4 1.0
N B:GLU59 4.1 16.4 1.0
CA B:VAL58 4.1 15.8 1.0
N B:VAL58 4.1 16.0 1.0
CA B:ILE55 4.2 15.3 1.0
N B:VAL57 4.2 13.8 1.0
OE1 B:GLU59 4.3 18.9 1.0
N B:ILE55 4.3 15.2 1.0
N B:ASN54 4.3 15.7 1.0
CA B:VAL57 4.4 15.1 1.0
CG B:GLU59 4.5 17.4 1.0
N B:ASP53 4.5 16.2 1.0
O B:HOH344 4.5 18.9 1.0
OE1 B:GLU62 4.5 16.7 1.0
CA B:ASN54 4.5 16.1 1.0
C B:ILE55 4.5 14.4 1.0
C B:VAL58 4.6 16.6 1.0
CG B:GLU52 4.6 14.6 1.0
CA B:GLU52 4.7 14.8 1.0
CB B:GLU59 4.8 17.0 1.0
CD B:GLU59 4.8 21.2 1.0
CB B:GLU52 4.8 14.3 1.0
CB B:ASN54 4.8 16.1 1.0
N B:ASN56 4.9 13.8 1.0
O B:HOH300 4.9 19.0 1.0
C B:ASP53 4.9 15.7 1.0
O B:ILE55 5.0 15.1 1.0

Reference:

D.Iyaguchi, S.Kawano, K.Takada, E.Toyota. Structural Basis For the Design of Novel Schiff Base Metal Chelate Inhibitors of Trypsin Bioorg.Med.Chem. V. 18 2076 2010.
ISSN: ISSN 0968-0896
PubMed: 20202854
DOI: 10.1016/J.BMC.2010.02.016
Page generated: Sat Dec 12 04:03:53 2020

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