Calcium in PDB 7jwx: Crystal Structure of Trypsin Bound O-Methyl Benzamidine

All present enzymatic activity of Crystal Structure of Trypsin Bound O-Methyl Benzamidine:
3.4.21.4;

The structure of Crystal Structure of Trypsin Bound O-Methyl Benzamidine, PDB code: 7jwx was solved by C.Packianathan, A.Laganowsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.58 / 2.38
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	189.27, 70.32, 137.74, 90, 133, 90
R / Rfree (%)	21.2 / 25.5

The structure of Crystal Structure of Trypsin Bound O-Methyl Benzamidine also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Trypsin Bound O-Methyl Benzamidine (pdb code 7jwx). 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 Trypsin Bound O-Methyl Benzamidine, PDB code: 7jwx:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Trypsin Bound O-Methyl Benzamidine


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 Trypsin Bound O-Methyl Benzamidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:44.3 occ:1.00 OE2 A:GLU62 2.3 31.6 1.0 O A:VAL57 2.4 30.2 1.0 O A:ASN54 2.4 28.7 1.0 OE1 A:GLU52 2.5 31.4 1.0 O A:HOH401 2.5 25.4 1.0 O A:HOH460 3.1 26.8 1.0 CD A:GLU62 3.2 31.6 1.0 CG A:GLU62 3.4 27.0 1.0 C A:ASN54 3.5 27.7 1.0 C A:VAL57 3.6 27.0 1.0 CD A:GLU52 3.6 31.4 1.0 N A:GLU59 4.0 31.4 1.0 OE1 A:GLU59 4.0 27.6 1.0 CG A:GLU59 4.2 36.0 1.0 OE2 A:GLU52 4.2 31.1 1.0 CB A:GLU59 4.2 30.6 1.0 CA A:ILE55 4.2 25.9 1.0 N A:ILE55 4.3 20.0 1.0 N A:VAL57 4.3 24.7 1.0 CA A:VAL58 4.4 31.4 1.0 N A:ASN54 4.4 24.3 1.0 OE1 A:GLU62 4.4 29.9 1.0 N A:ASP53 4.4 21.5 1.0 N A:VAL58 4.4 29.7 1.0 CA A:ASN54 4.4 26.7 1.0 CD A:GLU59 4.5 36.1 1.0 CA A:VAL57 4.6 24.9 1.0 C A:ILE55 4.6 24.9 1.0 CA A:GLU52 4.6 23.7 1.0 C A:VAL58 4.6 29.4 1.0 CG A:GLU52 4.7 24.7 1.0 CA A:GLU59 4.8 33.9 1.0 CB A:GLU52 4.8 26.7 1.0 CB A:ASN54 4.8 27.9 1.0 CB A:GLU62 4.8 27.9 1.0 N A:ASN56 4.9 27.9 1.0 C A:ASP53 5.0 23.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Trypsin Bound O-Methyl Benzamidine


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 Trypsin Bound O-Methyl Benzamidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:34.4 occ:1.00 OE2 B:GLU62 2.3 23.2 1.0 OE1 B:GLU52 2.4 25.6 1.0 O B:ASN54 2.4 23.7 1.0 O B:VAL57 2.4 31.6 1.0 O B:HOH464 3.0 26.7 1.0 CD B:GLU62 3.3 27.5 1.0 CG B:GLU62 3.4 23.1 1.0 C B:ASN54 3.4 24.3 1.0 CD B:GLU52 3.5 29.0 1.0 C B:VAL57 3.6 25.9 1.0 OE1 B:GLU59 3.8 29.6 1.0 N B:GLU59 4.0 27.5 1.0 OE2 B:GLU52 4.1 26.2 1.0 CD B:GLU59 4.2 28.0 1.0 CA B:ILE55 4.3 21.6 1.0 N B:ILE55 4.3 17.8 1.0 N B:ASN54 4.3 19.0 1.0 CG B:GLU59 4.3 28.7 1.0 CB B:GLU59 4.3 25.4 1.0 N B:ASP53 4.3 23.0 1.0 CA B:ASN54 4.4 26.4 1.0 N B:VAL57 4.4 24.1 1.0 N B:VAL58 4.4 22.9 1.0 CA B:VAL58 4.4 26.4 1.0 OE1 B:GLU62 4.5 24.5 1.0 CA B:VAL57 4.6 24.4 1.0 CA B:GLU52 4.6 23.9 1.0 C B:ILE55 4.6 22.4 1.0 CG B:GLU52 4.6 25.0 1.0 C B:VAL58 4.6 26.0 1.0 CB B:GLU52 4.7 26.7 1.0 CB B:ASN54 4.8 23.3 1.0 C B:ASP53 4.8 19.0 1.0 CA B:GLU59 4.8 25.6 1.0 CB B:GLU62 4.8 26.2 1.0 N B:ASN56 5.0 24.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Trypsin Bound O-Methyl Benzamidine


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 Trypsin Bound O-Methyl Benzamidine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:50.8 occ:1.00 OE2 C:GLU62 2.3 33.9 1.0 O C:ASN54 2.4 30.7 1.0 OE1 C:GLU52 2.4 35.0 1.0 O C:HOH402 2.4 31.6 1.0 O C:VAL57 2.4 37.0 1.0 CD C:GLU62 3.3 36.2 1.0 C C:VAL57 3.4 36.7 1.0 CD C:GLU52 3.5 33.9 1.0 CG C:GLU62 3.6 39.1 1.0 C C:ASN54 3.6 35.1 1.0 N C:GLU59 3.6 40.0 1.0 CA C:VAL58 3.7 40.1 1.0 N C:VAL58 3.9 41.5 1.0 OE2 C:GLU52 4.0 33.5 1.0 C C:VAL58 4.1 38.6 1.0 OE1 C:GLU59 4.2 41.3 1.0 CB C:GLU59 4.3 42.4 1.0 N C:ASN54 4.3 33.8 1.0 CG C:GLU59 4.4 41.8 1.0 CA C:ASN54 4.4 33.2 1.0 N C:VAL57 4.4 29.9 1.0 OE1 C:GLU62 4.4 40.3 1.0 CA C:VAL57 4.5 35.0 1.0 N C:ILE55 4.5 37.0 1.0 CB C:ASN54 4.6 33.4 1.0 CA C:GLU59 4.6 37.9 1.0 CA C:ILE55 4.7 32.8 1.0 N C:ASP53 4.7 27.3 1.0 CD C:GLU59 4.7 45.8 1.0 CG C:GLU52 4.7 27.4 1.0 CA C:GLU52 4.9 27.8 1.0 C C:ILE55 5.0 33.0 1.0 CB C:VAL58 5.0 41.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Trypsin Bound O-Methyl Benzamidine


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 Trypsin Bound O-Methyl Benzamidine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:54.3 occ:1.00 O D:VAL57 2.4 43.6 1.0 O D:HOH462 2.5 37.7 1.0 OE1 D:GLU52 2.5 35.9 1.0 O D:ASN54 2.5 37.3 1.0 OE2 D:GLU62 2.6 50.1 1.0 CD D:GLU62 3.3 51.9 1.0 C D:VAL57 3.5 43.3 1.0 C D:ASN54 3.6 37.5 1.0 CD D:GLU52 3.6 35.4 1.0 OE1 D:GLU62 3.7 52.8 1.0 CA D:VAL58 4.1 48.2 1.0 N D:GLU59 4.1 55.2 1.0 OE2 D:GLU52 4.1 34.8 1.0 N D:ASN54 4.2 33.5 1.0 N D:VAL58 4.2 47.7 1.0 N D:ASP53 4.3 33.5 1.0 O D:HOH453 4.4 36.1 1.0 CA D:ASN54 4.4 32.8 1.0 C D:VAL58 4.4 54.7 1.0 CG D:GLU62 4.4 46.8 1.0 N D:ILE55 4.5 33.8 1.0 N D:VAL57 4.5 36.0 1.0 CA D:ILE55 4.5 33.4 1.0 CG D:GLU59 4.6 65.3 1.0 CA D:VAL57 4.6 42.7 1.0 CB D:GLU59 4.7 57.3 1.0 OE1 D:GLU59 4.7 64.0 1.0 CA D:GLU52 4.7 34.4 1.0 CD D:GLU59 4.8 78.3 1.0 CB D:ASN54 4.8 32.2 1.0 CB D:GLU62 4.8 43.0 1.0 CG D:GLU52 4.8 33.3 1.0 C D:ILE55 4.8 39.7 1.0 C D:ASP53 4.9 32.1 1.0 CB D:GLU52 5.0 29.7 1.0

R.Y.Lyu, S.Joy, C.Packianathan, A.Laganowsky, K.Burgess. Small Molecule Peptidomimetic Trypsin Inhibitors: Validation of An Eko Binding Mode, But with A Twist To Be Published.