Calcium in PDB 6t0m: Cationic Trypsin in Complex with A D-Phe-Pro-Diaminopyridine Derivative

All present enzymatic activity of Cationic Trypsin in Complex with A D-Phe-Pro-Diaminopyridine Derivative:
3.4.21.4;

The structure of Cationic Trypsin in Complex with A D-Phe-Pro-Diaminopyridine Derivative, PDB code: 6t0m was solved by K.Ngo, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.22 / 1.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.454, 56.756, 66.691, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 17.1

The binding sites of Calcium atom in the Cationic Trypsin in Complex with A D-Phe-Pro-Diaminopyridine Derivative (pdb code 6t0m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Cationic Trypsin in Complex with A D-Phe-Pro-Diaminopyridine Derivative, PDB code: 6t0m:

Calcium binding site 1 out of 1 in the Cationic Trypsin in Complex with A D-Phe-Pro-Diaminopyridine Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cationic Trypsin in Complex with A D-Phe-Pro-Diaminopyridine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:13.4 occ:1.00 O A:VAL75 2.3 14.6 1.0 OE1 A:GLU70 2.3 14.1 1.0 O A:ASN72 2.3 13.3 1.0 OE2 A:GLU80 2.3 14.1 1.0 O A:HOH453 2.4 14.2 1.0 O A:HOH402 2.4 16.3 1.0 HG2 A:GLU80 3.3 19.3 1.0 HA A:VAL76 3.4 17.1 1.0 CD A:GLU70 3.4 14.2 1.0 CD A:GLU80 3.4 17.0 1.0 C A:VAL75 3.4 13.9 1.0 C A:ASN72 3.5 12.9 1.0 HA A:ILE73 3.5 15.8 1.0 H A:GLU77 3.5 18.3 1.0 H A:VAL75 3.6 16.1 1.0 CG A:GLU80 3.7 16.1 1.0 HG3 A:GLU77 3.7 20.5 1.0 HG3 A:GLU80 3.8 19.3 1.0 OE2 A:GLU70 3.8 14.3 1.0 H A:ASP71 3.9 16.9 1.0 HA A:GLU70 3.9 15.9 1.0 CA A:VAL76 4.1 14.3 1.0 N A:GLU77 4.2 15.2 1.0 N A:VAL76 4.2 14.0 1.0 HB3 A:ASN72 4.2 16.3 1.0 CA A:ILE73 4.2 13.2 1.0 N A:VAL75 4.2 13.4 1.0 HB2 A:GLU77 4.2 20.4 1.0 OE1 A:GLU77 4.3 17.6 1.0 H A:ASN72 4.3 16.9 1.0 N A:ILE73 4.3 12.5 1.0 N A:ASN72 4.4 14.0 1.0 CA A:VAL75 4.4 14.2 1.0 CA A:ASN72 4.4 12.6 1.0 HB3 A:GLU70 4.5 14.9 1.0 OE1 A:GLU80 4.5 15.5 1.0 C A:ILE73 4.5 12.4 1.0 CG A:GLU77 4.5 17.1 1.0 O A:HOH483 4.5 16.1 1.0 N A:ASP71 4.6 14.0 1.0 HB A:VAL75 4.6 15.8 1.0 C A:VAL76 4.6 16.3 1.0 CG A:GLU70 4.6 12.8 1.0 CA A:GLU70 4.7 13.3 1.0 CB A:GLU77 4.8 17.0 1.0 CD A:GLU77 4.8 21.3 1.0 CB A:ASN72 4.8 13.6 1.0 CB A:GLU70 4.8 12.4 1.0 O A:ILE73 4.9 12.9 1.0 N A:ASN74 4.9 12.1 1.0 HG22 A:VAL76 4.9 18.3 1.0 O A:DMS301 4.9 19.2 1.0 H A:VAL76 5.0 16.8 1.0 HZ A:PHE82 5.0 19.5 1.0 H A:ASN74 5.0 14.6 1.0 C A:ASP71 5.0 15.8 1.0

K.Ngo, C.Collins-Kautz, S.Gerstenecker, B.Wagner, A.Heine, G.Klebe. Protein-Induced Change in Ligand Protonation During Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins? J.Med.Chem. V. 63 3274 2020.
ISSN: ISSN 0022-2623
PubMed: 32011145
DOI: 10.1021/ACS.JMEDCHEM.9B02061