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Calcium in PDB 1y5u: Dianhydrosugar-Based Benzamidine, Factor Xa Specific Inhibitor in Complex with Bovine Trypsin Mutant

Enzymatic activity of Dianhydrosugar-Based Benzamidine, Factor Xa Specific Inhibitor in Complex with Bovine Trypsin Mutant

All present enzymatic activity of Dianhydrosugar-Based Benzamidine, Factor Xa Specific Inhibitor in Complex with Bovine Trypsin Mutant:
3.4.21.4;

Protein crystallography data

The structure of Dianhydrosugar-Based Benzamidine, Factor Xa Specific Inhibitor in Complex with Bovine Trypsin Mutant, PDB code: 1y5u was solved by A.Di Fenza, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.60
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 54.786, 54.786, 108.633, 90.00, 90.00, 120.00
R / Rfree (%) 15.7 / 21.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Dianhydrosugar-Based Benzamidine, Factor Xa Specific Inhibitor in Complex with Bovine Trypsin Mutant (pdb code 1y5u). 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 Dianhydrosugar-Based Benzamidine, Factor Xa Specific Inhibitor in Complex with Bovine Trypsin Mutant, PDB code: 1y5u:

Calcium binding site 1 out of 1 in 1y5u

Go back to Calcium Binding Sites List in 1y5u
Calcium binding site 1 out of 1 in the Dianhydrosugar-Based Benzamidine, Factor Xa Specific Inhibitor in Complex with Bovine Trypsin Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dianhydrosugar-Based Benzamidine, Factor Xa Specific Inhibitor in Complex with Bovine Trypsin Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Ca9

b:12.4
occ:1.00
 OE1 T:GLU70 2.2 13.5 1.0
O T:VAL75 2.2 11.6 1.0
OE2 T:GLU80 2.3 12.9 1.0
O T:HOH9200 2.3 10.3 1.0
O T:ASN72 2.3 13.2 1.0
O T:HOH9201 2.5 10.7 1.0
CD T:GLU70 3.3 15.6 1.0
CD T:GLU80 3.3 14.2 1.0
C T:VAL75 3.4 14.1 1.0
C T:ASN72 3.5 14.4 1.0
CG T:GLU80 3.7 15.7 1.0
OE2 T:GLU70 3.7 13.1 1.0
O4 T:PEG501 4.0 40.9 1.0
CA T:VAL76 4.1 13.5 1.0
N T:VAL76 4.1 13.9 1.0
N T:GLU77 4.1 11.9 1.0
CA T:ILE73 4.2 13.7 1.0
N T:VAL75 4.2 14.3 1.0
OE1 T:GLU77 4.3 15.9 1.0
N T:ILE73 4.4 12.0 1.0
N T:ASN72 4.4 13.7 1.0
CA T:VAL75 4.4 13.4 1.0
CA T:ASN72 4.4 14.7 1.0
OE1 T:GLU80 4.4 10.7 1.0
CG T:GLU77 4.5 13.8 1.0
C T:ILE73 4.5 13.9 1.0
O T:HOH9015 4.5 13.6 1.0
N T:ASP71 4.6 11.4 1.0
CG T:GLU70 4.6 10.6 1.0
C T:VAL76 4.6 18.9 1.0
CA T:GLU70 4.7 11.4 1.0
CB T:GLU77 4.8 12.9 1.0
CB T:ASN72 4.8 12.4 1.0
CD T:GLU77 4.8 19.4 1.0
CB T:GLU70 4.8 11.4 1.0
O T:ILE73 4.9 15.1 1.0
N T:ASN74 4.9 11.9 1.0
C T:ASP71 5.0 9.5 1.0
C4 T:PEG501 5.0 37.5 1.0

Reference:

A.Di Fenza, A.Heine, U.Koert, G.Klebe. Understanding Binding Selectivity Toward Trypsin and Factor Xa: the Role of Aromatic Interactions Chemmedchem V. 2 297 2007.
ISSN: ISSN 1860-7179
PubMed: 17191291
DOI: 10.1002/CMDC.200600185
Page generated: Tue Jul 8 03:47:35 2025

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