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Calcium in PDB 1qbo: Bovine Trypsin 7-[[6-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-2-Methyl- Benzimidazol-1-Yl]Methyl]Naphthalene-2-Carboximidamid Zk-806711 Inhibitor Complex

Enzymatic activity of Bovine Trypsin 7-[[6-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-2-Methyl- Benzimidazol-1-Yl]Methyl]Naphthalene-2-Carboximidamid Zk-806711 Inhibitor Complex

All present enzymatic activity of Bovine Trypsin 7-[[6-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-2-Methyl- Benzimidazol-1-Yl]Methyl]Naphthalene-2-Carboximidamid Zk-806711 Inhibitor Complex:
3.4.21.4;

Protein crystallography data

The structure of Bovine Trypsin 7-[[6-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-2-Methyl- Benzimidazol-1-Yl]Methyl]Naphthalene-2-Carboximidamid Zk-806711 Inhibitor Complex, PDB code: 1qbo was solved by M.Whitlow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 55.020, 55.020, 109.140, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 22.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Bovine Trypsin 7-[[6-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-2-Methyl- Benzimidazol-1-Yl]Methyl]Naphthalene-2-Carboximidamid Zk-806711 Inhibitor Complex (pdb code 1qbo). 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 Trypsin 7-[[6-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-2-Methyl- Benzimidazol-1-Yl]Methyl]Naphthalene-2-Carboximidamid Zk-806711 Inhibitor Complex, PDB code: 1qbo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1qbo

Go back to Calcium Binding Sites List in 1qbo
Calcium binding site 1 out of 2 in the Bovine Trypsin 7-[[6-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-2-Methyl- Benzimidazol-1-Yl]Methyl]Naphthalene-2-Carboximidamid Zk-806711 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bovine Trypsin 7-[[6-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-2-Methyl- Benzimidazol-1-Yl]Methyl]Naphthalene-2-Carboximidamid Zk-806711 Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:33.0
occ:1.00
 O A:VAL63 2.1 24.4 1.0
O A:HOH308 2.3 31.8 1.0
O A:ASN60 2.4 24.7 1.0
OE1 A:GLU58 2.4 25.8 1.0
OE2 A:GLU68 2.6 27.8 1.0
C A:VAL63 3.3 26.6 1.0
CD A:GLU58 3.5 23.9 1.0
C A:ASN60 3.6 24.7 1.0
CD A:GLU68 3.6 30.7 1.0
CG A:GLU68 3.8 32.4 1.0
OE1 A:GLU65 3.9 40.9 1.0
OE2 A:GLU58 3.9 25.3 1.0
CA A:VAL64 3.9 29.6 1.0
N A:VAL64 4.1 26.5 1.0
N A:GLU65 4.1 30.2 1.0
N A:VAL63 4.1 24.9 1.0
N A:ASN60 4.2 25.5 1.0
CG A:GLU65 4.2 39.4 1.0
CA A:VAL63 4.3 26.9 1.0
CD A:GLU65 4.4 41.1 1.0
CA A:ASN60 4.4 23.2 1.0
CA A:ILE61 4.4 22.9 1.0
N A:ASP59 4.4 24.6 1.0
N A:ILE61 4.4 22.4 1.0
C A:VAL64 4.6 29.7 1.0
C A:ILE61 4.6 23.3 1.0
OE1 A:GLU68 4.7 28.8 1.0
CA A:GLU58 4.8 22.0 1.0
CB A:ASN60 4.8 23.5 1.0
CG A:GLU58 4.8 25.3 1.0
O A:HOH332 4.8 46.7 1.0
N A:ASN62 4.8 21.8 1.0
CB A:VAL63 4.9 28.7 1.0
O A:HOH344 4.9 35.4 1.0
CB A:GLU65 4.9 37.3 1.0
C A:ASP59 5.0 26.4 1.0
CB A:GLU58 5.0 22.4 1.0
O A:ILE61 5.0 24.6 1.0

Calcium binding site 2 out of 2 in 1qbo

Go back to Calcium Binding Sites List in 1qbo
Calcium binding site 2 out of 2 in the Bovine Trypsin 7-[[6-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-2-Methyl- Benzimidazol-1-Yl]Methyl]Naphthalene-2-Carboximidamid Zk-806711 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bovine Trypsin 7-[[6-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-2-Methyl- Benzimidazol-1-Yl]Methyl]Naphthalene-2-Carboximidamid Zk-806711 Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca455

b:68.0
occ:0.63
 OD2 A:ASP59 2.7 38.4 1.0
OE2 A:GLU65 2.9 42.4 1.0
O A:HOH326 3.3 51.9 1.0
CG A:ASP59 3.6 38.0 1.0
CD A:GLU65 3.8 41.1 1.0
OE1 A:GLU65 3.9 40.9 1.0
O A:HOH421 4.1 41.7 0.8
CG1 A:VAL140 4.1 26.4 1.0
CB A:ASN60 4.1 23.5 1.0
CB A:ASP59 4.2 28.8 1.0
N A:ASN60 4.4 25.5 1.0
OD1 A:ASP59 4.5 41.6 1.0
CA A:ASN60 4.9 23.2 1.0
ND2 A:ASN60 4.9 24.4 1.0

Reference:

M.Whitlow, D.O.Arnaiz, B.O.Buckman, D.D.Davey, B.Griedel, W.J.Guilford, S.K.Koovakkat, A.Liang, R.Mohan, G.B.Phillips, M.Seto, K.J.Shaw, W.Xu, Z.Zhao, D.R.Light, M.M.Morrissey. Crystallographic Analysis of Potent and Selective Factor Xa Inhibitors Complexed to Bovine Trypsin. Acta Crystallogr.,Sect.D V. 55 1395 1999.
ISSN: ISSN 0907-4449
PubMed: 10417407
DOI: 10.1107/S0907444999007350
Page generated: Thu Jul 11 14:32:14 2024

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