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Calcium in PDB 1qbn: Bovine Trypsin 2-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1H-Imidazol-2-Yl)Phenoxy]Pyridine-4- Carboxylic Acid (Zk-806688) Complex

Enzymatic activity of Bovine Trypsin 2-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1H-Imidazol-2-Yl)Phenoxy]Pyridine-4- Carboxylic Acid (Zk-806688) Complex

All present enzymatic activity of Bovine Trypsin 2-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1H-Imidazol-2-Yl)Phenoxy]Pyridine-4- Carboxylic Acid (Zk-806688) Complex:
3.4.21.4;

Protein crystallography data

The structure of Bovine Trypsin 2-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1H-Imidazol-2-Yl)Phenoxy]Pyridine-4- Carboxylic Acid (Zk-806688) Complex, PDB code: 1qbn 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 (%) 15.6 / 21.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Bovine Trypsin 2-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1H-Imidazol-2-Yl)Phenoxy]Pyridine-4- Carboxylic Acid (Zk-806688) Complex (pdb code 1qbn). 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 2-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1H-Imidazol-2-Yl)Phenoxy]Pyridine-4- Carboxylic Acid (Zk-806688) Complex, PDB code: 1qbn:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1qbn

Go back to Calcium Binding Sites List in 1qbn
Calcium binding site 1 out of 2 in the Bovine Trypsin 2-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1H-Imidazol-2-Yl)Phenoxy]Pyridine-4- Carboxylic Acid (Zk-806688) 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 2-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1H-Imidazol-2-Yl)Phenoxy]Pyridine-4- Carboxylic Acid (Zk-806688) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:22.6
occ:0.97
 O A:VAL63 2.2 19.1 1.0
OE1 A:GLU58 2.3 19.0 1.0
O A:ASN60 2.3 16.5 1.0
OE2 A:GLU68 2.4 15.9 1.0
O A:HOH308 2.4 17.2 1.0
O A:HOH333 2.6 18.1 1.0
C A:VAL63 3.4 19.7 1.0
CD A:GLU58 3.4 19.9 1.0
CD A:GLU68 3.5 19.8 1.0
C A:ASN60 3.5 16.9 1.0
CG A:GLU68 3.8 21.5 1.0
OE2 A:GLU58 4.0 20.4 1.0
N A:GLU65 4.1 22.2 1.0
OE1 A:GLU65 4.1 27.8 1.0
CA A:VAL64 4.1 22.5 1.0
N A:ASN60 4.2 17.4 1.0
N A:VAL64 4.2 20.9 1.0
N A:VAL63 4.3 18.4 1.0
CA A:ILE61 4.3 17.7 1.0
N A:ASP59 4.4 16.6 1.0
N A:ILE61 4.4 17.1 1.0
CA A:ASN60 4.4 16.6 1.0
CG A:GLU65 4.4 26.3 1.0
CA A:VAL63 4.4 18.9 1.0
O A:HOH332 4.5 21.5 1.0
OE1 A:GLU68 4.6 17.8 1.0
C A:ILE61 4.6 18.6 1.0
CD A:GLU65 4.6 28.8 1.0
C A:VAL64 4.6 22.7 1.0
CG A:GLU58 4.7 18.8 1.0
CB A:GLU65 4.7 24.5 1.0
CA A:GLU58 4.7 16.3 1.0
CB A:ASN60 4.8 19.6 1.0
N A:ASN62 4.9 17.6 1.0
CB A:GLU58 4.9 16.5 1.0
C A:ASP59 4.9 16.5 1.0
O A:HOH344 4.9 30.5 1.0

Calcium binding site 2 out of 2 in 1qbn

Go back to Calcium Binding Sites List in 1qbn
Calcium binding site 2 out of 2 in the Bovine Trypsin 2-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1H-Imidazol-2-Yl)Phenoxy]Pyridine-4- Carboxylic Acid (Zk-806688) 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 2-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1H-Imidazol-2-Yl)Phenoxy]Pyridine-4- Carboxylic Acid (Zk-806688) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca455

b:55.3
occ:0.87
 OD2 A:ASP59 2.5 25.5 1.0
OE2 A:GLU65 2.6 31.6 1.0
O A:HOH326 3.2 37.5 1.0
CD A:GLU65 3.4 28.8 1.0
OE1 A:GLU65 3.4 27.8 1.0
CG A:ASP59 3.6 22.6 1.0
CB A:ASP59 4.0 18.1 1.0
CG1 A:VAL140 4.1 19.6 1.0
CB A:ASN60 4.1 19.6 1.0
O A:HOH421 4.1 27.9 1.0
N A:ASN60 4.2 17.4 1.0
OD1 A:ASP59 4.6 23.8 1.0
CA A:ASN60 4.7 16.6 1.0
CG A:GLU65 4.8 26.3 1.0
CB A:ALA15 4.8 26.5 1.0
C A:ASP59 4.9 16.5 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 14:31:05 2024

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