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Calcium in PDB 1qb1: Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974)

Enzymatic activity of Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974)

All present enzymatic activity of Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974):
3.4.21.4;

Protein crystallography data

The structure of Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974), PDB code: 1qb1 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 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.160, 63.780, 69.350, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.7

Other elements in 1qb1:

The structure of Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974) also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974) (pdb code 1qb1). 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 Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974), PDB code: 1qb1:

Calcium binding site 1 out of 1 in 1qb1

Go back to Calcium Binding Sites List in 1qb1
Calcium binding site 1 out of 1 in the Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bovine Trypsin with 1-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-6- [3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4- Yl]Piperidine-3-Carboxylic Acid (Zk-806974) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:13.3
occ:1.00
 O A:VAL63 2.2 14.5 1.0
O A:ASN60 2.2 10.8 1.0
OE1 A:GLU58 2.3 11.9 1.0
OE2 A:GLU68 2.4 11.5 1.0
O A:HOH323 2.5 14.6 1.0
O A:HOH340 2.5 12.6 1.0
CD A:GLU58 3.3 16.3 1.0
CD A:GLU68 3.4 10.2 1.0
C A:ASN60 3.4 11.8 1.0
C A:VAL63 3.4 13.3 1.0
CG A:GLU68 3.7 14.8 1.0
OE2 A:GLU58 3.7 14.9 1.0
CA A:VAL64 4.2 14.4 1.0
N A:GLU65 4.2 15.5 1.0
CA A:ILE61 4.2 13.4 1.0
N A:VAL64 4.2 10.9 1.0
N A:VAL63 4.2 17.3 1.0
N A:ILE61 4.3 12.6 1.0
OE1 A:GLU65 4.3 16.5 1.0
N A:ASN60 4.4 13.2 1.0
CG A:GLU65 4.4 21.9 1.0
CA A:ASN60 4.4 12.8 1.0
CA A:VAL63 4.4 16.5 1.0
O A:HOH319 4.4 15.8 1.0
C A:ILE61 4.5 13.1 1.0
OE1 A:GLU68 4.6 13.4 1.0
N A:ASP59 4.6 13.7 1.0
C A:VAL64 4.7 16.2 1.0
CG A:GLU58 4.7 13.0 1.0
O A:HOH342 4.7 23.5 1.0
CD A:GLU65 4.7 23.1 1.0
CB A:ASN60 4.7 14.2 1.0
N A:ASN62 4.8 13.6 1.0
CB A:GLU65 4.9 19.2 1.0
CA A:GLU58 4.9 12.3 1.0
O A:ILE61 4.9 13.4 1.0
CB A:GLU58 5.0 10.1 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 14:24:31 2024

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