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Calcium in PDB 1qb9: Bovine Trypsin 7-[[2-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-9H- Carbozol-9-Yl] Methyl]Naphthalene-2-Carboximidamide (Zk-806450) Complex

Enzymatic activity of Bovine Trypsin 7-[[2-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-9H- Carbozol-9-Yl] Methyl]Naphthalene-2-Carboximidamide (Zk-806450) Complex

All present enzymatic activity of Bovine Trypsin 7-[[2-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-9H- Carbozol-9-Yl] Methyl]Naphthalene-2-Carboximidamide (Zk-806450) Complex:
3.4.21.4;

Protein crystallography data

The structure of Bovine Trypsin 7-[[2-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-9H- Carbozol-9-Yl] Methyl]Naphthalene-2-Carboximidamide (Zk-806450) Complex, PDB code: 1qb9 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 (°) 54.510, 54.510, 108.710, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 27.8

Other elements in 1qb9:

The structure of Bovine Trypsin 7-[[2-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-9H- Carbozol-9-Yl] Methyl]Naphthalene-2-Carboximidamide (Zk-806450) Complex also contains other interesting chemical elements:

Potassium (K) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Bovine Trypsin 7-[[2-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-9H- Carbozol-9-Yl] Methyl]Naphthalene-2-Carboximidamide (Zk-806450) Complex (pdb code 1qb9). 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-[[2-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-9H- Carbozol-9-Yl] Methyl]Naphthalene-2-Carboximidamide (Zk-806450) Complex, PDB code: 1qb9:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1qb9

Go back to Calcium Binding Sites List in 1qb9
Calcium binding site 1 out of 2 in the Bovine Trypsin 7-[[2-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-9H- Carbozol-9-Yl] Methyl]Naphthalene-2-Carboximidamide (Zk-806450) 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-[[2-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-9H- Carbozol-9-Yl] Methyl]Naphthalene-2-Carboximidamide (Zk-806450) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:29.9
occ:1.00
 O A:VAL63 2.3 21.4 1.0
OE2 A:GLU68 2.4 20.8 1.0
OE1 A:GLU58 2.4 25.9 1.0
O A:ASN60 2.4 17.7 1.0
O A:HOH308 2.4 21.4 1.0
O A:HOH333 2.7 29.3 1.0
CD A:GLU68 3.4 23.5 1.0
C A:VAL63 3.5 23.0 1.0
C A:ASN60 3.6 21.3 1.0
CD A:GLU58 3.6 21.9 1.0
CG A:GLU68 3.7 23.6 1.0
OE1 A:GLU65 3.8 45.2 1.0
CA A:VAL64 4.0 27.8 1.0
N A:GLU65 4.0 31.7 1.0
OE2 A:GLU58 4.1 19.3 1.0
N A:ASN60 4.1 23.0 1.0
N A:VAL64 4.2 24.2 1.0
N A:ASP59 4.2 19.4 1.0
CA A:ASN60 4.4 21.8 1.0
O A:HOH332 4.4 44.8 1.0
N A:VAL63 4.4 20.8 1.0
N A:ILE61 4.5 20.7 1.0
C A:VAL64 4.5 27.9 1.0
CA A:ILE61 4.5 20.5 1.0
OE1 A:GLU68 4.5 24.4 1.0
CA A:VAL63 4.5 21.3 1.0
CD A:GLU65 4.5 43.5 1.0
CG A:GLU65 4.6 41.7 1.0
CA A:GLU58 4.6 17.9 1.0
CB A:ASN60 4.7 24.6 1.0
C A:ILE61 4.7 21.1 1.0
CG A:GLU58 4.8 23.2 1.0
CB A:VAL63 4.9 23.7 1.0
CB A:GLU65 4.9 37.9 1.0
C A:ASP59 4.9 20.8 1.0
CB A:GLU58 4.9 18.4 1.0

Calcium binding site 2 out of 2 in 1qb9

Go back to Calcium Binding Sites List in 1qb9
Calcium binding site 2 out of 2 in the Bovine Trypsin 7-[[2-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-9H- Carbozol-9-Yl] Methyl]Naphthalene-2-Carboximidamide (Zk-806450) 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-[[2-[[1-(1-Iminoethyl)Piperidin-4-Yl]Oxy]-9H- Carbozol-9-Yl] Methyl]Naphthalene-2-Carboximidamide (Zk-806450) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:63.9
occ:0.64
 OE2 A:GLU65 2.3 42.9 1.0
OD2 A:ASP59 2.6 39.3 1.0
O A:HOH326 2.9 38.0 1.0
CD A:GLU65 3.2 43.5 1.0
OE1 A:GLU65 3.3 45.2 1.0
CG A:ASP59 3.6 31.6 1.0
CB A:ASN60 3.8 24.6 1.0
CB A:ASP59 4.1 22.7 1.0
CG1 A:VAL140 4.1 22.3 1.0
O A:HOH421 4.2 32.8 1.0
N A:ASN60 4.3 23.0 1.0
CG A:GLU65 4.5 41.7 1.0
OD1 A:ASP59 4.6 30.4 1.0
CA A:ASN60 4.6 21.8 1.0
ND2 A:ASN60 4.8 25.1 1.0
CG A:ASN60 4.9 24.0 1.0
C A:ASP59 4.9 20.8 1.0
CB A:ALA15 5.0 39.0 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: Sat Dec 12 03:16:05 2020

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