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Calcium in PDB 2bfn: The Crystal Structure of the Complex of the Haloalkane Dehalogenase Linb with the Product of Dehalogenation Reaction 1,2-Dichloropropane.

Enzymatic activity of The Crystal Structure of the Complex of the Haloalkane Dehalogenase Linb with the Product of Dehalogenation Reaction 1,2-Dichloropropane.

All present enzymatic activity of The Crystal Structure of the Complex of the Haloalkane Dehalogenase Linb with the Product of Dehalogenation Reaction 1,2-Dichloropropane.:
3.8.1.5;

Protein crystallography data

The structure of The Crystal Structure of the Complex of the Haloalkane Dehalogenase Linb with the Product of Dehalogenation Reaction 1,2-Dichloropropane., PDB code: 2bfn was solved by P.Banas, M.Otyepka, P.Jerabek, J.Vevodova, M.Bohac, J.Damborsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.55 / 1.6
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.571, 72.142, 73.311, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 17.1

Other elements in 2bfn:

The structure of The Crystal Structure of the Complex of the Haloalkane Dehalogenase Linb with the Product of Dehalogenation Reaction 1,2-Dichloropropane. also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of the Complex of the Haloalkane Dehalogenase Linb with the Product of Dehalogenation Reaction 1,2-Dichloropropane. (pdb code 2bfn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The Crystal Structure of the Complex of the Haloalkane Dehalogenase Linb with the Product of Dehalogenation Reaction 1,2-Dichloropropane., PDB code: 2bfn:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2bfn

Go back to Calcium Binding Sites List in 2bfn
Calcium binding site 1 out of 3 in the The Crystal Structure of the Complex of the Haloalkane Dehalogenase Linb with the Product of Dehalogenation Reaction 1,2-Dichloropropane.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of the Complex of the Haloalkane Dehalogenase Linb with the Product of Dehalogenation Reaction 1,2-Dichloropropane. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1299

b:5.4
occ:1.00
 OE1 A:GLN165 2.3 7.2 1.0
OD1 A:ASP166 2.4 6.5 1.0
OD2 A:ASP166 2.5 7.5 1.0
O A:HOH2207 2.6 31.5 1.0
CG A:ASP166 2.8 6.1 1.0
O A:HOH2208 3.4 27.0 1.0
CD A:GLN165 3.4 10.5 1.0
CG A:GLN165 3.9 9.5 1.0
CB A:ASP166 4.3 4.9 1.0
O A:HOH2202 4.3 25.9 1.0
OE2 A:GLU161 4.4 14.2 0.7
O A:HOH2203 4.5 7.7 1.0
NE2 A:GLN165 4.5 13.9 1.0
CB A:GLN165 4.8 7.2 1.0
O A:HOH2205 4.8 15.4 1.0
CG A:GLU161 4.9 11.8 1.0
OE2 A:GLU161 5.0 13.1 0.3

Calcium binding site 2 out of 3 in 2bfn

Go back to Calcium Binding Sites List in 2bfn
Calcium binding site 2 out of 3 in the The Crystal Structure of the Complex of the Haloalkane Dehalogenase Linb with the Product of Dehalogenation Reaction 1,2-Dichloropropane.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of the Complex of the Haloalkane Dehalogenase Linb with the Product of Dehalogenation Reaction 1,2-Dichloropropane. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1300

b:12.4
occ:1.00
 OD1 A:ASP149 2.1 10.3 0.3
O A:HOH2185 2.3 7.9 1.0
O A:HOH2186 2.3 22.2 1.0
OD1 A:ASP149 2.4 9.7 0.7
OE1 A:GLN152 2.4 9.4 1.0
CG A:ASP149 3.3 10.8 0.3
CG A:ASP149 3.4 11.9 0.7
CD A:GLN152 3.5 6.8 1.0
O A:HOH2181 4.0 30.9 1.0
NE2 A:GLN152 4.0 6.6 1.0
OD2 A:ASP149 4.0 13.5 0.7
OD2 A:ASP149 4.0 10.6 0.3
CB A:ASP149 4.3 9.8 1.0
CA A:ASP149 4.3 9.5 1.0
O A:HOH2182 4.4 26.4 1.0
O A:HOH2180 4.5 11.0 1.0
CG A:GLN152 4.8 6.1 1.0
N A:ASP149 4.8 9.4 1.0

Calcium binding site 3 out of 3 in 2bfn

Go back to Calcium Binding Sites List in 2bfn
Calcium binding site 3 out of 3 in the The Crystal Structure of the Complex of the Haloalkane Dehalogenase Linb with the Product of Dehalogenation Reaction 1,2-Dichloropropane.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of the Complex of the Haloalkane Dehalogenase Linb with the Product of Dehalogenation Reaction 1,2-Dichloropropane. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1301

b:12.4
occ:0.50
 O A:HOH2038 2.4 12.9 1.0
O A:HOH2039 2.4 13.8 1.0
O A:HOH2019 2.5 22.5 1.0
O A:HOH2040 2.5 22.2 1.0
OD1 A:ASP30 4.2 9.5 1.0
O A:HOH2148 4.3 21.6 1.0
OD1 A:ASP100 4.4 8.2 1.0
OD2 A:ASP30 4.4 10.0 1.0
CG A:ASP30 4.7 8.9 1.0
O A:HOH2020 5.0 25.2 1.0

Reference:

M.Minincova, Z.Prokop, J.Vevodova, Y.Nagata, J.Damborsky. Weak Activity of Haloalkane Dehalogenase Linb with 1,2,3-Trichloropropane Revealed By X-Ray Crystallography and Microcalorimetry Appl.Environ.Microbiol. V. 73 2005 2007.
ISSN: ISSN 0099-2240
PubMed: 17259360
DOI: 10.1128/AEM.02416-06
Page generated: Sat Dec 12 03:32:24 2020

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