Calcium in PDB 1iz8: Re-Refinement of the Structure of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution

The structure of Re-Refinement of the Structure of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution, PDB code: 1iz8 was solved by V.A.Streltsov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.94 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	50.227, 71.721, 73.319, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 24.8

The structure of Re-Refinement of the Structure of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Calcium atom in the Re-Refinement of the Structure of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution (pdb code 1iz8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Re-Refinement of the Structure of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution, PDB code: 1iz8:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Re-Refinement of the Structure of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Re-Refinement of the Structure of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:17.4 occ:1.00 O A:PRO175 2.4 16.2 1.0 O A:HOH1007 2.4 10.3 1.0 O A:HOH1028 2.4 12.8 1.0 O A:ILE178 2.4 12.0 1.0 C A:PRO175 3.5 16.1 1.0 C A:ILE178 3.6 14.4 1.0 N A:ILE178 4.2 12.6 1.0 CA A:GLY176 4.2 9.0 1.0 N A:GLY176 4.3 14.5 1.0 C A:GLY176 4.3 13.3 1.0 O A:GLY176 4.4 18.7 1.0 CA A:ILE178 4.4 13.7 1.0 CA A:PRO175 4.5 12.6 1.0 O A:HOH1041 4.5 11.0 1.0 O A:ARG180 4.5 19.8 1.0 CB A:ILE178 4.6 16.9 1.0 N A:LEU179 4.6 15.5 1.0 C A:LEU179 4.7 21.1 1.0 CA A:LEU179 4.7 18.3 1.0 O A:LEU179 4.9 22.1 1.0 N A:LEU177 4.9 15.5 1.0 CB A:PRO175 5.0 13.1 1.0

Calcium binding site 2 out of 3 in the Re-Refinement of the Structure of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Re-Refinement of the Structure of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:36.6 occ:0.25 O A:HOH1271 2.0 47.1 1.0 O A:HOH1236 2.2 23.8 1.0 O A:HOH1231 2.3 26.8 1.0 O A:HOH1272 2.8 29.4 1.0 O A:HOH1211 3.8 34.5 1.0 OD1 A:ASP30 4.0 22.2 1.0 OD2 A:ASP30 4.4 14.5 1.0 OD1 A:ASP100 4.5 11.8 1.0 O A:HOH1232 4.6 24.2 1.0 CG A:ASP30 4.6 20.0 1.0

Calcium binding site 3 out of 3 in the Re-Refinement of the Structure of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Re-Refinement of the Structure of Hydrolytic Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 with 1,3-Propanediol, A Product of Debromidation of Dibrompropane, at 2.0A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:15.9 occ:0.25 OD2 A:ASP149 1.9 37.0 1.0 O A:HOH1003 2.0 7.3 1.0 O A:HOH1276 2.3 26.6 1.0 O A:HOH1117 2.6 18.8 1.0 OE1 A:GLN152 2.6 18.5 1.0 CG A:ASP149 2.6 35.4 1.0 OD1 A:ASP149 3.2 37.4 1.0 CB A:ASP149 3.6 29.4 1.0 O A:HOH1218 3.7 26.9 1.0 CD A:GLN152 3.7 18.4 1.0 CA A:ASP149 3.8 22.9 1.0 O A:HOH1273 4.1 33.2 1.0 NE2 A:GLN152 4.3 11.2 1.0 O A:HOH1027 4.4 25.8 1.0 N A:ASP149 4.5 20.2 1.0 CG A:GLN152 4.9 17.5 1.0

V.A.Streltsov, Z.Prokop, J.Damborsky, Y.Nagata, A.Oakley, M.C.J.Wilce. Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26: X-Ray Crystallographic Studies of Dehalogenation of Brominated Substrates Biochemistry V. 42 10104 2003.
ISSN: ISSN 0006-2960
PubMed: 12939138
DOI: 10.1021/BI027280A