Calcium in PDB 3whn: Hemerythrin-Like Domain of Dcrh I119H Mutant (Met)

The structure of Hemerythrin-Like Domain of Dcrh I119H Mutant (Met), PDB code: 3whn was solved by Y.Okamoto, A.Onoda, H.Sugimoto, Y.Takano, S.Hirota, D.M.Kurtz Jr., Y.Shiro, T.Hayashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.573, 44.082, 46.715, 92.71, 102.59, 90.02
R / Rfree (%)	19.3 / 24.8

The structure of Hemerythrin-Like Domain of Dcrh I119H Mutant (Met) also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the Hemerythrin-Like Domain of Dcrh I119H Mutant (Met) (pdb code 3whn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Hemerythrin-Like Domain of Dcrh I119H Mutant (Met), PDB code: 3whn:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Hemerythrin-Like Domain of Dcrh I119H Mutant (Met)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Hemerythrin-Like Domain of Dcrh I119H Mutant (Met) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:12.9 occ:1.00 O A:HOH339 2.4 18.4 1.0 O A:HOH433 2.4 8.4 1.0 OD1 A:ASP100 2.4 18.6 1.0 O A:HOH440 2.5 10.0 1.0 O A:HOH311 2.5 13.7 1.0 CG A:ASP100 3.5 17.7 1.0 OD2 A:ASP100 3.9 16.2 1.0 O A:ALA98 4.7 14.3 1.0 CB A:ASP100 4.8 16.9 1.0

Calcium binding site 2 out of 2 in the Hemerythrin-Like Domain of Dcrh I119H Mutant (Met)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Hemerythrin-Like Domain of Dcrh I119H Mutant (Met) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:25.0 occ:1.00 O B:HOH333 2.3 18.1 1.0 O B:HOH380 2.4 26.5 1.0 NH2 B:ARG131 2.4 18.0 1.0 O B:HOH401 2.4 30.7 1.0 O B:HOH410 2.5 32.9 1.0 O B:ASN15 2.5 8.8 1.0 CZ B:ARG131 3.6 20.3 1.0 C B:ASN15 3.6 9.2 1.0 OE2 B:GLU127 3.9 16.7 1.0 NH1 B:ARG131 4.1 17.2 1.0 N B:ASN15 4.2 11.0 1.0 OD2 B:ASP20 4.3 10.1 1.0 CA B:ASN15 4.5 9.7 1.0 N B:LEU16 4.5 8.5 1.0 CA B:LEU16 4.6 9.0 1.0 CD B:PRO17 4.6 9.0 1.0 NE B:ARG131 4.6 20.2 1.0 C B:LEU16 4.6 8.8 1.0 N B:PRO17 4.7 9.1 1.0 CB B:ALA14 4.7 14.7 1.0 C B:ALA14 4.9 12.5 1.0 CG B:PRO17 4.9 9.6 1.0

Y.Okamoto, A.Onoda, H.Sugimoto, Y.Takano, S.Hirota, D.M.Kurtz Jr., Y.Shiro, T.Hayashi. H2O2-Dependent Substrate Oxidation By An Engineered Diiron Site in A Bacterial Hemerythrin Chem.Commun.(Camb.) 2014.
ISSN: ESSN 1364-548X
PubMed: 24400317
DOI: 10.1039/C3CC48108E