Chlorine in PDB 3agu: Hemerythrin-Like Domain of Dcrh (Semimet-R)

The structure of Hemerythrin-Like Domain of Dcrh (Semimet-R), PDB code: 3agu was solved by A.Onoda, Y.Okamoto, H.Sugimoto, E.Mizohata, T.Inoue, 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 / 1.81
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.425, 44.903, 48.076, 95.21, 103.98, 89.95
R / Rfree (%)	24.7 / 29.2

The structure of Hemerythrin-Like Domain of Dcrh (Semimet-R) also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

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

Chlorine binding site 1 out of 2 in the Hemerythrin-Like Domain of Dcrh (Semimet-R)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hemerythrin-Like Domain of Dcrh (Semimet-R) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:11.2 occ:1.00 CL A:CFO201 0.0 11.2 1.0 FE2 A:CFO201 2.4 8.9 1.0 O A:CFO201 3.1 5.7 1.0 NE2 A:HIS23 3.2 9.2 1.0 CD2 A:HIS23 3.3 7.3 1.0 OD2 A:ASP123 3.3 7.3 1.0 NE2 A:HIS59 3.4 8.4 1.0 CD1 A:LEU115 3.6 17.5 1.0 CG1 A:ILE119 3.7 8.2 1.0 CD2 A:HIS59 3.7 6.4 1.0 CD2 A:HIS118 3.7 9.0 1.0 CD1 A:LEU26 4.1 10.9 1.0 CD1 A:ILE119 4.2 9.2 1.0 CE1 A:PHE60 4.2 8.9 1.0 CE1 A:HIS23 4.4 9.5 1.0 CG A:LEU115 4.4 16.7 1.0 CG A:ASP123 4.5 8.4 1.0 CG A:HIS23 4.5 8.2 1.0 CE1 A:HIS59 4.5 7.6 1.0 NE2 A:HIS118 4.6 9.9 1.0 CZ3 A:TRP114 4.7 12.7 1.0 CG A:HIS118 4.7 9.8 1.0 OE2 A:GLU63 4.7 5.8 1.0 FE1 A:CFO201 4.7 6.9 1.0 CG A:HIS59 5.0 8.2 1.0 CD1 A:PHE60 5.0 8.0 1.0

Chlorine binding site 2 out of 2 in the Hemerythrin-Like Domain of Dcrh (Semimet-R)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hemerythrin-Like Domain of Dcrh (Semimet-R) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:10.5 occ:1.00 CL B:CFO201 0.0 10.5 1.0 FE2 B:CFO201 2.4 9.3 1.0 O B:CFO201 3.0 7.1 1.0 NE2 B:HIS23 3.3 9.2 1.0 NE2 B:HIS59 3.4 8.1 1.0 OD2 B:ASP123 3.4 6.7 1.0 CD2 B:HIS23 3.4 7.5 1.0 CD1 B:LEU115 3.6 17.4 1.0 CG1 B:ILE119 3.7 8.6 1.0 CD2 B:HIS59 3.7 6.5 1.0 CD2 B:HIS118 3.7 8.9 1.0 CE1 B:PHE60 4.1 8.2 1.0 CD1 B:LEU26 4.2 10.5 1.0 CD1 B:ILE119 4.3 9.2 1.0 CE1 B:HIS23 4.5 9.2 1.0 CG B:LEU115 4.5 16.5 1.0 CG B:ASP123 4.5 8.7 1.0 CZ3 B:TRP114 4.6 12.8 1.0 NE2 B:HIS118 4.6 10.8 1.0 CE1 B:HIS59 4.6 7.0 1.0 CG B:HIS23 4.6 8.6 1.0 CG B:HIS118 4.7 9.7 1.0 FE1 B:CFO201 4.7 7.8 1.0 OE2 B:GLU63 4.8 5.3 1.0 CD1 B:PHE60 4.9 7.9 1.0 OD1 B:ASP123 5.0 9.1 1.0 CG B:HIS59 5.0 7.8 1.0 CZ B:PHE60 5.0 6.8 1.0 N B:ILE119 5.0 10.5 1.0

A.Onoda, Y.Okamoto, H.Sugimoto, E.Mizohata, T.Inoue, Y.Shiro, T.Hayashi. Characteristics of Diiron Site with Large Cavity in Hemerythrin-Like Domain of Dcrh To Be Published.