Zinc in PDB 2o6p: Crystal Structure of the Heme-Isdc Complex

The structure of Crystal Structure of the Heme-Isdc Complex, PDB code: 2o6p was solved by K.H.Sharp, S.Schneider, A.Cockayne, M.Paoli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.99 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.489, 70.441, 88.685, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 22.2

The structure of Crystal Structure of the Heme-Isdc Complex also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Crystal Structure of the Heme-Isdc Complex (pdb code 2o6p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Heme-Isdc Complex, PDB code: 2o6p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Heme-Isdc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Heme-Isdc Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:22.1 occ:0.75 O1A B:HEM190 2.1 32.1 1.0 O A:HOH1053 2.1 28.3 1.0 O A:HOH1065 2.2 20.3 1.0 ND1 A:HIS134 2.2 20.1 1.0 CGA B:HEM190 2.9 29.4 1.0 O2A B:HEM190 2.9 32.9 1.0 CE1 A:HIS134 3.2 20.1 1.0 CG A:HIS134 3.3 18.9 1.0 CB A:HIS134 3.6 17.9 1.0 CMA B:HEM190 3.8 20.7 1.0 CA A:HIS134 3.8 17.3 1.0 N A:HIS135 4.0 17.2 1.0 O A:HIS135 4.3 17.5 1.0 C3A B:HEM190 4.3 19.6 1.0 CBA B:HEM190 4.3 27.0 1.0 NE2 A:HIS134 4.3 18.9 1.0 CD2 A:HIS134 4.4 18.1 1.0 O A:ASP133 4.5 17.6 1.0 C A:HIS134 4.5 17.8 1.0 CD1 B:ILE48 4.5 18.5 0.5 O A:HOH1074 4.5 39.1 1.0 C2A B:HEM190 4.6 20.6 1.0 CAA B:HEM190 4.7 22.4 1.0 CE1 A:TYR136 5.0 15.8 1.0 N A:HIS134 5.0 16.9 1.0 CD1 B:ILE48 5.0 17.4 0.5 C A:HIS135 5.0 17.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Heme-Isdc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Heme-Isdc Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:40.4 occ:0.75 NE2 A:HIS135 2.1 24.9 0.8 OD1 A:ASP133 2.1 20.6 1.0 O A:HOH1083 2.2 51.8 1.0 CE1 A:HIS135 2.9 24.7 0.8 CG A:ASP133 3.0 18.4 1.0 OD2 A:ASP133 3.2 20.1 1.0 CD2 A:HIS135 3.2 24.1 0.8 O A:HOH1084 3.3 28.3 1.0 O A:HOH1082 3.8 50.1 1.0 ND1 A:HIS135 4.1 24.7 0.8 CG A:HIS135 4.3 21.8 0.8 O A:HOH1085 4.4 30.0 1.0 CB A:ASP133 4.4 17.4 1.0 C A:ASP133 4.5 17.1 1.0 O A:ASP133 4.5 17.6 1.0 N A:HIS134 4.7 16.9 1.0 CA A:ASP133 4.8 17.0 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Heme-Isdc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Heme-Isdc Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:18.5 occ:1.00 OD1 B:ASP133 2.0 18.5 1.0 NE2 B:HIS135 2.0 18.0 1.0 CG B:ASP133 2.8 18.2 1.0 OD2 B:ASP133 3.0 19.2 1.0 CD2 B:HIS135 3.0 16.6 1.0 CE1 B:HIS135 3.0 17.4 1.0 O B:HOH1009 3.7 19.4 1.0 ND1 B:HIS135 4.1 16.2 1.0 CG B:HIS135 4.2 16.1 1.0 CB B:ASP133 4.3 18.4 1.0 O B:HOH1017 4.3 24.3 1.0 C B:ASP133 4.4 17.3 1.0 O B:ASP133 4.4 17.5 1.0 N B:HIS134 4.7 16.7 1.0 O B:HOH1026 4.8 30.0 1.0 CA B:ASP133 4.8 17.8 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Heme-Isdc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Heme-Isdc Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:23.9 occ:0.75 NE2 B:HIS134 2.0 21.8 1.0 O1A A:HEM190 2.0 27.1 1.0 O B:HOH1051 2.3 31.2 1.0 O B:HOH1103 2.3 21.6 1.0 CGA A:HEM190 2.9 25.7 1.0 CE1 B:HIS134 3.0 22.5 1.0 CD2 B:HIS134 3.0 20.0 1.0 O2A A:HEM190 3.1 27.8 1.0 O A:HOH1059 4.1 39.7 1.0 ND1 B:HIS134 4.1 20.7 1.0 CG B:HIS134 4.1 18.7 1.0 CD1 B:TYR132 4.2 17.6 1.0 CBA A:HEM190 4.3 24.0 1.0 CE1 B:TYR132 4.4 17.9 1.0 N B:ASP133 4.7 17.8 1.0 CAA A:HEM190 4.8 21.5 1.0 CA B:TYR132 4.8 19.9 1.0 CG B:TYR132 4.9 18.5 1.0 O B:ASP133 5.0 17.5 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Heme-Isdc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Heme-Isdc Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:17.7 occ:1.00 O B:GLY28 2.2 16.9 1.0 N B:GLY28 2.2 17.4 1.0 C B:GLY28 2.9 17.3 1.0 CA B:GLY28 2.9 17.5 1.0 N B:SER29 4.2 17.8 1.0 CA B:SER29 5.0 18.5 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Heme-Isdc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Heme-Isdc Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1005 b:21.3 occ:0.75 O B:HOH1088 2.0 21.0 1.0 NZ B:LYS58 2.0 23.3 1.0 O B:HOH1098 2.4 15.5 0.5 O B:HOH1098 2.9 14.0 0.5 CE B:LYS58 3.0 23.3 1.0 O B:HOH1076 4.1 23.8 1.0 OG B:SER31 4.1 18.8 1.0 O B:HOH1099 4.3 24.0 0.5 CD B:LYS58 4.3 22.5 1.0 O B:HOH1099 4.6 31.1 0.5 CB B:SER31 4.8 18.9 1.0 O B:HOH1102 4.9 27.5 1.0

K.H.Sharp, S.Schneider, A.Cockayne, M.Paoli. Crystal Structure of the Heme-Isdc Complex, the Central Conduit of the Isd Iron/Heme Uptake System in Staphylococcus Aureus. J. Biol. Chem. V. 282 10625 2007.
ISSN: ISSN 0021-9258
PubMed: 17287214
DOI: 10.1074/JBC.M700234200