Cadmium in PDB 1rtx: Crystal Structure of Synechocystis Hemoglobin with A Covalent Heme Linkage

The structure of Crystal Structure of Synechocystis Hemoglobin with A Covalent Heme Linkage, PDB code: 1rtx was solved by J.A.Hoy, S.Kundu, J.T.Trent, S.Ramaswamy, M.S.Hargrove, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.76 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.500, 46.000, 61.000, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 22.4

The structure of Crystal Structure of Synechocystis Hemoglobin with A Covalent Heme Linkage also contains other interesting chemical elements:

Potassium	(K)	1 atom
Iron	(Fe)	1 atom

The binding sites of Cadmium atom in the Crystal Structure of Synechocystis Hemoglobin with A Covalent Heme Linkage (pdb code 1rtx). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of Synechocystis Hemoglobin with A Covalent Heme Linkage, PDB code: 1rtx:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Crystal Structure of Synechocystis Hemoglobin with A Covalent Heme Linkage


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Synechocystis Hemoglobin with A Covalent Heme Linkage within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd126 b:23.3 occ:1.00 ND1 A:HIS77 2.2 20.9 1.0 ND1 A:HIS33 2.4 22.2 1.0 O A:HIS33 2.6 22.0 1.0 CE1 A:HIS77 3.0 24.5 1.0 CE1 A:HIS33 3.3 22.3 1.0 C A:HIS33 3.3 21.4 1.0 CG A:HIS77 3.3 23.7 1.0 CG A:HIS33 3.4 22.0 1.0 CB A:HIS33 3.7 22.7 1.0 CB A:HIS77 3.8 23.2 1.0 N A:PHE34 4.0 21.6 1.0 CA A:HIS33 4.1 22.2 1.0 NE2 A:HIS77 4.2 22.4 1.0 CA A:PHE34 4.2 21.2 1.0 CD2 A:HIS77 4.3 21.9 1.0 NE2 A:HIS33 4.4 20.8 1.0 CA A:HIS77 4.5 24.5 1.0 CD2 A:HIS33 4.5 20.5 1.0 O A:HIS77 4.9 23.9 1.0 C A:PHE34 4.9 21.4 1.0 CD1 A:PHE34 4.9 22.3 1.0

Cadmium binding site 2 out of 2 in the Crystal Structure of Synechocystis Hemoglobin with A Covalent Heme Linkage


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Synechocystis Hemoglobin with A Covalent Heme Linkage within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd127 b:38.4 occ:1.00 O A:HOH131 2.2 35.6 1.0 O A:HOH130 2.2 34.4 1.0 OD1 A:ASP120 2.3 28.5 1.0 OD2 A:ASP120 2.7 28.6 1.0 CG A:ASP120 2.8 30.5 1.0 O A:HOH208 3.8 54.8 1.0 CA A:GLY63 4.1 29.7 1.0 O A:ALA116 4.1 32.4 1.0 CB A:ASP120 4.3 28.3 1.0 C A:GLY63 4.5 29.5 1.0 O A:GLY63 4.7 28.6 1.0 NE A:ARG67 4.8 40.0 1.0 C A:ALA116 5.0 33.0 1.0

J.A.Hoy, S.Kundu, J.T.Trent, S.Ramaswamy, M.S.Hargrove. The Crystal Structure of Synechocystis Hemoglobin with A Covalent Heme Linkage. J.Biol.Chem. V. 279 16535 2004.
ISSN: ISSN 0021-9258
PubMed: 14736872
DOI: 10.1074/JBC.M313707200