Cadmium in PDB 4gje: Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium

The structure of Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium, PDB code: 4gje was solved by X.Zhang, M.Paetzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.98 / 1.60
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	49.627, 49.627, 116.313, 90.00, 90.00, 120.00
R / Rfree (%)	12.1 / 15

The structure of Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Cadmium atom in the Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium (pdb code 4gje). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium, PDB code: 4gje:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in the Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium


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 the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd101 b:19.8 occ:1.00 OXT A:ACT109 2.3 22.1 1.0 OD1 A:ASP33 2.3 21.6 1.0 O A:CYS35 2.4 18.8 1.0 O A:HOH224 2.4 26.3 1.0 OD2 A:ASP33 2.5 22.0 1.0 SG A:CYS35 2.6 18.5 1.0 CG A:ASP33 2.7 20.5 1.0 C A:ACT109 3.2 22.0 1.0 C A:CYS35 3.2 17.2 1.0 CH3 A:ACT109 3.4 23.7 1.0 CB A:CYS35 3.7 17.8 1.0 CA A:CYS35 3.7 18.5 1.0 N A:CYS35 3.7 18.2 1.0 O A:HOH225 3.7 20.4 1.0 CB A:ASP33 4.3 20.0 1.0 O A:ACT109 4.3 24.2 1.0 N A:ILE36 4.3 17.4 1.0 CA A:ILE36 4.8 17.4 1.0 N A:GLY34 4.8 19.0 1.0 C A:ILE36 4.9 19.5 1.0 C A:GLY34 5.0 18.8 1.0

Cadmium binding site 2 out of 7 in the Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium


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 the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd102 b:25.4 occ:0.60 O A:HOH235 1.6 24.3 1.0 O A:HOH236 1.9 35.4 1.0 OD2 A:ASP65 2.1 39.7 1.0 OE1 A:GLU76 2.3 22.9 1.0 OE2 A:GLU76 2.5 27.8 1.0 O A:THR71 2.6 24.6 1.0 O A:HOH209 2.7 52.0 1.0 CD A:GLU76 2.8 19.0 1.0 CG A:ASP65 3.3 42.7 0.5 C A:THR71 3.6 21.1 1.0 OG1 A:THR71 3.9 27.4 1.0 CA A:VAL72 4.0 18.1 1.0 OD1 A:ASP65 4.1 45.5 0.5 N A:VAL72 4.2 18.4 1.0 N A:GLU66 4.2 42.9 1.0 CG A:GLU76 4.3 18.0 1.0 CB A:ASP65 4.3 42.3 1.0 N A:ASP73 4.4 16.5 1.0 OE1 A:GLU66 4.5 35.5 1.0 CA A:ASP65 4.6 41.6 1.0 C A:VAL72 4.7 16.3 1.0 CA A:THR71 4.7 23.3 1.0 CB A:GLU66 4.8 39.4 1.0 CB A:THR71 4.8 24.1 1.0 C A:ASP65 4.9 43.4 1.0 CB A:GLU76 4.9 17.9 1.0

Cadmium binding site 3 out of 7 in the Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd103 b:20.2 occ:1.00 O A:HOH226 2.2 28.2 1.0 OE2 A:GLU40 2.3 20.4 1.0 O A:PHE27 2.3 19.1 1.0 O A:HOH225 2.3 20.4 1.0 OE1 A:GLU40 2.4 19.4 1.0 CD A:GLU40 2.7 20.0 1.0 C A:PHE27 3.4 20.7 1.0 CG A:GLU40 4.2 19.1 1.0 CA A:PHE27 4.2 19.0 1.0 N A:VAL28 4.3 22.0 1.0 CA A:VAL28 4.3 23.5 1.0 CB A:PHE27 4.4 19.4 1.0 O A:HOH241 4.4 23.0 1.0 O A:HOH227 4.4 37.8 1.0 OXT A:ACT109 4.5 22.1 1.0 O A:ACT109 4.6 24.2 1.0 CA A:ILE36 4.7 17.4 1.0 CG2 A:ILE36 4.9 18.4 1.0 N A:SER37 4.9 18.7 1.0 CG1 A:VAL28 4.9 29.6 1.0 C A:ACT109 5.0 22.0 1.0 CB A:ILE36 5.0 16.1 1.0

Cadmium binding site 4 out of 7 in the Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd104 b:20.4 occ:1.00 OD2 A:ASP87 2.2 20.1 1.0 OE1 A:GLU56 2.2 22.1 1.0 OE2 A:GLU56 2.4 24.4 1.0 SG A:CYS84 2.5 19.0 1.0 CD A:GLU56 2.6 23.3 1.0 CG A:ASP87 3.1 16.7 1.0 OD1 A:ASP87 3.2 19.7 1.0 CD A:CD105 3.5 18.5 1.0 CB A:CYS84 3.6 18.3 1.0 CA A:PRO52 3.7 21.3 1.0 CA A:CYS84 3.8 18.0 1.0 O A:HOH234 3.9 39.4 1.0 CB A:PRO52 4.1 19.6 1.0 O A:CYS84 4.2 17.6 1.0 CG A:GLU56 4.2 22.3 1.0 N A:PRO52 4.4 19.4 1.0 CB A:ASP87 4.5 19.2 1.0 C A:CYS84 4.5 16.8 1.0 O A:ASN51 4.8 20.9 1.0 C A:ASN51 4.8 19.7 1.0 N A:THR53 4.8 24.2 1.0 C A:PRO52 4.9 20.0 1.0 CB A:GLU56 4.9 22.5 1.0 N A:CYS84 5.0 17.1 1.0

Cadmium binding site 5 out of 7 in the Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd105 b:18.5 occ:1.00 O A:CYS84 2.2 17.6 1.0 OD1 A:ASP87 2.4 19.7 1.0 OE1 A:GLN50 2.5 19.1 1.0 SG A:CYS84 2.6 19.0 1.0 C A:CYS84 3.1 16.8 1.0 CG A:ASP87 3.4 16.7 1.0 CD A:GLN50 3.5 18.6 1.0 CD A:CD104 3.5 20.4 1.0 CB A:CYS84 3.6 18.3 1.0 CA A:CYS84 3.7 18.0 1.0 OD2 A:ASP87 3.7 20.1 1.0 N A:MET85 4.0 15.8 1.0 CB A:GLN50 4.2 18.4 1.0 NE2 A:GLN50 4.2 22.0 1.0 N A:ASN51 4.3 19.8 1.0 CA A:MET85 4.3 16.2 1.0 CG A:GLN50 4.4 19.8 1.0 CA A:GLN50 4.5 19.7 1.0 C A:ASP87 4.6 20.1 1.0 N A:ASP87 4.6 18.1 1.0 CB A:ASP87 4.7 19.2 1.0 N A:ASP88 4.7 20.5 1.0 C A:MET85 4.8 16.9 1.0 CA A:ASP87 4.8 18.2 1.0 C A:GLN50 4.9 19.0 1.0 O A:ASP87 4.9 20.3 1.0

Cadmium binding site 6 out of 7 in the Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd106 b:19.9 occ:1.00 OD2 A:ASP73 2.2 20.5 1.0 OE2 A:GLU66 2.2 31.6 1.0 OD2 A:ASP75 2.3 23.1 1.0 OD1 A:ASP75 2.5 19.6 1.0 OD1 A:ASP73 2.6 18.0 1.0 CG A:ASP75 2.7 19.9 1.0 OE1 A:GLU66 2.8 35.5 1.0 CG A:ASP73 2.8 15.7 1.0 CD A:GLU66 2.9 33.6 1.0 CB A:ASP75 4.2 17.9 1.0 CB A:ASP73 4.3 18.2 1.0 CG A:GLU76 4.3 18.0 1.0 CG A:GLU66 4.4 36.9 1.0 N A:GLU76 4.5 17.4 1.0 OD1 A:ASP2 4.5 51.8 1.0 CD A:GLU76 4.7 19.0 1.0 N A:ASP75 4.8 17.3 1.0 CE1 A:TYR5 4.8 37.6 1.0 OE2 A:GLU76 4.9 27.8 1.0 CA A:ASP75 4.9 17.4 1.0

Cadmium binding site 7 out of 7 in the Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of the Refolded Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd107 b:31.0 occ:0.65 O A:HOH246 1.9 46.6 1.0 O A:HOH247 2.4 47.2 1.0 OE2 A:GLU59 2.4 33.2 1.0 O A:HOH245 2.5 63.2 1.0 OE1 A:GLU59 2.5 33.3 1.0 CD A:GLU59 2.8 28.7 1.0 O A:HOH248 2.9 13.6 1.0 O A:HOH243 4.1 78.2 1.0 CG A:GLU59 4.3 29.6 1.0 OD2 A:ASP62 4.8 41.5 1.0

X.L.Zhang, G.F.Tibbits, M.Paetzel. The Structure of Cardiac Troponin C Regulatory Domain with Bound Cd(2+) Reveals A Closed Conformation and Unique Ion Coordination. Acta Crystallogr.,Sect.D V. 69 722 2013.
ISSN: ISSN 0907-4449
PubMed: 23633581
DOI: 10.1107/S0907444913001182