Cadmium in PDB 4gjg: Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) in Complex with Cadmium.

The structure of Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) in Complex with Cadmium., PDB code: 4gjg 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)	42.94 / 2.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	49.583, 49.583, 115.141, 90.00, 90.00, 120.00
R / Rfree (%)	14.4 / 19.8

The structure of Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) in Complex with Cadmium. also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Cadmium atom in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) in Complex with Cadmium. (pdb code 4gjg). 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 Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) in Complex with Cadmium., PDB code: 4gjg:
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 Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) 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 Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) in Complex with Cadmium. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd101 b:32.4 occ:1.00 O A:HOH202 2.0 33.3 1.0 OE2 A:GLU40 2.2 32.0 1.0 OE1 A:GLU40 2.3 29.7 1.0 O A:PHE27 2.4 32.7 1.0 O A:HOH201 2.4 32.6 1.0 CD A:GLU40 2.6 30.4 1.0 C A:PHE27 3.5 31.8 1.0 CG A:GLU40 4.1 27.8 1.0 CA A:PHE27 4.3 30.9 1.0 O A:HOH204 4.3 35.0 1.0 N A:ILE28 4.4 32.1 1.0 CB A:PHE27 4.4 29.3 1.0 CA A:ILE28 4.5 31.4 1.0 OXT A:ACT111 4.7 41.0 1.0 CA A:ILE36 4.7 25.9 1.0 O A:ACT111 4.7 43.9 1.0 O A:CYS35 4.9 25.6 1.0 CG2 A:ILE36 4.9 25.9 1.0 N A:SER37 4.9 27.2 1.0 CB A:GLU40 5.0 29.4 1.0 CB A:ILE36 5.0 24.7 1.0 O A:HOH232 5.0 65.0 1.0 C A:ACT111 5.0 40.1 1.0

Cadmium binding site 2 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) 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 Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) in Complex with Cadmium. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd102 b:32.8 occ:1.00 OD2 A:ASP87 2.1 34.8 1.0 OE1 A:GLU56 2.3 36.4 1.0 OE2 A:GLU56 2.3 35.0 1.0 SG A:CYS84 2.5 28.9 1.0 CD A:GLU56 2.6 34.8 1.0 CG A:ASP87 3.0 31.4 1.0 OD1 A:ASP87 3.2 30.2 1.0 CD A:CD103 3.5 28.4 1.0 CB A:CYS84 3.6 27.9 1.0 CA A:CYS84 3.8 27.6 1.0 CA A:PRO52 3.9 32.7 1.0 CG A:GLU56 4.1 32.9 1.0 CB A:PRO52 4.2 30.6 1.0 O A:CYS84 4.2 29.9 1.0 O A:HOH223 4.3 57.2 1.0 CB A:ASP87 4.4 29.5 1.0 N A:PRO52 4.5 32.0 1.0 C A:CYS84 4.5 28.2 1.0 O A:ASN51 4.8 32.2 1.0 C A:ASN51 4.8 32.0 1.0 CB A:GLU56 4.9 34.7 1.0 C A:PRO52 5.0 35.3 1.0

Cadmium binding site 3 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) 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 Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) in Complex with Cadmium. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd103 b:28.4 occ:1.00 O A:CYS84 2.2 29.9 1.0 OD1 A:ASP87 2.3 30.2 1.0 OE1 A:GLN50 2.4 33.6 1.0 SG A:CYS84 2.5 28.9 1.0 C A:CYS84 3.0 28.2 1.0 CG A:ASP87 3.3 31.4 1.0 CD A:GLN50 3.5 32.3 1.0 CD A:CD102 3.5 32.8 1.0 CB A:CYS84 3.6 27.9 1.0 CA A:CYS84 3.7 27.6 1.0 OD2 A:ASP87 3.7 34.8 1.0 N A:MET85 4.0 26.3 1.0 CB A:GLN50 4.1 29.5 1.0 N A:ASN51 4.3 31.6 1.0 CG A:GLN50 4.3 28.8 1.0 CA A:MET85 4.3 27.0 1.0 NE2 A:GLN50 4.4 31.6 1.0 CA A:GLN50 4.4 30.9 1.0 N A:ASP87 4.5 28.9 1.0 CB A:ASP87 4.6 29.5 1.0 C A:ASP87 4.6 31.6 1.0 N A:ASP88 4.6 31.6 1.0 CA A:ASP87 4.8 30.2 1.0 C A:MET85 4.8 28.7 1.0 C A:GLN50 4.9 32.6 1.0 O A:ASP87 5.0 33.0 1.0

Cadmium binding site 4 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) 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 Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) in Complex with Cadmium. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd104 b:29.3 occ:1.00 OXT A:ACT111 1.9 41.0 1.0 OD1 A:ASP33 2.3 29.8 1.0 O A:CYS35 2.5 25.6 1.0 SG A:CYS35 2.5 28.5 1.0 OD2 A:ASP33 2.5 29.5 1.0 O A:HOH203 2.6 41.2 1.0 CG A:ASP33 2.8 28.7 1.0 C A:ACT111 2.9 40.1 1.0 C A:CYS35 3.3 26.1 1.0 CH3 A:ACT111 3.4 41.9 1.0 O A:HOH201 3.7 32.6 1.0 CB A:CYS35 3.7 27.5 1.0 CA A:CYS35 3.7 26.4 1.0 N A:CYS35 3.7 26.5 1.0 O A:ACT111 3.9 43.9 1.0 CB A:ASP33 4.3 29.1 1.0 N A:ILE36 4.3 24.3 1.0 CA A:ILE36 4.7 25.9 1.0 N A:GLY34 4.8 27.7 1.0 C A:GLY34 5.0 27.6 1.0 C A:ILE36 5.0 26.5 1.0 CA A:ASP33 5.0 30.1 1.0

Cadmium binding site 5 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) 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 Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) in Complex with Cadmium. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd105 b:28.9 occ:1.00 OE2 A:GLU66 2.2 43.9 1.0 OD2 A:ASP73 2.2 29.8 1.0 OD2 A:ASP75 2.3 29.9 1.0 OD1 A:ASP75 2.4 27.8 1.0 OD1 A:ASP73 2.6 26.1 1.0 CG A:ASP75 2.7 26.8 1.0 CG A:ASP73 2.8 27.4 1.0 CD A:GLU66 3.0 49.4 1.0 OE1 A:GLU66 3.2 52.2 1.0 CB A:ASP75 4.2 26.1 1.0 CB A:ASP73 4.3 25.6 1.0 CG A:GLU76 4.4 29.7 1.0 CG A:GLU66 4.4 52.7 1.0 CD A:GLU76 4.5 36.0 1.0 N A:GLU76 4.6 27.7 1.0 OE2 A:GLU76 4.6 40.8 1.0 N A:ASP75 4.8 25.5 1.0 CE1 A:TYR5 4.8 45.1 1.0 CA A:ASP75 4.9 25.7 1.0

Cadmium binding site 6 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) 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 Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) in Complex with Cadmium. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd106 b:84.7 occ:0.70 OE1 A:GLU59 2.2 63.0 1.0 O A:HOH206 2.5 0.3 1.0 OE2 A:GLU59 2.8 59.9 1.0 CD A:GLU59 2.8 56.7 1.0 O A:HOH205 3.4 94.7 1.0 O A:HOH208 3.5 51.4 1.0 O A:HOH207 4.1 98.0 1.0 CG A:GLU59 4.4 46.9 1.0 OD2 A:ASP62 4.6 40.1 0.5 CB A:GLU59 5.0 38.1 1.0

Cadmium binding site 7 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) 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 Amino-Terminal Domain of Human Cardiac Troponin C Mutant D2N/V28I/L29Q/G30D (Niqd) in Complex with Cadmium. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd107 b:41.5 occ:0.60 O A:HOH210 1.8 81.0 1.0 O A:HOH209 2.0 83.7 1.0 OD2 A:ASP65 2.3 47.0 0.5 OE1 A:GLU76 2.4 37.0 1.0 OE2 A:GLU76 2.6 40.8 1.0 O A:THR71 2.6 34.6 1.0 O A:HOH211 2.7 56.6 1.0 CD A:GLU76 2.9 36.0 1.0 CG A:ASP65 3.3 51.4 0.5 C A:THR71 3.6 33.8 1.0 OD1 A:ASP65 3.8 53.2 0.5 OG1 A:THR71 3.9 36.5 1.0 CA A:VAL72 4.1 27.9 1.0 N A:VAL72 4.2 29.8 1.0 CB A:ASP65 4.3 52.2 1.0 CG A:GLU76 4.4 29.7 1.0 N A:ASP73 4.4 24.8 1.0 N A:GLU66 4.6 54.1 1.0 OE1 A:GLU66 4.6 52.2 1.0 CA A:ASP65 4.6 52.2 1.0 CA A:THR71 4.7 35.6 1.0 C A:VAL72 4.8 27.4 1.0 CB A:THR71 4.8 35.2 1.0 N A:THR71 4.9 37.7 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