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Cadmium in PDB 3swb: Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.7 A Resolution

Protein crystallography data

The structure of Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.7 A Resolution, PDB code: 3swb was solved by X.L.Zhang, M.Paetzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.12 / 1.67
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 49.793, 49.793, 117.475, 90.00, 90.00, 120.00
R / Rfree (%) 13.5 / 16.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.7 A Resolution (pdb code 3swb). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.7 A Resolution, PDB code: 3swb:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 3swb

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Cadmium binding site 1 out of 6 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.7 A Resolution


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 in Complex with Cadmium at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd101

b:18.2
occ:1.00
OE2 A:GLU40 2.3 17.5 1.0
O A:HOH119 2.3 21.1 1.0
OE1 A:GLU40 2.4 16.0 1.0
O A:HOH122 2.4 20.4 1.0
O A:PHE27 2.4 17.7 1.0
CD A:GLU40 2.6 14.4 1.0
C A:PHE27 3.5 17.3 1.0
CG A:GLU40 4.2 16.7 1.0
N A:VAL28 4.3 19.5 1.0
CA A:VAL28 4.3 20.8 1.0
CA A:PHE27 4.3 15.5 1.0
OXT A:ACT93 4.4 26.5 1.0
O A:HOH97 4.4 23.7 1.0
O A:HOH120 4.4 36.4 1.0
CB A:PHE27 4.5 16.3 1.0
CH3 A:ACT93 4.6 26.5 1.0
CA A:ILE36 4.7 15.1 1.0
C A:ACT93 4.8 27.3 1.0
O A:HOH132 4.8 40.1 1.0
CG2 A:ILE36 4.9 14.8 1.0
N A:SER37 4.9 17.0 1.0
CG1 A:VAL28 4.9 26.8 1.0
CB A:GLU40 5.0 17.3 1.0
CB A:ILE36 5.0 14.1 1.0
O A:CYS35 5.0 16.5 1.0

Cadmium binding site 2 out of 6 in 3swb

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Cadmium binding site 2 out of 6 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.7 A Resolution


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 in Complex with Cadmium at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd102

b:17.7
occ:1.00
OD1 A:ASP87 2.2 16.4 1.0
OE1 A:GLU56 2.3 19.7 1.0
OE2 A:GLU56 2.3 20.9 1.0
SG A:CYS84 2.5 14.6 1.0
CD A:GLU56 2.6 18.5 1.0
CG A:ASP87 3.0 12.7 1.0
OD2 A:ASP87 3.1 15.8 1.0
CD A:CD103 3.5 13.8 1.0
CB A:CYS84 3.6 14.0 1.0
CA A:CYS84 3.8 13.6 1.0
CA A:PRO52 3.9 16.8 1.0
CB A:PRO52 4.1 15.8 1.0
CG A:GLU56 4.1 19.5 1.0
O A:CYS84 4.3 12.6 1.0
CB A:ASP87 4.4 14.1 1.0
N A:PRO52 4.5 14.5 1.0
C A:CYS84 4.5 11.6 1.0
O A:ASN51 4.8 15.1 1.0
C A:ASN51 4.9 14.8 1.0
CB A:GLU56 4.9 20.1 1.0
N A:CYS84 5.0 12.2 1.0
N A:THR53 5.0 21.7 1.0

Cadmium binding site 3 out of 6 in 3swb

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Cadmium binding site 3 out of 6 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.7 A Resolution


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 in Complex with Cadmium at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd103

b:13.8
occ:1.00
OD2 A:ASP87 2.3 15.8 1.0
OE1 A:GLN50 2.3 16.1 1.0
O A:CYS84 2.4 12.6 1.0
SG A:CYS84 2.6 14.6 1.0
C A:CYS84 3.1 11.6 1.0
CG A:ASP87 3.3 12.7 1.0
CD A:GLN50 3.4 13.4 1.0
CD A:CD102 3.5 17.7 1.0
CB A:CYS84 3.5 14.0 1.0
CA A:CYS84 3.6 13.6 1.0
OD1 A:ASP87 3.7 16.4 1.0
N A:MET85 4.1 11.9 1.0
NE2 A:GLN50 4.2 15.9 1.0
CB A:GLN50 4.3 13.7 1.0
N A:ASN51 4.3 13.6 1.0
CA A:MET85 4.4 11.8 1.0
CG A:GLN50 4.4 13.0 1.0
O A:HOH99 4.4 25.5 1.0
CA A:GLN50 4.6 12.7 1.0
CB A:ASP87 4.6 14.1 1.0
N A:ASP87 4.6 12.8 1.0
C A:ASP87 4.6 13.2 1.0
N A:ASP88 4.7 13.9 1.0
CA A:ASP87 4.8 12.6 1.0
C A:MET85 4.8 12.1 1.0
O A:ASP87 4.9 13.8 1.0

Cadmium binding site 4 out of 6 in 3swb

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Cadmium binding site 4 out of 6 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.7 A Resolution


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 in Complex with Cadmium at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd104

b:19.2
occ:1.00
OXT A:ACT93 2.3 26.5 1.0
OD1 A:ASP33 2.3 20.4 1.0
OD2 A:ASP33 2.4 20.7 1.0
O A:HOH95 2.4 21.2 1.0
O A:CYS35 2.4 16.5 1.0
SG A:CYS35 2.6 17.9 1.0
CG A:ASP33 2.7 19.4 1.0
C A:ACT93 3.1 27.3 1.0
O A:ACT93 3.1 30.7 1.0
C A:CYS35 3.3 15.0 1.0
CB A:CYS35 3.6 16.0 1.0
CA A:CYS35 3.7 15.7 1.0
N A:CYS35 3.7 15.7 1.0
O A:HOH122 3.7 20.4 1.0
CB A:ASP33 4.2 19.3 1.0
N A:ILE36 4.3 15.1 1.0
CH3 A:ACT93 4.5 26.5 1.0
CA A:ILE36 4.7 15.1 1.0
N A:GLY34 4.9 17.8 1.0
C A:ILE36 4.9 16.0 1.0
C A:GLY34 5.0 17.6 1.0
CA A:ASP33 5.0 19.8 1.0

Cadmium binding site 5 out of 6 in 3swb

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Cadmium binding site 5 out of 6 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.7 A Resolution


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 in Complex with Cadmium at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd105

b:19.9
occ:1.00
OD2 A:ASP73 2.3 19.8 1.0
OE2 A:GLU66 2.3 36.4 1.0
OD2 A:ASP75 2.3 22.1 1.0
OD1 A:ASP75 2.4 20.1 1.0
OE1 A:GLU66 2.4 29.8 1.0
OD1 A:ASP73 2.5 18.1 1.0
CG A:ASP75 2.7 16.2 1.0
CD A:GLU66 2.8 29.9 1.0
CG A:ASP73 2.8 17.4 1.0
CB A:ASP75 4.2 15.6 1.0
CB A:ASP73 4.3 16.2 1.0
CG A:GLU66 4.3 33.2 0.5
CG A:GLU76 4.4 16.8 1.0
N A:GLU76 4.6 14.5 1.0
CD A:GLU76 4.7 22.5 1.0
N A:ASP75 4.8 15.3 1.0
OE2 A:GLU76 4.9 29.8 1.0
OD2 A:ASP2 4.9 39.6 0.5
CA A:ASP75 5.0 15.3 1.0

Cadmium binding site 6 out of 6 in 3swb

Go back to Cadmium Binding Sites List in 3swb
Cadmium binding site 6 out of 6 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.7 A Resolution


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 in Complex with Cadmium at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd106

b:28.0
occ:0.60
O A:HOH129 2.3 42.0 1.0
O A:HOH143 2.3 39.0 1.0
OE1 A:GLU59 2.4 34.0 1.0
OE2 A:GLU59 2.4 34.7 1.0
O A:HOH144 2.5 43.7 1.0
CD A:GLU59 2.7 29.5 1.0
O A:HOH125 4.2 46.9 1.0
CG A:GLU59 4.3 26.9 1.0
OD2 A:ASP62 4.9 38.3 1.0

Reference:

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
Page generated: Fri Aug 28 14:00:32 2020
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