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Cadmium in PDB 3sd6: Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution.

Protein crystallography data

The structure of Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution., PDB code: 3sd6 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) 42.93 / 1.37
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 49.576, 49.576, 116.041, 90.00, 90.00, 120.00
R / Rfree (%) 13.3 / 14.8

Other elements in 3sd6:

The structure of Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution. also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

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 1.4 Resolution. (pdb code 3sd6). 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 in Complex with Cadmium at 1.4 Resolution., PDB code: 3sd6:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 3sd6

Go back to Cadmium Binding Sites List in 3sd6
Cadmium binding site 1 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 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 1.4 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd101

b:19.1
occ:1.00
 OE2 A:GLU40 2.3 19.2 1.0
O A:PHE27 2.3 18.9 1.0
O A:HOH125 2.3 19.3 1.0
O A:HOH145 2.3 26.5 1.0
OE1 A:GLU40 2.4 18.4 1.0
CD A:GLU40 2.7 18.1 1.0
C A:PHE27 3.4 20.2 1.0
CG A:GLU40 4.2 17.8 1.0
CA A:PHE27 4.3 18.4 1.0
N A:VAL28 4.3 21.5 1.0
CA A:VAL28 4.3 22.2 1.0
O A:HOH99 4.3 22.2 1.0
CB A:PHE27 4.4 18.5 1.0
O A:HOH122 4.5 34.1 1.0
OXT A:ACT90 4.6 21.4 1.0
O A:ACT90 4.7 25.7 1.0
CA A:ILE36 4.7 16.6 1.0
CG2 A:ILE36 4.9 18.4 1.0
N A:SER37 4.9 18.3 1.0
O A:CYS35 4.9 16.8 1.0
CG1 A:VAL28 5.0 28.4 1.0
CB A:GLU40 5.0 19.2 1.0

Cadmium binding site 2 out of 7 in 3sd6

Go back to Cadmium Binding Sites List in 3sd6
Cadmium binding site 2 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 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 1.4 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd102

b:18.2
occ:1.00
 OD2 A:ASP87 2.2 19.2 1.0
OE1 A:GLU56 2.3 19.7 1.0
OE2 A:GLU56 2.3 23.1 1.0
SG A:CYS84 2.5 16.2 1.0
CD A:GLU56 2.7 20.7 1.0
CG A:ASP87 3.0 16.6 1.0
OD1 A:ASP87 3.1 19.7 1.0
CD A:CD103 3.5 16.0 1.0
CB A:CYS84 3.6 15.9 1.0
CA A:PRO52 3.7 19.0 1.0
CA A:CYS84 3.8 15.0 1.0
O A:HOH142 4.0 36.4 1.0
O A:HOH139 4.0 41.3 1.0
CB A:PRO52 4.1 19.5 1.0
CG A:GLU56 4.2 19.2 1.0
O A:CYS84 4.2 15.1 1.0
N A:PRO52 4.4 18.6 1.0
CB A:ASP87 4.4 16.4 1.0
C A:CYS84 4.5 14.4 1.0
O A:ASN51 4.8 19.2 1.0
C A:ASN51 4.8 18.7 1.0
N A:THR53 4.8 23.6 1.0
C A:PRO52 4.9 19.9 1.0
CB A:GLU56 4.9 19.5 1.0
N A:CYS84 5.0 14.4 1.0
CD A:PRO52 5.0 18.5 1.0

Cadmium binding site 3 out of 7 in 3sd6

Go back to Cadmium Binding Sites List in 3sd6
Cadmium binding site 3 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 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 1.4 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd103

b:16.0
occ:1.00
 O A:CYS84 2.3 15.1 1.0
OD1 A:ASP87 2.3 19.7 1.0
OE1 A:GLN50 2.4 18.5 1.0
SG A:CYS84 2.5 16.2 1.0
C A:CYS84 3.0 14.4 1.0
CG A:ASP87 3.3 16.6 1.0
CD A:GLN50 3.4 18.2 1.0
CD A:CD102 3.5 18.2 1.0
CB A:CYS84 3.5 15.9 1.0
CA A:CYS84 3.6 15.0 1.0
OD2 A:ASP87 3.7 19.2 1.0
N A:MET85 4.0 14.2 1.0
CB A:GLN50 4.2 19.6 1.0
NE2 A:GLN50 4.2 20.3 1.0
N A:ASN51 4.3 18.7 1.0
CG A:GLN50 4.3 18.8 1.0
CA A:MET85 4.3 14.3 1.0
CA A:GLN50 4.5 18.3 1.0
O A:HOH150 4.6 38.7 1.0
CB A:ASP87 4.6 16.4 1.0
N A:ASP87 4.6 15.4 1.0
C A:ASP87 4.6 17.2 1.0
N A:ASP88 4.7 17.3 1.0
C A:MET85 4.8 15.8 1.0
CA A:ASP87 4.8 16.1 1.0
C A:GLN50 4.9 19.2 1.0
O A:ASP87 5.0 19.1 1.0

Cadmium binding site 4 out of 7 in 3sd6

Go back to Cadmium Binding Sites List in 3sd6
Cadmium binding site 4 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 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 1.4 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd104

b:18.5
occ:1.00
 OD1 A:ASP33 2.3 19.2 1.0
OXT A:ACT90 2.3 21.4 1.0
O A:HOH97 2.4 23.4 1.0
O A:CYS35 2.5 16.8 1.0
OD2 A:ASP33 2.5 20.2 1.0
SG A:CYS35 2.5 17.1 1.0
CG A:ASP33 2.7 17.3 1.0
C A:ACT90 3.2 24.6 1.0
C A:CYS35 3.3 15.9 1.0
CH3 A:ACT90 3.4 28.0 1.0
CA A:CYS35 3.6 17.1 1.0
CB A:CYS35 3.7 17.6 1.0
N A:CYS35 3.7 15.5 1.0
O A:HOH125 3.7 19.3 1.0
CB A:ASP33 4.2 19.7 1.0
O A:ACT90 4.3 25.7 1.0
N A:ILE36 4.3 16.6 1.0
CA A:ILE36 4.8 16.6 1.0
N A:GLY34 4.9 16.9 1.0
C A:ILE36 4.9 18.5 1.0
C A:GLY34 5.0 16.7 1.0
CA A:ASP33 5.0 19.6 1.0

Cadmium binding site 5 out of 7 in 3sd6

Go back to Cadmium Binding Sites List in 3sd6
Cadmium binding site 5 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 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 1.4 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd105

b:18.4
occ:1.00
 OD2 A:ASP73 2.3 19.8 1.0
OD2 A:ASP75 2.3 19.9 1.0
OE2 A:GLU66 2.4 31.9 1.0
OD1 A:ASP75 2.4 19.4 1.0
OD1 A:ASP73 2.6 17.8 1.0
CG A:ASP75 2.7 16.9 1.0
OE1 A:GLU66 2.8 35.3 1.0
CG A:ASP73 2.8 17.0 1.0
CD A:GLU66 3.0 27.5 0.5
CB A:ASP75 4.2 16.4 1.0
CB A:ASP73 4.3 18.3 1.0
CG A:GLU76 4.3 16.0 1.0
CG A:GLU66 4.4 28.1 0.5
N A:GLU76 4.6 16.0 1.0
CD A:GLU76 4.6 17.2 1.0
OE2 A:GLU76 4.7 27.9 1.0
N A:ASP75 4.8 16.3 1.0
CE1 A:TYR5 4.9 33.4 1.0
CA A:ASP75 4.9 15.6 1.0

Cadmium binding site 6 out of 7 in 3sd6

Go back to Cadmium Binding Sites List in 3sd6
Cadmium binding site 6 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 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 1.4 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd106

b:26.6
occ:0.60
 OE2 A:GLU59 2.3 30.5 1.0
O A:HOH133 2.4 37.9 1.0
O A:HOH131 2.4 34.7 1.0
O A:HOH132 2.4 38.2 1.0
OE1 A:GLU59 2.5 32.7 1.0
O A:HOH146 2.7 19.5 1.0
CD A:GLU59 2.7 25.1 1.0
CG A:GLU59 4.2 27.1 1.0
O A:HOH134 4.2 50.2 1.0
OD2 A:ASP62 4.8 36.7 1.0

Cadmium binding site 7 out of 7 in 3sd6

Go back to Cadmium Binding Sites List in 3sd6
Cadmium binding site 7 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution.


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 in Complex with Cadmium at 1.4 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd107

b:21.6
occ:0.50
 O A:HOH148 2.0 29.8 1.0
O A:HOH147 2.1 31.8 1.0
OD2 A:ASP65 2.2 30.7 0.5
OE1 A:GLU76 2.3 20.6 1.0
O A:THR71 2.5 23.2 1.0
OE2 A:GLU76 2.6 27.9 1.0
O A:HOH151 2.6 44.4 1.0
CD A:GLU76 2.8 17.2 1.0
CG A:ASP65 3.4 39.2 0.5
C A:THR71 3.6 19.9 1.0
OG1 A:THR71 3.8 30.8 1.0
CA A:VAL72 4.0 16.2 1.0
N A:VAL72 4.1 17.8 1.0
OD1 A:ASP65 4.1 41.5 0.5
N A:GLU66 4.2 38.8 1.0
CG A:GLU76 4.3 16.0 1.0
N A:ASP73 4.3 14.9 1.0
CB A:ASP65 4.4 37.7 1.0
OE1 A:GLU66 4.5 35.3 1.0
CA A:ASP65 4.6 38.2 1.0
C A:VAL72 4.6 14.9 1.0
CA A:THR71 4.7 23.2 1.0
CB A:THR71 4.7 24.1 1.0
CB A:GLU66 4.9 35.2 0.5
C A:ASP65 4.9 39.8 1.0
CB A:GLU76 4.9 16.0 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 Jul 19 16:27:34 2024

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