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Cadmium in PDB 3rv5: Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid

Protein crystallography data

The structure of Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid, PDB code: 3rv5 was solved by A.Y.Li, J.Lee, D.Borek, Z.Otwinowski, G.Tibbits, M.Paetzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.01 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 51.844, 81.783, 100.469, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 28.1

Other elements in 3rv5:

The structure of Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid (pdb code 3rv5). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 21 binding sites of Cadmium where determined in the Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid, PDB code: 3rv5:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 21 in 3rv5

Go back to Cadmium Binding Sites List in 3rv5
Cadmium binding site 1 out of 21 in the Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid


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 Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd101

b:22.3
occ:1.00
 OD2 A:ASP33 2.1 16.7 1.0
O A:GLY30 2.2 26.5 1.0
OE1 A:GLU40 2.4 25.6 1.0
OD1 A:ASP33 2.4 26.9 1.0
SG A:CYS35 2.5 25.3 1.0
O A:CYS35 2.5 21.4 1.0
OE2 A:GLU40 2.6 22.3 1.0
CG A:ASP33 2.6 21.8 1.0
CD A:GLU40 2.8 20.2 1.0
C A:CYS35 3.3 20.6 1.0
C A:GLY30 3.3 24.5 1.0
O A:HOH118 3.6 29.8 1.0
CB A:CYS35 3.7 21.0 1.0
CA A:CYS35 3.8 21.6 1.0
O A:HOH113 3.9 40.5 1.0
N A:CYS35 3.9 22.4 1.0
CB A:ASP33 4.1 22.9 1.0
N A:ILE36 4.1 21.9 1.0
CD A:CD103 4.1 29.9 1.0
CA A:GLY30 4.2 24.6 1.0
CA A:ILE36 4.3 22.2 1.0
N A:ALA31 4.3 24.3 1.0
CG A:GLU40 4.3 22.6 1.0
O A:HOH119 4.4 23.3 1.0
CA A:ALA31 4.5 23.2 1.0
O A:HOH115 4.6 28.6 1.0
N A:SER37 4.6 22.8 1.0
N A:ASP33 4.8 23.2 1.0
C A:ILE36 4.8 22.4 1.0
CA A:ASP33 4.9 24.9 1.0

Cadmium binding site 2 out of 21 in 3rv5

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Cadmium binding site 2 out of 21 in the Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid


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 Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd102

b:25.9
occ:1.00
 OD2 A:ASP65 2.1 30.1 1.0
OD1 A:ASP67 2.3 29.1 1.0
OG A:SER69 2.3 27.4 1.0
O A:HOH110 2.3 21.4 1.0
OE1 A:GLU76 2.3 31.1 1.0
O A:THR71 2.4 29.6 1.0
OE2 A:GLU76 2.6 30.0 1.0
CD A:GLU76 2.8 27.7 1.0
CG A:ASP67 3.1 30.2 1.0
CG A:ASP65 3.2 32.9 1.0
OD2 A:ASP67 3.3 30.4 1.0
CB A:SER69 3.4 30.1 1.0
C A:THR71 3.5 27.2 1.0
OD1 A:ASP65 3.9 32.8 1.0
N A:SER69 3.9 32.0 1.0
O A:HOH123 4.1 16.3 1.0
CA A:VAL72 4.1 23.3 1.0
CB A:ASP65 4.2 32.9 1.0
CA A:SER69 4.2 30.3 1.0
CG A:GLU76 4.3 23.4 1.0
N A:VAL72 4.3 25.1 1.0
N A:THR71 4.3 28.8 1.0
CA A:ASP65 4.3 34.1 1.0
N A:ASP73 4.3 21.5 1.0
N A:ASP67 4.4 32.8 1.0
CB A:ASP67 4.5 31.6 1.0
CA A:THR71 4.6 27.4 1.0
N A:GLY70 4.6 31.2 1.0
C A:VAL72 4.7 22.5 1.0
C A:ASP65 4.7 35.6 1.0
N A:GLU66 4.7 34.8 1.0
N A:GLY68 4.7 33.1 1.0
C A:SER69 4.8 31.1 1.0
OG1 A:THR71 4.8 23.4 1.0
CA A:ASP67 4.8 33.2 1.0
OD1 A:ASP73 4.8 22.0 1.0
C A:ASP67 4.9 33.5 1.0
CB A:GLU76 4.9 20.4 1.0

Cadmium binding site 3 out of 21 in 3rv5

Go back to Cadmium Binding Sites List in 3rv5
Cadmium binding site 3 out of 21 in the Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid


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 Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd103

b:29.9
occ:1.00
 O A:HOH119 2.1 23.3 1.0
O A:HOH115 2.1 28.6 1.0
SG A:CYS35 2.7 25.3 1.0
O A:HOH118 3.2 29.8 1.0
CB A:CYS35 3.5 21.0 1.0
O A:HOH116 4.0 26.8 1.0
OD2 A:ASP33 4.1 16.7 1.0
CD A:CD101 4.1 22.3 1.0
CG A:ASP33 4.2 21.8 1.0
OD1 A:ASP33 4.3 26.9 1.0
CG2 A:THR71 4.3 22.6 1.0
OG1 A:THR71 4.4 23.4 1.0
CB A:THR71 4.7 27.7 1.0
CA A:CYS35 4.8 21.6 1.0
CB A:ASP33 5.0 22.9 1.0

Cadmium binding site 4 out of 21 in 3rv5

Go back to Cadmium Binding Sites List in 3rv5
Cadmium binding site 4 out of 21 in the Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid


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 Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd104

b:29.1
occ:1.00
 O A:HOH132 2.1 19.8 1.0
OD2 A:ASP73 2.1 23.1 1.0
OD1 A:ASP75 2.4 25.8 1.0
O A:HOH127 2.4 27.2 1.0
OD2 A:ASP75 2.5 26.1 1.0
O A:HOH120 2.6 24.4 1.0
CG A:ASP75 2.8 23.3 1.0
CG A:ASP73 3.0 23.0 1.0
OD1 A:ASP73 3.1 22.0 1.0
O A:HOH114 4.1 8.0 1.0
CG A:GLU76 4.3 23.4 1.0
OD2 A:ASP67 4.3 30.4 1.0
OE1 A:GLU66 4.3 32.8 1.0
OE2 A:GLU76 4.4 30.0 1.0
CB A:ASP75 4.4 21.2 1.0
CB A:ASP73 4.4 20.9 1.0
CD A:GLU76 4.6 27.7 1.0
O B:GLU32 4.7 23.2 1.0
CG B:GLU32 4.8 22.6 1.0
O B:HOH141 4.8 51.5 1.0
N A:GLU76 4.9 19.4 1.0
O A:HOH110 5.0 21.4 1.0

Cadmium binding site 5 out of 21 in 3rv5

Go back to Cadmium Binding Sites List in 3rv5
Cadmium binding site 5 out of 21 in the Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid


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 Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd105

b:52.3
occ:1.00
 OE2 A:GLU66 2.3 39.3 1.0
O A:HOH140 2.4 49.2 1.0
O C:HOH123 2.5 49.4 1.0
OE1 A:GLU66 2.8 32.8 1.0
O C:HOH138 2.9 34.7 1.0
CD A:GLU66 2.9 36.0 1.0
OE2 B:GLU32 3.7 31.8 1.0
O B:HOH148 4.0 34.4 1.0
CD B:CD105 4.3 37.9 1.0
O C:HOH115 4.4 27.4 1.0
CG A:GLU66 4.4 37.5 1.0
O C:HOH137 4.5 36.7 1.0
O A:HOH127 4.6 27.2 1.0
O C:HOH124 4.7 22.4 1.0
CD B:GLU32 4.7 25.2 1.0
OD2 A:ASP75 4.9 26.1 1.0

Cadmium binding site 6 out of 21 in 3rv5

Go back to Cadmium Binding Sites List in 3rv5
Cadmium binding site 6 out of 21 in the Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid


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 Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd101

b:25.6
occ:1.00
 OE2 B:GLU40 2.4 27.7 1.0
OE1 B:GLU40 2.4 28.7 1.0
O B:GLY30 2.4 25.2 1.0
O B:CYS35 2.4 27.0 1.0
OD1 B:ASP33 2.5 31.5 1.0
OD2 B:ASP33 2.5 31.5 1.0
SG B:CYS35 2.6 32.1 1.0
CD B:GLU40 2.7 28.6 1.0
CG B:ASP33 2.9 25.7 1.0
C B:CYS35 3.2 24.8 1.0
C B:GLY30 3.5 22.5 1.0
CB B:CYS35 3.8 22.9 1.0
CA B:CYS35 3.8 25.1 1.0
N B:CYS35 3.9 23.4 1.0
CD B:CD103 3.9 31.5 1.0
N B:ILE36 4.1 24.7 1.0
N B:SER37 4.1 24.6 1.0
CA B:ILE36 4.2 24.5 1.0
CG B:GLU40 4.2 26.2 1.0
O B:HOH146 4.2 30.0 1.0
CA B:GLY30 4.3 21.6 1.0
O B:HOH143 4.4 16.8 1.0
N B:ALA31 4.4 21.7 1.0
CB B:ASP33 4.4 22.3 1.0
CA B:ALA31 4.5 21.1 1.0
C B:ILE36 4.5 25.0 1.0
N B:ASP33 5.0 20.8 1.0
OG B:SER37 5.0 30.5 1.0
CB B:SER37 5.0 25.5 1.0

Cadmium binding site 7 out of 21 in 3rv5

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Cadmium binding site 7 out of 21 in the Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid


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 Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd102

b:28.3
occ:1.00
 OE1 B:GLU76 2.2 39.1 1.0
OD1 B:ASP65 2.2 34.1 1.0
O B:HOH110 2.2 20.2 1.0
OG B:SER69 2.3 31.5 1.0
OD1 B:ASP67 2.4 38.8 1.0
O B:THR71 2.5 31.3 1.0
OE2 B:GLU76 2.5 40.4 1.0
CD B:GLU76 2.7 35.2 1.0
CG B:ASP65 3.2 32.6 1.0
CG B:ASP67 3.3 36.0 1.0
OD2 B:ASP67 3.5 30.7 1.0
CB B:SER69 3.5 30.6 1.0
C B:THR71 3.6 28.3 1.0
N B:SER69 3.9 32.1 1.0
OD2 B:ASP65 4.0 33.7 1.0
CA B:ASP65 4.0 35.4 1.0
CB B:ASP65 4.0 35.2 1.0
CG B:GLU76 4.2 30.6 1.0
CA B:SER69 4.2 31.4 1.0
N B:ASP73 4.2 23.4 1.0
N B:THR71 4.3 29.0 1.0
C B:ASP65 4.3 38.1 1.0
CA B:VAL72 4.4 25.3 1.0
N B:VAL72 4.4 26.9 1.0
OG1 B:THR71 4.4 28.3 1.0
N B:ASP67 4.4 38.0 1.0
CA B:THR71 4.5 29.3 1.0
CB B:ASP67 4.6 36.5 1.0
O B:ASP65 4.6 39.1 1.0
N B:GLY70 4.7 31.9 1.0
N B:GLU66 4.7 38.8 1.0
C B:VAL72 4.8 24.2 1.0
C B:SER69 4.8 31.5 1.0
N B:GLY68 4.8 36.0 1.0
C B:ASP67 4.8 36.2 1.0
CA B:ASP67 4.9 37.3 1.0
CG B:ASP73 4.9 23.7 1.0
CB B:GLU76 4.9 26.4 1.0
OD1 B:ASP73 4.9 23.0 1.0

Cadmium binding site 8 out of 21 in 3rv5

Go back to Cadmium Binding Sites List in 3rv5
Cadmium binding site 8 out of 21 in the Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd103

b:31.5
occ:1.00
 O B:HOH144 2.2 32.3 1.0
O B:HOH119 2.5 23.8 1.0
O B:HOH147 2.5 28.0 1.0
O B:HOH150 2.5 27.2 1.0
SG B:CYS35 2.6 32.1 1.0
O B:HOH146 2.6 30.0 1.0
CB B:CYS35 3.2 22.9 1.0
OD2 B:ASP33 3.6 31.5 1.0
O B:HOH118 3.8 26.4 1.0
CG B:ASP33 3.8 25.7 1.0
CD B:CD101 3.9 25.6 1.0
OD1 B:ASP33 4.1 31.5 1.0
CA B:CYS35 4.4 25.1 1.0
CG2 B:THR71 4.4 29.6 1.0
N B:CYS35 4.5 23.4 1.0
OG1 B:THR71 4.6 28.3 1.0
CB B:ASP33 4.7 22.3 1.0
CB B:THR71 4.8 27.4 1.0
O B:ASP33 4.9 22.5 1.0
C B:CYS35 5.0 24.8 1.0

Cadmium binding site 9 out of 21 in 3rv5

Go back to Cadmium Binding Sites List in 3rv5
Cadmium binding site 9 out of 21 in the Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd104

b:28.2
occ:1.00
 O B:HOH138 2.2 19.0 1.0
OD1 B:ASP75 2.2 25.4 1.0
O B:HOH114 2.2 21.4 1.0
OD2 B:ASP73 2.2 31.0 1.0
O B:HOH113 2.3 23.8 1.0
O B:HOH115 2.4 25.1 1.0
OD2 B:ASP75 2.5 31.7 1.0
CG B:ASP75 2.7 27.5 1.0
CG B:ASP73 3.0 23.7 1.0
OD1 B:ASP73 3.0 23.0 1.0
O B:HOH125 3.8 29.6 1.0
O B:HOH123 3.9 14.8 1.0
OD2 B:ASP67 4.1 30.7 1.0
CB B:ASP75 4.3 24.5 1.0
OE2 B:GLU76 4.4 40.4 1.0
CB B:ASP73 4.5 20.9 1.0
CG B:GLU76 4.6 30.6 1.0
CG A:GLU32 4.6 27.8 1.0
CD B:GLU76 4.8 35.2 1.0
O A:GLU32 4.8 24.8 1.0
CG B:ASP67 4.8 36.0 1.0
CA A:GLU32 4.8 24.5 1.0
N B:GLU76 4.9 24.7 1.0

Cadmium binding site 10 out of 21 in 3rv5

Go back to Cadmium Binding Sites List in 3rv5
Cadmium binding site 10 out of 21 in the Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Human Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd105

b:37.9
occ:1.00
 O B:HOH142 2.3 35.5 1.0
OE2 C:GLU15 2.3 32.6 1.0
O C:HOH138 2.4 34.7 1.0
OE2 B:GLU32 2.4 31.8 1.0
O B:HOH148 2.4 34.4 1.0
OE1 B:GLU32 2.6 32.8 1.0
CD B:GLU32 2.8 25.2 1.0
CD C:GLU15 3.3 30.1 1.0
OE1 C:GLU15 3.5 28.1 1.0
O B:HOH121 3.6 43.8 1.0
O C:HOH124 4.2 22.4 1.0
CD1 B:LEU29 4.2 25.6 1.0
CD A:CD105 4.3 52.3 1.0
CG B:GLU32 4.4 22.6 1.0
O C:HOH123 4.5 49.4 1.0
O B:HOH136 4.6 29.6 1.0
CG C:GLU15 4.7 32.8 1.0

Reference:

A.Y.Li, J.Lee, D.Borek, Z.Otwinowski, G.F.Tibbits, M.Paetzel. Crystal Structure of Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid Reveals Novel Conformation. J.Mol.Biol. V. 413 699 2011.
ISSN: ISSN 0022-2836
PubMed: 21920370
DOI: 10.1016/J.JMB.2011.08.049
Page generated: Sun Jan 24 09:56:00 2021

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