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Cadmium in PDB 4gjf: Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant L29Q in Complex with Cadmium

Protein crystallography data

The structure of Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant L29Q in Complex with Cadmium, PDB code: 4gjf 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) 42.65 / 1.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 49.250, 49.250, 113.378, 90.00, 90.00, 120.00
R / Rfree (%) 14.2 / 17.8

Other elements in 4gjf:

The structure of Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant L29Q in Complex with Cadmium also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant L29Q in Complex with Cadmium (pdb code 4gjf). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant L29Q in Complex with Cadmium, PDB code: 4gjf:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 4gjf

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Cadmium binding site 1 out of 8 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant L29Q 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 L29Q in Complex with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd102

b:32.6
occ:1.00
O A:HOH201 2.0 32.3 1.0
O A:HOH210 2.2 32.4 1.0
OE2 A:GLU40 2.3 31.1 1.0
OE1 A:GLU40 2.4 28.2 1.0
O A:PHE27 2.5 33.2 1.0
CD A:GLU40 2.6 32.1 1.0
C A:PHE27 3.6 33.6 1.0
CG A:GLU40 4.1 33.0 1.0
O A:HOH217 4.4 32.7 1.0
CA A:PHE27 4.4 32.0 1.0
OXT A:ACT110 4.5 34.7 1.0
N A:VAL28 4.5 33.5 1.0
O A:ACT110 4.5 38.3 1.0
CA A:VAL28 4.5 35.1 1.0
CB A:PHE27 4.6 30.9 1.0
O A:HOH235 4.6 66.2 1.0
CA A:ILE36 4.7 28.0 1.0
CG2 A:ILE36 4.8 28.3 1.0
O A:CYS35 4.9 26.2 1.0
CB A:ILE36 4.9 27.4 1.0
C A:ACT110 4.9 36.9 1.0
N A:SER37 4.9 31.9 1.0
CB A:GLU40 5.0 34.0 1.0

Cadmium binding site 2 out of 8 in 4gjf

Go back to Cadmium Binding Sites List in 4gjf
Cadmium binding site 2 out of 8 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant L29Q 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 L29Q in Complex with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd103

b:29.8
occ:1.00
OXT A:ACT110 2.2 34.7 1.0
OD1 A:ASP33 2.3 28.1 1.0
O A:CYS35 2.4 26.2 1.0
OD2 A:ASP33 2.5 28.6 1.0
O A:HOH202 2.5 35.5 1.0
SG A:CYS35 2.6 27.2 1.0
CG A:ASP33 2.8 27.6 1.0
C A:ACT110 3.1 36.9 1.0
C A:CYS35 3.2 26.6 1.0
CH3 A:ACT110 3.4 38.0 1.0
N A:CYS35 3.7 26.6 1.0
CA A:CYS35 3.7 25.5 1.0
CB A:CYS35 3.7 26.7 1.0
O A:HOH210 3.8 32.4 1.0
O A:ACT110 4.3 38.3 1.0
CB A:ASP33 4.3 28.4 1.0
N A:ILE36 4.3 25.4 1.0
CA A:ILE36 4.7 28.0 1.0
N A:GLY34 4.8 28.3 1.0
C A:GLY34 4.9 28.3 1.0

Cadmium binding site 3 out of 8 in 4gjf

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Cadmium binding site 3 out of 8 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant L29Q 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 L29Q in Complex with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd104

b:30.4
occ:1.00
O A:CYS84 2.3 31.6 1.0
OD1 A:ASP87 2.3 30.4 1.0
OE1 A:GLN50 2.5 33.6 1.0
SG A:CYS84 2.6 29.1 1.0
C A:CYS84 3.0 29.1 1.0
CG A:ASP87 3.3 34.3 1.0
CD A:CD105 3.5 33.3 1.0
CD A:GLN50 3.5 36.0 1.0
CB A:CYS84 3.6 29.4 1.0
CA A:CYS84 3.6 29.4 1.0
OD2 A:ASP87 3.7 32.3 1.0
N A:MET85 4.0 28.9 1.0
CB A:GLN50 4.1 31.9 1.0
N A:ASN51 4.3 33.2 1.0
CA A:MET85 4.3 28.3 1.0
NE2 A:GLN50 4.4 37.1 1.0
CG A:GLN50 4.4 31.7 1.0
CA A:GLN50 4.5 33.4 1.0
N A:ASP88 4.5 33.1 1.0
CB A:ASP87 4.6 32.6 1.0
N A:ASP87 4.6 30.7 1.0
C A:ASP87 4.6 34.1 1.0
C A:MET85 4.7 30.3 1.0
CA A:ASP87 4.8 33.2 1.0
C A:GLN50 4.9 34.9 1.0
O A:MET85 5.0 29.4 1.0

Cadmium binding site 4 out of 8 in 4gjf

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Cadmium binding site 4 out of 8 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant L29Q 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 L29Q in Complex with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd105

b:33.3
occ:1.00
OD2 A:ASP87 2.2 32.3 1.0
OE2 A:GLU56 2.3 33.6 1.0
OE1 A:GLU56 2.4 33.7 1.0
SG A:CYS84 2.5 29.1 1.0
CD A:GLU56 2.7 31.3 1.0
CG A:ASP87 3.0 34.3 1.0
OD1 A:ASP87 3.2 30.4 1.0
CD A:CD104 3.5 30.4 1.0
CB A:CYS84 3.6 29.4 1.0
CA A:CYS84 3.8 29.4 1.0
CA A:PRO52 3.8 36.3 1.0
O A:HOH228 4.1 61.7 1.0
CG A:GLU56 4.2 33.3 1.0
CB A:PRO52 4.3 34.5 1.0
O A:CYS84 4.3 31.6 1.0
N A:PRO52 4.4 35.5 1.0
CB A:ASP87 4.4 32.6 1.0
C A:CYS84 4.5 29.1 1.0
C A:ASN51 4.8 34.3 1.0
O A:ASN51 4.8 33.9 1.0
CB A:GLU56 5.0 36.2 1.0
C A:PRO52 5.0 39.4 1.0
N A:CYS84 5.0 28.1 1.0
N A:THR53 5.0 43.1 1.0

Cadmium binding site 5 out of 8 in 4gjf

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Cadmium binding site 5 out of 8 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant L29Q 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 L29Q in Complex with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd106

b:30.7
occ:1.00
OE2 A:GLU66 1.9 49.9 1.0
OD2 A:ASP73 2.1 35.4 1.0
OD2 A:ASP75 2.2 28.2 1.0
OD1 A:ASP75 2.5 27.9 1.0
CG A:ASP75 2.7 27.5 1.0
OD1 A:ASP73 2.7 24.3 1.0
CD A:GLU66 2.8 52.7 1.0
CG A:ASP73 2.8 28.2 1.0
OE1 A:GLU66 2.9 51.7 1.0
CB A:ASP75 4.2 26.3 1.0
CG A:GLU66 4.3 58.9 1.0
CB A:ASP73 4.3 26.6 1.0
CG A:GLU76 4.4 28.8 1.0
CD A:GLU76 4.6 33.1 1.0
N A:GLU76 4.6 27.3 1.0
OE2 A:GLU76 4.7 36.9 1.0
N A:ASP75 4.8 26.2 1.0
CE1 A:TYR5 4.9 46.5 1.0
CA A:ASP75 5.0 27.1 1.0

Cadmium binding site 6 out of 8 in 4gjf

Go back to Cadmium Binding Sites List in 4gjf
Cadmium binding site 6 out of 8 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant L29Q 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 L29Q in Complex with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd107

b:38.8
occ:0.60
O A:HOH203 2.1 0.6 1.0
O A:HOH204 2.2 50.5 1.0
OE2 A:GLU59 2.4 50.7 1.0
OE1 A:GLU59 2.5 52.9 1.0
O A:HOH209 2.6 46.9 1.0
CD A:GLU59 2.8 48.1 1.0
O A:HOH208 3.1 31.6 1.0
CG A:GLU59 4.3 43.4 1.0
OD2 A:ASP62 4.7 53.9 1.0

Cadmium binding site 7 out of 8 in 4gjf

Go back to Cadmium Binding Sites List in 4gjf
Cadmium binding site 7 out of 8 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant L29Q 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 L29Q in Complex with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd108

b:46.1
occ:0.60
O A:HOH206 1.7 42.6 1.0
O A:HOH207 2.1 96.8 1.0
OD2 A:ASP65 2.2 62.9 1.0
OE1 A:GLU76 2.4 32.9 1.0
O A:HOH205 2.4 87.2 1.0
O A:THR71 2.6 32.9 1.0
OE2 A:GLU76 2.6 36.9 1.0
CD A:GLU76 2.9 33.1 1.0
CG A:ASP65 3.2 64.4 1.0
C A:THR71 3.7 33.2 1.0
OD1 A:ASP65 3.7 71.4 1.0
OG1 A:THR71 3.7 36.7 1.0
O A:HOH241 4.0 74.7 0.5
N A:GLU66 4.1 61.2 1.0
CA A:VAL72 4.2 27.7 1.0
N A:VAL72 4.3 28.6 1.0
CA A:ASP65 4.3 59.7 1.0
CB A:ASP65 4.3 60.7 1.0
CG A:GLU76 4.4 28.8 1.0
OE1 A:GLU66 4.5 51.7 1.0
N A:ASP73 4.5 26.6 1.0
CA A:THR71 4.7 35.2 1.0
C A:ASP65 4.8 60.6 1.0
CB A:THR71 4.8 35.3 1.0
C A:VAL72 4.8 28.0 1.0
N A:THR71 4.9 39.7 1.0
CB A:GLU66 5.0 61.2 1.0
CD A:GLU66 5.0 52.7 1.0

Cadmium binding site 8 out of 8 in 4gjf

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Cadmium binding site 8 out of 8 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C Mutant L29Q in Complex with Cadmium


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 the Amino-Terminal Domain of Human Cardiac Troponin C Mutant L29Q in Complex with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd109

b:41.5
occ:0.70
OE1 A:GLU19 2.3 56.1 1.0
OE2 A:GLU19 2.4 52.7 1.0
O A:HOH224 2.5 46.9 1.0
CD A:GLU19 2.7 50.4 1.0
O A:HOH212 2.7 94.5 1.0
O A:HOH233 4.1 63.8 1.0
O A:HOH211 4.1 37.0 1.0
CG A:GLU19 4.2 42.9 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: Sat Dec 12 08:24:36 2020

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