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Calcium in PDB 1j1e: Crystal Structure of the 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form

Protein crystallography data

The structure of Crystal Structure of the 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form, PDB code: 1j1e was solved by S.Takeda, A.Yamashita, K.Maeda, Y.Maeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.299, 169.506, 68.538, 90.00, 102.38, 90.00
R / Rfree (%) 25.1 / 30.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form (pdb code 1j1e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form, PDB code: 1j1e:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1j1e

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Calcium binding site 1 out of 6 in the Crystal Structure of the 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:78.1
occ:1.00
 OD2 A:ASP67 2.1 0.3 1.0
OG A:SER69 2.3 95.2 1.0
OE2 A:GLU76 2.4 57.6 1.0
OE1 A:GLU76 2.4 57.6 1.0
CD A:GLU76 2.7 57.6 1.0
CG A:ASP67 2.9 0.3 1.0
O A:THR71 2.9 59.7 1.0
OD2 A:ASP65 3.0 0.4 1.0
OD1 A:ASP67 3.2 0.3 1.0
CB A:SER69 3.2 95.2 1.0
OD2 A:ASP73 3.3 0.5 1.0
CG A:ASP65 4.0 0.4 1.0
C A:THR71 4.1 59.7 1.0
CG A:ASP73 4.1 0.5 1.0
N A:ASP67 4.2 94.0 1.0
CB A:ASP67 4.2 0.3 1.0
CG A:GLU76 4.2 57.6 1.0
N A:ASP73 4.2 50.9 1.0
N A:SER69 4.3 98.5 1.0
CA A:SER69 4.3 98.5 1.0
CB A:ASP73 4.4 0.5 1.0
N A:GLU66 4.4 89.0 1.0
CA A:ASP65 4.6 0.5 1.0
CA A:ASP67 4.7 94.0 1.0
OD1 A:ASP65 4.7 0.4 1.0
CA A:VAL72 4.7 46.2 1.0
OG1 A:THR71 4.8 47.7 1.0
CB A:ASP65 4.8 0.4 1.0
N A:THR71 4.8 59.7 1.0
C A:VAL72 4.9 46.2 1.0
N A:VAL72 4.9 46.2 1.0
C A:ASP67 4.9 94.0 1.0
CA A:ASP73 5.0 50.9 1.0
CB A:GLU76 5.0 57.6 1.0

Calcium binding site 2 out of 6 in 1j1e

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Calcium binding site 2 out of 6 in the Crystal Structure of the 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:78.1
occ:1.00
 OD1 A:ASN107 1.9 70.2 1.0
OE2 A:GLU116 2.2 67.9 1.0
OE1 A:GLU116 2.2 67.9 1.0
CD A:GLU116 2.3 67.9 1.0
O A:TYR111 2.5 73.4 1.0
OD2 A:ASP109 2.7 0.8 1.0
CG A:ASN107 2.8 70.2 1.0
OD1 A:ASP105 2.9 51.7 1.0
OD1 A:ASP109 3.1 0.8 1.0
CG A:ASP109 3.1 0.8 1.0
ND2 A:ASN107 3.3 70.2 1.0
OD1 A:ASP113 3.6 76.1 1.0
CG A:GLU116 3.7 67.9 1.0
C A:TYR111 3.8 73.4 1.0
CG A:ASP105 4.0 51.7 1.0
CB A:ASN107 4.0 70.2 1.0
CG A:ASP113 4.1 76.1 1.0
N A:ASN107 4.1 56.9 1.0
N A:ASP113 4.2 69.7 1.0
CA A:ASP105 4.2 51.6 1.0
N A:LYS106 4.4 76.9 1.0
CA A:ILE112 4.4 73.9 1.0
CB A:ASP109 4.5 0.8 1.0
CB A:ASP105 4.5 51.7 1.0
C A:ASP105 4.6 51.6 1.0
CA A:ASN107 4.6 56.9 1.0
CB A:ASP113 4.6 76.1 1.0
N A:ILE112 4.6 73.9 1.0
N A:ASP109 4.6 51.0 1.0
N A:TYR111 4.7 73.4 1.0
CA A:TYR111 4.7 73.4 1.0
C A:ILE112 4.8 73.9 1.0
OD2 A:ASP113 4.8 76.1 1.0
CB A:GLU116 4.8 67.9 1.0
C A:ASN107 4.9 56.9 1.0
N A:ALA108 4.9 56.1 1.0
CB A:TYR111 5.0 43.9 1.0

Calcium binding site 3 out of 6 in 1j1e

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Calcium binding site 3 out of 6 in the Crystal Structure of the 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:78.1
occ:1.00
 OD2 A:ASP141 2.0 87.5 1.0
OE1 A:GLU152 2.1 99.3 1.0
OD1 A:ASN143 2.3 0.8 1.0
O A:ARG147 2.5 0.2 1.0
OE2 A:GLU152 2.6 99.3 1.0
CD A:GLU152 2.6 99.3 1.0
ND2 A:ASN143 2.7 0.8 1.0
CG A:ASN143 2.8 0.8 1.0
OD1 A:ASP145 2.8 84.5 1.0
OD2 A:ASP145 3.2 84.5 1.0
CG A:ASP141 3.2 87.5 1.0
CG A:ASP145 3.2 84.5 1.0
C A:ARG147 3.6 0.2 1.0
CA A:ASP141 3.8 82.8 1.0
OD1 A:ASP141 4.0 87.5 1.0
CA A:ILE148 4.0 88.3 1.0
N A:ASP149 4.0 54.1 1.0
CB A:ASP141 4.0 87.5 1.0
OD2 A:ASP149 4.1 82.5 1.0
CG A:GLU152 4.1 99.3 1.0
N A:ASP145 4.1 0.9 1.0
CB A:ASN143 4.2 0.8 1.0
N A:ASN144 4.2 0.3 1.0
N A:ILE148 4.3 88.3 1.0
C A:ASP141 4.3 82.8 1.0
N A:ASN143 4.3 98.0 1.0
CB A:ASP145 4.5 84.5 1.0
C A:ILE148 4.5 88.3 1.0
N A:LYS142 4.6 97.7 1.0
CA A:ASN143 4.7 98.0 1.0
CG A:ASP149 4.7 82.5 1.0
N A:ARG147 4.7 0.2 1.0
CA A:ARG147 4.8 0.2 1.0
C A:ASN143 4.8 98.0 1.0
CA A:ASP145 4.8 0.9 1.0
CB A:GLU152 4.9 99.3 1.0
N A:ASP141 4.9 82.8 1.0
CB A:ASP149 4.9 82.5 1.0
O A:ASP141 4.9 82.8 1.0
CA A:ASN144 4.9 0.3 1.0
O A:GLY140 5.0 90.4 1.0

Calcium binding site 4 out of 6 in 1j1e

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Calcium binding site 4 out of 6 in the Crystal Structure of the 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:78.1
occ:1.00
 OD2 D:ASP67 2.0 0.2 1.0
OE1 D:GLU76 2.2 0.8 1.0
OD2 D:ASP65 2.3 0.4 1.0
OE2 D:GLU76 2.4 0.8 1.0
OG D:SER69 2.5 0.8 1.0
CD D:GLU76 2.6 0.8 1.0
O D:THR71 2.8 0.6 1.0
CG D:ASP67 2.8 0.2 1.0
OD2 D:ASP73 3.0 0.3 1.0
CG D:ASP65 3.1 0.4 1.0
OD1 D:ASP67 3.3 0.2 1.0
CB D:SER69 3.5 0.8 1.0
OD1 D:ASP65 3.6 0.4 1.0
N D:SER69 3.6 0.3 1.0
C D:THR71 3.8 0.6 1.0
CG D:ASP73 3.8 0.3 1.0
N D:ASP67 3.8 0.5 1.0
CB D:ASP67 4.0 0.2 1.0
N D:GLU66 4.1 0.8 1.0
CG D:GLU76 4.1 0.8 1.0
N D:GLY68 4.1 0.3 1.0
CA D:ASP65 4.1 0.4 1.0
CB D:ASP65 4.1 0.4 1.0
CA D:SER69 4.1 0.3 1.0
CA D:ASP67 4.2 0.5 1.0
C D:ASP67 4.2 0.5 1.0
OD1 D:ASP73 4.3 0.3 1.0
N D:ASP73 4.4 86.0 1.0
OG1 D:THR71 4.4 92.3 1.0
N D:THR71 4.5 0.6 1.0
C D:ASP65 4.5 0.4 1.0
N D:VAL72 4.6 0.1 1.0
C D:GLY68 4.6 0.3 1.0
CA D:VAL72 4.6 0.1 1.0
CA D:THR71 4.7 0.6 1.0
CA D:GLY68 4.8 0.3 1.0
C D:GLU66 4.8 0.8 1.0
C D:SER69 4.8 0.3 1.0
CB D:ASP73 4.8 0.3 1.0
N D:GLY70 4.8 0.6 1.0
O D:ASP67 4.9 0.5 1.0
C D:VAL72 4.9 0.1 1.0
CB D:GLU76 5.0 0.8 1.0

Calcium binding site 5 out of 6 in 1j1e

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Calcium binding site 5 out of 6 in the Crystal Structure of the 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:78.1
occ:1.00
 OD1 D:ASP109 2.2 91.2 1.0
OD1 D:ASN107 2.2 0.1 1.0
O D:TYR111 2.4 60.4 1.0
OD2 D:ASP105 2.5 65.2 1.0
OE2 D:GLU116 2.7 0.1 1.0
CG D:ASN107 2.8 0.1 1.0
ND2 D:ASN107 2.8 0.1 1.0
OE1 D:GLU116 2.8 0.1 1.0
CD D:GLU116 3.0 0.1 1.0
CG D:ASP109 3.2 91.2 1.0
C D:TYR111 3.6 60.4 1.0
CG D:ASP105 3.6 65.2 1.0
OD1 D:ASP113 3.8 0.2 1.0
OD2 D:ASP109 3.8 91.2 1.0
CB D:ASP109 4.1 91.2 1.0
CB D:ASN107 4.1 0.1 1.0
OD1 D:ASP105 4.2 65.2 1.0
CG D:ASP113 4.3 0.2 1.0
N D:TYR111 4.3 60.4 1.0
N D:ASN107 4.3 79.8 1.0
N D:ASP109 4.3 0.8 1.0
N D:ASP113 4.4 0.7 1.0
CA D:TYR111 4.4 60.4 1.0
CG D:GLU116 4.4 0.1 1.0
CB D:TYR111 4.6 46.5 1.0
N D:ILE112 4.6 87.4 1.0
CB D:ASP113 4.6 0.2 1.0
CA D:ASP105 4.6 70.3 1.0
CB D:ASP105 4.6 65.2 1.0
CA D:ASN107 4.7 79.8 1.0
CA D:ILE112 4.7 87.4 1.0
N D:ALA108 4.7 70.7 1.0
CA D:ASP109 4.8 0.8 1.0
C D:ASP105 4.8 70.3 1.0
C D:ASN107 4.9 79.8 1.0
N D:LYS106 4.9 84.4 1.0
N D:GLY110 4.9 68.9 1.0
OD2 D:ASP113 4.9 0.2 1.0
C D:ILE112 5.0 87.4 1.0

Calcium binding site 6 out of 6 in 1j1e

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Calcium binding site 6 out of 6 in the Crystal Structure of the 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca203

b:78.1
occ:1.00
 OD1 D:ASN143 2.2 0.6 1.0
O D:ARG147 2.3 0.2 1.0
OD2 D:ASP145 2.5 0.6 1.0
OE2 D:GLU152 2.5 93.3 1.0
OE1 D:GLU152 2.6 93.3 1.0
CD D:GLU152 2.8 93.3 1.0
OD2 D:ASP141 3.0 0.4 1.0
CG D:ASP145 3.0 0.6 1.0
CG D:ASN143 3.1 0.6 1.0
OD1 D:ASP145 3.2 0.6 1.0
ND2 D:ASN143 3.4 0.6 1.0
C D:ARG147 3.6 0.2 1.0
OD1 D:ASP149 3.9 0.8 1.0
OD2 D:ASP149 4.0 0.8 1.0
N D:ASP145 4.2 0.2 1.0
CG D:ASP149 4.2 0.8 1.0
CG D:ASP141 4.2 0.4 1.0
CB D:ASP145 4.3 0.6 1.0
CG D:GLU152 4.3 93.3 1.0
CA D:ILE148 4.3 72.6 1.0
N D:ILE148 4.4 72.6 1.0
N D:ASP149 4.4 85.8 1.0
CA D:ASP141 4.5 0.9 1.0
N D:ASN143 4.5 0.7 1.0
CB D:ASN143 4.5 0.6 1.0
N D:ARG147 4.6 0.2 1.0
N D:ASN144 4.6 98.5 1.0
CA D:ASP145 4.6 0.2 1.0
CA D:ARG147 4.6 0.2 1.0
CG D:ARG147 4.7 96.0 1.0
C D:ILE148 4.7 72.6 1.0
N D:LYS142 4.8 78.4 1.0
C D:ASP141 4.8 0.9 1.0
C D:ASP145 4.9 0.2 1.0
CA D:ASN143 5.0 0.7 1.0
CB D:ASP141 5.0 0.4 1.0

Reference:

S.Takeda, A.Yamashita, K.Maeda, Y.Maeda. Structure of the Core Domain of Human Cardiac Troponin in the CA2+-Saturated Form Nature V. 424 35 2003.
ISSN: ISSN 0028-0836
PubMed: 12840750
DOI: 10.1038/NATURE01780
Page generated: Thu Jul 11 10:33:38 2024

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