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Calcium in PDB 1j1d: Crystal Structure of the 46KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form

Protein crystallography data

The structure of Crystal Structure of the 46KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form, PDB code: 1j1d 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) 40.00 / 2.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.346, 167.860, 69.707, 90.00, 101.35, 90.00
R / Rfree (%) 26.4 / 29.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the 46KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form (pdb code 1j1d). 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 46KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form, PDB code: 1j1d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1j1d

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Calcium binding site 1 out of 6 in the Crystal Structure of the 46KDA 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 46KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:68.4
occ:1.00
 OE2 A:GLU76 2.3 63.7 1.0
OE1 A:GLU76 2.4 58.4 1.0
OG A:SER69 2.4 71.9 1.0
OD2 A:ASP65 2.5 73.7 1.0
OD2 A:ASP67 2.5 71.7 1.0
CD A:GLU76 2.6 60.5 1.0
O A:THR71 2.6 69.0 1.0
CG A:ASP67 3.2 73.5 1.0
OD2 A:ASP73 3.3 68.9 1.0
OD1 A:ASP67 3.3 71.7 1.0
C A:THR71 3.6 68.1 1.0
CG A:ASP65 3.6 73.8 1.0
CB A:SER69 3.7 73.9 1.0
CG A:GLU76 4.0 59.8 1.0
OG1 A:THR71 4.2 71.7 1.0
CA A:VAL72 4.3 64.5 1.0
N A:VAL72 4.3 66.8 1.0
CA A:ASP65 4.3 74.6 1.0
CG A:ASP73 4.4 66.1 1.0
N A:GLU66 4.4 78.4 1.0
N A:THR71 4.4 69.7 1.0
N A:ASP73 4.4 63.3 1.0
OD1 A:ASP65 4.4 70.5 1.0
N A:ASP67 4.5 75.9 1.0
CB A:ASP65 4.6 73.9 1.0
CB A:ASP67 4.6 74.6 1.0
CA A:THR71 4.6 69.1 1.0
N A:SER69 4.7 77.0 1.0
C A:VAL72 4.7 64.4 1.0
CA A:SER69 4.7 74.3 1.0
CB A:GLU76 4.9 60.5 1.0
C A:ASP65 4.9 76.7 1.0
N A:GLY70 5.0 71.1 1.0

Calcium binding site 2 out of 6 in 1j1d

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Calcium binding site 2 out of 6 in the Crystal Structure of the 46KDA 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 46KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:67.0
occ:1.00
 OE1 A:GLU116 2.0 60.4 1.0
OD1 A:ASN107 2.1 75.1 1.0
OD2 A:ASP109 2.1 68.4 1.0
OD1 A:ASP105 2.2 77.1 1.0
O A:TYR111 2.5 59.1 1.0
CD A:GLU116 2.6 63.1 1.0
OE2 A:GLU116 2.6 59.9 1.0
CG A:ASP109 2.8 68.9 1.0
OD1 A:ASP109 2.9 72.4 1.0
CG A:ASN107 3.1 73.7 1.0
CG A:ASP105 3.3 74.1 1.0
C A:TYR111 3.7 58.5 1.0
ND2 A:ASN107 3.8 72.4 1.0
CA A:ASP105 4.0 73.5 1.0
CG A:GLU116 4.1 66.7 1.0
CB A:ASP105 4.1 73.7 1.0
OD2 A:ASP105 4.2 72.3 1.0
CB A:ASP109 4.2 66.2 1.0
CB A:ASN107 4.3 71.2 1.0
N A:ASP109 4.3 62.9 1.0
C A:ASP105 4.3 73.6 1.0
N A:ASN107 4.4 71.2 1.0
N A:ASP113 4.4 80.0 1.0
N A:TYR111 4.4 54.4 1.0
OD1 A:ASP113 4.4 93.9 1.0
CA A:ILE112 4.5 68.1 1.0
CA A:TYR111 4.5 54.9 1.0
N A:ILE112 4.6 63.2 1.0
N A:ALA108 4.7 64.8 1.0
O A:ASP105 4.7 74.4 1.0
CA A:ASN107 4.7 69.0 1.0
N A:LYS106 4.8 73.5 1.0
CA A:ASP109 4.8 62.9 1.0
CB A:ASP113 4.8 88.2 1.0
CB A:TYR111 4.8 51.7 1.0
CB A:GLU116 4.9 74.9 1.0
C A:ILE112 4.9 73.8 1.0
CG A:ASP113 4.9 91.6 1.0
C A:ASN107 4.9 67.6 1.0
N A:GLY110 5.0 59.8 1.0

Calcium binding site 3 out of 6 in 1j1d

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Calcium binding site 3 out of 6 in the Crystal Structure of the 46KDA 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 46KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:95.9
occ:1.00
 O A:ARG147 1.9 79.7 1.0
OD1 A:ASN143 2.1 86.2 1.0
OE1 A:GLU152 2.3 74.0 1.0
OD1 A:ASP145 2.5 92.8 1.0
OD1 A:ASP141 2.8 89.1 1.0
CG A:ASN143 2.8 86.5 1.0
C A:ARG147 2.9 78.7 1.0
ND2 A:ASN143 2.9 85.0 1.0
CD A:GLU152 3.5 72.9 1.0
CA A:ILE148 3.5 75.9 1.0
N A:ILE148 3.6 77.7 1.0
CG A:ASP145 3.7 91.0 1.0
CA A:ARG147 3.9 78.2 1.0
N A:ARG147 3.9 81.1 1.0
CG A:ASP141 3.9 88.3 1.0
N A:ASP145 4.0 90.2 1.0
OD1 A:ASP149 4.1 73.3 1.0
N A:ASP149 4.1 73.9 1.0
N A:ASN144 4.1 91.1 1.0
OE2 A:GLU152 4.1 72.5 1.0
CA A:ASP141 4.2 86.1 1.0
CG A:ARG147 4.2 67.2 1.0
CB A:ASN143 4.3 87.8 1.0
OD2 A:ASP145 4.3 89.2 1.0
C A:ILE148 4.4 75.1 1.0
N A:ASN143 4.5 89.6 1.0
CB A:ARG147 4.5 74.1 1.0
CB A:ASP141 4.6 87.2 1.0
CG A:GLU152 4.6 72.1 1.0
CA A:ASP145 4.7 88.7 1.0
CA A:ASN144 4.7 91.6 1.0
C A:ASP145 4.7 87.0 1.0
N A:LYS142 4.7 87.2 1.0
C A:ASN144 4.7 91.5 1.0
CB A:ILE148 4.7 75.3 1.0
CB A:ASP145 4.8 89.5 1.0
C A:ASP141 4.8 86.3 1.0
CG1 A:ILE148 4.8 74.0 1.0
CA A:ASN143 4.8 89.7 1.0
C A:ASN143 4.8 90.6 1.0
OD2 A:ASP141 4.9 87.4 1.0
O A:ASP145 4.9 88.2 1.0
N A:GLY146 5.0 85.4 1.0

Calcium binding site 4 out of 6 in 1j1d

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Calcium binding site 4 out of 6 in the Crystal Structure of the 46KDA 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 46KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:92.7
occ:1.00
 OG D:SER69 2.2 92.4 1.0
O D:THR71 2.3 84.4 1.0
OE2 D:GLU76 2.4 73.5 1.0
OD2 D:ASP67 2.5 0.0 1.0
OE1 D:GLU76 2.5 74.8 1.0
OD2 D:ASP65 2.6 93.2 1.0
CD D:GLU76 2.8 73.3 1.0
OD1 D:ASP67 3.2 0.7 1.0
CG D:ASP67 3.2 0.6 1.0
C D:THR71 3.4 84.4 1.0
CB D:SER69 3.5 95.0 1.0
CG D:ASP65 3.5 94.0 1.0
N D:SER69 3.7 97.0 1.0
OD1 D:ASP65 3.9 93.9 1.0
OD2 D:ASP73 4.0 82.0 1.0
CA D:SER69 4.0 95.6 1.0
N D:THR71 4.1 89.2 1.0
OG1 D:THR71 4.2 85.9 1.0
CG D:GLU76 4.3 70.9 1.0
CA D:THR71 4.3 86.3 1.0
CG D:ASP73 4.3 80.7 1.0
N D:VAL72 4.3 81.8 1.0
C D:SER69 4.4 95.0 1.0
CA D:VAL72 4.4 78.2 1.0
N D:ASP73 4.4 75.8 1.0
OD1 D:ASP73 4.5 81.2 1.0
N D:GLY68 4.5 0.0 1.0
N D:GLY70 4.5 94.0 1.0
CB D:ASP65 4.6 93.9 1.0
CB D:ASP67 4.6 1.0 1.0
CA D:ASP65 4.8 94.3 1.0
C D:GLY68 4.8 98.1 1.0
CB D:THR71 4.9 86.0 1.0
N D:ASP67 4.9 0.1 1.0
C D:VAL72 4.9 76.6 1.0

Calcium binding site 5 out of 6 in 1j1d

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Calcium binding site 5 out of 6 in the Crystal Structure of the 46KDA 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 46KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:79.4
occ:1.00
 OD1 D:ASN107 2.1 85.0 1.0
OD1 D:ASP109 2.1 81.5 1.0
O D:TYR111 2.3 80.2 1.0
OE2 D:GLU116 2.4 82.7 1.0
OD2 D:ASP105 2.6 80.6 1.0
OE1 D:GLU116 2.8 82.6 1.0
CD D:GLU116 2.9 83.4 1.0
CG D:ASP109 2.9 81.6 1.0
OD2 D:ASP109 3.1 82.9 1.0
CG D:ASN107 3.2 83.0 1.0
C D:TYR111 3.5 79.6 1.0
OD2 D:ASP113 3.5 92.4 1.0
ND2 D:ASN107 3.8 81.9 1.0
CG D:ASP105 3.8 80.2 1.0
N D:ASP113 4.0 87.6 1.0
CG D:ASP113 4.1 91.7 1.0
CA D:ILE112 4.2 84.2 1.0
CG D:GLU116 4.2 84.8 1.0
N D:ILE112 4.3 81.7 1.0
CB D:ASP109 4.3 80.5 1.0
CB D:ASN107 4.4 82.2 1.0
N D:ASN107 4.4 82.5 1.0
CA D:ASP105 4.5 80.0 1.0
OD1 D:ASP105 4.5 77.8 1.0
CA D:TYR111 4.5 78.0 1.0
N D:TYR111 4.5 78.1 1.0
C D:ILE112 4.6 86.1 1.0
N D:ASP109 4.6 80.4 1.0
CB D:ASP113 4.6 90.3 1.0
CB D:ASP105 4.7 79.5 1.0
OD1 D:ASP113 4.7 91.6 1.0
C D:ASP105 4.8 80.8 1.0
CB D:TYR111 4.9 75.0 1.0
CA D:ASN107 4.9 81.9 1.0
N D:LYS106 4.9 82.7 1.0
CA D:ASP113 4.9 90.0 1.0
CA D:ASP109 5.0 79.8 1.0
CB D:GLU116 5.0 86.6 1.0

Calcium binding site 6 out of 6 in 1j1d

Go back to Calcium Binding Sites List in 1j1d
Calcium binding site 6 out of 6 in the Crystal Structure of the 46KDA 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 46KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca203

b:79.4
occ:1.00
 OD2 D:ASP145 2.0 94.2 1.0
OE1 D:GLU152 2.2 67.9 1.0
OD1 D:ASP145 2.3 94.8 1.0
CG D:ASP145 2.4 93.3 1.0
OD1 D:ASN143 2.4 95.4 1.0
OE2 D:GLU152 2.4 66.5 1.0
O D:ARG147 2.5 85.6 1.0
CD D:GLU152 2.6 67.5 1.0
OD2 D:ASP141 2.7 89.4 1.0
CG D:ASN143 3.3 94.2 1.0
ND2 D:ASN143 3.6 94.6 1.0
C D:ARG147 3.6 85.4 1.0
CB D:ASP145 3.7 92.2 1.0
CG D:ASP141 3.8 89.4 1.0
N D:ASP145 4.0 92.0 1.0
CG D:GLU152 4.1 66.5 1.0
CA D:ASP141 4.1 89.4 1.0
CA D:ILE148 4.1 80.0 1.0
N D:ILE148 4.3 82.8 1.0
C D:ASP141 4.3 89.0 1.0
N D:ASP149 4.3 76.2 1.0
N D:ASN144 4.4 90.9 1.0
CB D:ASP141 4.4 89.1 1.0
OD2 D:ASP149 4.4 74.9 1.0
CA D:ASP145 4.5 90.8 1.0
N D:ASN143 4.5 89.0 1.0
OD1 D:ASP141 4.6 89.3 1.0
N D:ARG147 4.6 87.9 1.0
O D:ASP141 4.6 89.4 1.0
CB D:ASN143 4.7 92.2 1.0
CA D:ARG147 4.7 87.0 1.0
C D:ILE148 4.7 78.4 1.0
N D:LYS142 4.8 88.4 1.0
CB D:GLU152 4.9 67.3 1.0
CA D:ASN143 5.0 90.3 1.0
O D:GLY140 5.0 91.8 1.0
N D:GLY146 5.0 88.0 1.0
C D:ASN144 5.0 92.1 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 10:33:37 2024

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