Calcium in PDB 1ytz: Crystal Structure of Skeletal Muscle Troponin in the CA2+- Activated State

The structure of Crystal Structure of Skeletal Muscle Troponin in the CA2+- Activated State, PDB code: 1ytz was solved by M.V.Vinogradova, D.B.Stone, G.G.Malanina, C.Karatzaferi, R.Cooke, R.A.Mendelson, R.J.Fletterick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 3.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	138.608, 138.608, 83.676, 90.00, 90.00, 90.00
R / Rfree (%)	28.9 / 33.8

The binding sites of Calcium atom in the Crystal Structure of Skeletal Muscle Troponin in the CA2+- Activated State (pdb code 1ytz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Skeletal Muscle Troponin in the CA2+- Activated State, PDB code: 1ytz:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Skeletal Muscle Troponin in the CA2+- Activated State


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 Skeletal Muscle Troponin in the CA2+- Activated State within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:33.6 occ:1.00 OD2 C:ASP109 2.3 55.1 1.0 OD1 C:ASN107 2.5 58.0 1.0 OD1 C:ASP105 2.6 48.5 1.0 CG C:ASP109 2.9 56.2 1.0 OE1 C:GLU116 2.9 42.1 1.0 O C:PHE111 2.9 49.9 1.0 OE2 C:GLU116 3.0 42.2 1.0 OD1 C:ASP109 3.0 58.1 1.0 CG C:ASN107 3.2 57.6 1.0 CB C:ASN107 3.2 56.5 1.0 CD C:GLU116 3.3 41.5 1.0 C C:PHE111 3.4 48.4 1.0 O C:ASP105 3.5 55.0 1.0 CG C:ASP105 3.8 50.1 1.0 N C:PHE111 3.9 49.2 1.0 N C:ILE112 3.9 46.7 1.0 OD2 C:ASP113 4.0 46.9 1.0 CA C:PHE111 4.1 49.5 1.0 CB C:ASP109 4.1 54.4 1.0 CA C:ILE112 4.2 43.4 1.0 CB C:PHE111 4.2 52.5 1.0 C C:ASP105 4.3 53.1 1.0 N C:ASP109 4.3 51.1 1.0 CA C:ASP105 4.3 50.0 1.0 OD2 C:ASP105 4.5 51.7 1.0 N C:ASP113 4.5 44.3 1.0 ND2 C:ASN107 4.6 59.7 1.0 CA C:ASN107 4.6 56.6 1.0 N C:GLY110 4.6 49.1 1.0 CA C:ASP109 4.6 51.4 1.0 CB C:ASP105 4.7 49.1 1.0 CG C:ASP113 4.8 48.2 1.0 N C:ALA108 4.8 54.2 1.0 C C:ASN107 4.8 56.0 1.0 CG C:GLU116 4.8 40.7 1.0 C C:ASP109 4.8 50.9 1.0 O C:LYS106 4.9 55.0 1.0 C C:ILE112 4.9 43.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Skeletal Muscle Troponin in the CA2+- Activated State


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 Skeletal Muscle Troponin in the CA2+- Activated State within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:41.8 occ:1.00 OD1 C:ASP145 2.4 59.7 1.0 OD1 C:ASN143 2.5 78.3 1.0 OD2 C:ASP141 2.7 60.1 1.0 OE2 C:GLU152 2.7 55.5 1.0 O C:ARG147 2.8 62.2 1.0 OE1 C:GLU152 2.8 51.8 1.0 CD C:GLU152 3.1 52.5 1.0 ND2 C:ASN143 3.1 76.9 1.0 CG C:ASN143 3.1 76.6 1.0 CG C:ASP141 3.2 60.8 1.0 CG C:ASP145 3.4 62.4 1.0 C C:ARG147 3.4 61.1 1.0 OD2 C:ASP145 3.6 61.3 1.0 OD1 C:ASP141 3.7 59.2 1.0 NE2 T:GLN243 3.8 0.2 1.0 CA C:ILE148 3.9 58.2 1.0 N C:ILE148 3.9 59.2 1.0 CB C:ASP141 4.1 61.2 1.0 N C:ASP149 4.1 58.0 1.0 CA C:ASP141 4.2 63.1 1.0 N C:ARG147 4.2 62.7 1.0 CA C:ARG147 4.3 63.0 1.0 C C:ILE148 4.5 58.5 1.0 N C:ASP145 4.5 66.2 1.0 CB C:ASN143 4.6 74.2 1.0 CG C:GLU152 4.6 51.1 1.0 N C:ASN143 4.6 70.6 1.0 CB C:ARG147 4.7 66.0 1.0 CB C:ASP145 4.7 65.1 1.0 C C:ASP141 4.8 66.7 1.0 N C:LYS142 4.8 68.9 1.0 CD T:GLN243 4.8 0.9 1.0 N C:GLY146 4.8 64.3 1.0 CA C:ASN143 5.0 72.0 1.0 N C:ASN144 5.0 70.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Skeletal Muscle Troponin in the CA2+- Activated State


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 Skeletal Muscle Troponin in the CA2+- Activated State within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:74.5 occ:1.00 O C:ASP35 2.5 72.8 1.0 OD2 C:ASP29 2.6 71.7 1.0 OE1 C:GLU40 2.6 73.6 1.0 OD1 C:ASP31 2.7 82.6 1.0 OE2 C:GLU40 2.9 72.3 1.0 CD C:GLU40 3.1 72.3 1.0 OD2 C:ASP31 3.1 82.8 1.0 CG C:ASP31 3.3 82.2 1.0 CG C:ASP29 3.3 73.3 1.0 C C:ASP35 3.5 73.3 1.0 OD1 C:ASP29 3.6 73.1 1.0 N C:ASP35 3.8 75.2 1.0 N C:GLY34 4.2 77.5 1.0 N C:GLY33 4.2 81.2 1.0 CA C:ASP35 4.2 75.0 1.0 CA C:GLY33 4.4 79.5 1.0 CG C:GLU40 4.5 69.8 1.0 N C:ILE36 4.5 71.5 1.0 CB C:ASP29 4.5 73.1 1.0 OD1 C:ASP35 4.6 78.9 1.0 CG C:ASP35 4.7 78.5 1.0 CA C:ILE36 4.8 69.4 1.0 CB C:ASP31 4.8 81.6 1.0 CA C:ASP29 4.8 73.5 1.0 C C:GLY33 4.8 78.5 1.0 N C:SER37 4.8 68.1 1.0 N C:GLY32 4.9 83.1 1.0 C C:GLY34 4.9 76.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Skeletal Muscle Troponin in the CA2+- Activated State


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 Skeletal Muscle Troponin in the CA2+- Activated State within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca204 b:80.5 occ:1.00 OE1 C:GLU76 2.6 58.1 1.0 OG C:SER69 2.6 69.1 1.0 OD1 C:ASP67 2.7 84.2 1.0 OE2 C:GLU76 3.0 56.5 1.0 OD1 C:ASP65 3.0 67.9 1.0 CD C:GLU76 3.1 58.6 1.0 OD2 C:ASP67 3.1 83.6 1.0 O C:THR71 3.2 62.9 1.0 CG C:ASP67 3.2 82.7 1.0 OD2 C:ASP73 3.2 77.6 1.0 CB C:SER69 3.4 70.8 1.0 OG1 C:THR71 3.7 56.9 1.0 C C:THR71 3.9 62.2 1.0 CG C:ASP73 4.2 76.6 1.0 N C:ASP73 4.2 68.7 1.0 CG C:ASP65 4.3 72.4 1.0 CA C:ILE72 4.4 65.4 1.0 CG C:GLU76 4.4 59.6 1.0 N C:ILE72 4.5 63.4 1.0 CB C:ASP73 4.5 73.3 1.0 CB C:ASP67 4.6 81.0 1.0 C C:ILE72 4.6 67.0 1.0 CA C:SER69 4.7 71.6 1.0 CA C:THR71 4.8 60.7 1.0 N C:THR71 4.8 61.4 1.0 CB C:THR71 4.8 58.9 1.0 N C:SER69 4.8 74.0 1.0

M.V.Vinogradova, D.B.Stone, G.G.Malanina, C.Karatzaferi, R.Cooke, R.A.Mendelson, R.J.Fletterick. CA2+-Regulated Structural Changes in Troponin Proc.Natl.Acad.Sci.Usa V. 102 5038 2005.
ISSN: ISSN 0027-8424
PubMed: 15784741
DOI: 10.1073/PNAS.0408882102