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Calcium in PDB 6dae: 2.0 Angstrom Crystal Structure of the D95V Ca/Cam:CAV1.2 Iq Domain Complex

Protein crystallography data

The structure of 2.0 Angstrom Crystal Structure of the D95V Ca/Cam:CAV1.2 Iq Domain Complex, PDB code: 6dae was solved by K.Wang, J.Lu, F.Van Petegem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.04 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.148, 69.615, 86.078, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22.6

Calcium Binding Sites:

The binding sites of Calcium atom in the 2.0 Angstrom Crystal Structure of the D95V Ca/Cam:CAV1.2 Iq Domain Complex (pdb code 6dae). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the 2.0 Angstrom Crystal Structure of the D95V Ca/Cam:CAV1.2 Iq Domain Complex, PDB code: 6dae:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6dae

Go back to Calcium Binding Sites List in 6dae
Calcium binding site 1 out of 6 in the 2.0 Angstrom Crystal Structure of the D95V Ca/Cam:CAV1.2 Iq Domain Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 2.0 Angstrom Crystal Structure of the D95V Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:16.6
occ:1.00
 OD1 A:ASP20 2.3 16.2 1.0
O A:THR26 2.3 17.1 1.0
OD1 A:ASP22 2.4 19.2 1.0
OD1 A:ASP24 2.4 22.1 1.0
O A:HOH650 2.4 16.4 1.0
OE1 A:GLU31 2.5 15.6 1.0
OE2 A:GLU31 2.5 14.4 1.0
CD A:GLU31 2.8 15.7 1.0
CG A:ASP22 3.3 23.9 1.0
CG A:ASP24 3.3 23.8 1.0
CG A:ASP20 3.4 18.9 1.0
C A:THR26 3.5 16.4 1.0
OD2 A:ASP22 3.6 22.8 1.0
OD2 A:ASP24 3.9 22.9 1.0
OG1 A:THR26 3.9 19.9 1.0
CA A:ASP20 4.0 15.4 1.0
CB A:ASP20 4.1 14.3 1.0
N A:THR26 4.2 15.9 1.0
N A:ASP24 4.2 21.6 1.0
CG A:GLU31 4.3 16.0 1.0
OD2 A:ASP20 4.3 19.1 1.0
CB A:ASP24 4.3 17.7 1.0
CA A:THR26 4.4 14.5 1.0
C A:ASP20 4.4 16.6 1.0
N A:ILE27 4.5 11.4 1.0
N A:ASP22 4.5 17.8 1.0
O A:HOH601 4.6 36.6 1.0
CB A:ASP22 4.6 23.6 1.0
CA A:ILE27 4.6 19.1 1.0
CA A:ASP24 4.7 19.2 1.0
N A:GLY23 4.7 19.6 1.0
O A:HOH635 4.7 19.1 1.0
CB A:THR26 4.8 18.4 1.0
N A:GLY25 4.8 17.4 1.0
N A:LYS21 4.8 17.0 1.0
CG2 A:THR28 4.8 13.2 1.0
O A:ASP20 4.9 15.3 1.0
C A:ASP24 4.9 18.3 1.0
CA A:ASP22 4.9 21.1 1.0
O A:HOH651 4.9 27.3 1.0
C A:ASP22 4.9 22.2 1.0
N A:THR28 5.0 16.5 1.0

Calcium binding site 2 out of 6 in 6dae

Go back to Calcium Binding Sites List in 6dae
Calcium binding site 2 out of 6 in the 2.0 Angstrom Crystal Structure of the D95V Ca/Cam:CAV1.2 Iq Domain Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 2.0 Angstrom Crystal Structure of the D95V Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:18.7
occ:1.00
 OD1 A:ASP56 2.4 16.0 1.0
OD1 A:ASP58 2.4 21.3 1.0
O A:HOH653 2.5 17.6 1.0
O A:HOH618 2.5 17.7 1.0
OD1 A:ASN60 2.5 15.5 1.0
O A:THR62 2.5 16.3 1.0
OE1 A:GLU67 2.5 14.7 1.0
OE2 A:GLU67 2.6 16.6 1.0
CD A:GLU67 2.9 17.2 1.0
CG A:ASN60 3.3 17.7 1.0
CG A:ASP58 3.4 21.1 1.0
CG A:ASP56 3.5 20.7 1.0
C A:THR62 3.6 18.0 1.0
ND2 A:ASN60 3.7 19.6 1.0
OD2 A:ASP58 3.8 22.4 1.0
OD2 A:ASP56 4.2 17.9 1.0
CB A:ASP56 4.3 19.6 1.0
N A:ASP64 4.3 16.7 1.0
CA A:ASP56 4.3 20.1 1.0
N A:ASP58 4.4 21.1 1.0
OG1 A:THR62 4.4 15.5 1.0
CG A:GLU67 4.4 14.5 1.0
CA A:ILE63 4.4 18.1 1.0
N A:THR62 4.4 15.1 1.0
N A:ILE63 4.4 16.8 1.0
N A:ASN60 4.5 18.9 1.0
O A:HOH686 4.5 24.8 1.0
OD2 A:ASP64 4.5 19.0 1.0
CB A:ASN60 4.6 18.5 1.0
CA A:THR62 4.6 13.6 1.0
CG A:ASP64 4.6 21.4 1.0
C A:ASP56 4.7 24.4 1.0
CB A:ASP58 4.7 19.3 1.0
N A:GLY59 4.7 22.4 1.0
N A:ALA57 4.7 18.8 1.0
C A:ILE63 4.8 17.5 1.0
OD1 A:ASP64 4.9 16.0 1.0
CA A:ASP58 4.9 24.9 1.0
CA A:ASN60 4.9 22.0 1.0

Calcium binding site 3 out of 6 in 6dae

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Calcium binding site 3 out of 6 in the 2.0 Angstrom Crystal Structure of the D95V Ca/Cam:CAV1.2 Iq Domain Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 2.0 Angstrom Crystal Structure of the D95V Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:33.4
occ:1.00
 OD1 A:ASP131 2.3 42.3 1.0
OD1 A:ASP129 2.3 32.7 1.0
O A:GLN135 2.4 33.9 1.0
OD1 A:ASP133 2.4 39.6 1.0
O A:HOH664 2.4 32.6 1.0
OE1 A:GLU140 2.5 36.5 1.0
OE2 A:GLU140 2.5 35.4 1.0
CD A:GLU140 2.8 36.8 1.0
CG A:ASP133 3.3 42.3 1.0
CG A:ASP131 3.3 45.9 1.0
CG A:ASP129 3.4 36.4 1.0
C A:GLN135 3.5 31.2 1.0
OD2 A:ASP133 3.6 41.7 1.0
OD2 A:ASP131 3.8 47.1 1.0
CA A:ASP129 4.2 33.2 1.0
N A:ASP133 4.2 45.9 1.0
N A:ASP131 4.3 51.5 1.0
OD2 A:ASP129 4.3 37.5 1.0
N A:GLN135 4.3 31.7 1.0
CB A:ASP129 4.3 36.0 1.0
N A:VAL136 4.3 29.4 1.0
CG A:GLU140 4.3 36.0 1.0
CA A:VAL136 4.3 29.1 1.0
CA A:GLN135 4.4 33.1 1.0
N A:GLY132 4.4 51.0 1.0
C A:ASP129 4.4 39.3 1.0
N A:ILE130 4.4 39.3 1.0
CB A:ASP133 4.5 43.4 1.0
CB A:ASP131 4.5 49.2 1.0
N A:ASN137 4.6 28.1 1.0
O A:HOH647 4.7 49.2 1.0
CB A:GLN135 4.7 37.8 1.0
CA A:ASP131 4.7 51.3 1.0
C A:ASP131 4.8 54.4 1.0
CA A:ASP133 4.8 43.4 1.0
N A:GLY134 5.0 37.6 1.0
C A:VAL136 5.0 27.8 1.0

Calcium binding site 4 out of 6 in 6dae

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Calcium binding site 4 out of 6 in the 2.0 Angstrom Crystal Structure of the D95V Ca/Cam:CAV1.2 Iq Domain Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 2.0 Angstrom Crystal Structure of the D95V Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:22.9
occ:1.00
 OD1 B:ASP22 2.3 28.7 1.0
O B:THR26 2.3 24.5 1.0
OD1 B:ASP20 2.3 18.7 1.0
OD1 B:ASP24 2.4 28.9 1.0
O B:HOH634 2.4 22.4 1.0
OE2 B:GLU31 2.5 21.2 1.0
OE1 B:GLU31 2.5 24.1 1.0
CD B:GLU31 2.8 22.9 1.0
CG B:ASP22 3.2 36.1 1.0
CG B:ASP24 3.3 29.5 1.0
CG B:ASP20 3.4 19.3 1.0
C B:THR26 3.5 22.9 1.0
OD2 B:ASP22 3.5 42.1 1.0
OD2 B:ASP24 3.9 35.0 1.0
OG1 B:THR26 4.1 33.9 1.0
N B:THR26 4.1 16.8 1.0
CA B:ASP20 4.1 17.4 1.0
N B:ASP24 4.2 25.6 1.0
CB B:ASP20 4.2 18.9 1.0
OD2 B:ASP20 4.3 18.5 1.0
CG B:GLU31 4.3 22.8 1.0
CA B:THR26 4.3 15.2 1.0
N B:ASP22 4.4 22.9 1.0
CB B:ASP24 4.4 25.2 1.0
C B:ASP20 4.4 21.2 1.0
N B:ILE27 4.5 18.1 1.0
CB B:ASP22 4.5 30.7 1.0
N B:GLY23 4.6 25.8 1.0
CA B:ILE27 4.6 18.9 1.0
N B:LYS21 4.6 20.3 1.0
CA B:ASP24 4.7 27.1 1.0
N B:GLY25 4.7 21.9 1.0
CA B:ASP22 4.8 24.1 1.0
C B:ASP22 4.8 25.4 1.0
CG2 B:THR28 4.9 22.9 1.0
C B:ASP24 4.9 23.8 1.0
CB B:THR26 4.9 26.8 1.0
N B:THR28 4.9 19.4 1.0
O B:ASP20 5.0 21.9 1.0
O B:HOH603 5.0 25.4 1.0

Calcium binding site 5 out of 6 in 6dae

Go back to Calcium Binding Sites List in 6dae
Calcium binding site 5 out of 6 in the 2.0 Angstrom Crystal Structure of the D95V Ca/Cam:CAV1.2 Iq Domain Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 2.0 Angstrom Crystal Structure of the D95V Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:19.4
occ:1.00
 OD1 B:ASP56 2.3 24.7 1.0
OD1 B:ASN60 2.3 22.1 1.0
O B:THR62 2.4 17.7 1.0
OD1 B:ASP58 2.5 25.5 1.0
O B:HOH627 2.5 20.5 1.0
OE1 B:GLU67 2.5 15.6 1.0
O B:HOH608 2.5 27.2 1.0
OE2 B:GLU67 2.6 21.1 1.0
CD B:GLU67 2.9 15.7 1.0
CG B:ASN60 3.2 29.0 1.0
CG B:ASP58 3.4 25.7 1.0
CG B:ASP56 3.4 26.1 1.0
C B:THR62 3.6 18.6 1.0
ND2 B:ASN60 3.7 24.0 1.0
OD2 B:ASP58 3.7 26.1 1.0
CB B:ASP56 4.2 22.8 1.0
OD2 B:ASP56 4.2 28.9 1.0
CA B:ASP56 4.3 18.9 1.0
N B:ASP64 4.3 16.3 1.0
N B:ASN60 4.4 30.7 1.0
N B:THR62 4.4 20.6 1.0
CG B:GLU67 4.4 16.3 1.0
CB B:ASN60 4.4 29.6 1.0
N B:ILE63 4.4 16.4 1.0
CA B:ILE63 4.4 17.2 1.0
N B:ASP58 4.5 28.3 1.0
OG1 B:THR62 4.5 23.1 1.0
CA B:THR62 4.6 20.9 1.0
O A:HOH620 4.6 45.4 1.0
OD2 B:ASP64 4.6 26.4 1.0
CB B:ASP58 4.6 27.6 1.0
C B:ASP56 4.7 24.7 1.0
CG B:ASP64 4.7 24.9 1.0
N B:GLY59 4.7 25.6 1.0
N B:ALA57 4.7 21.0 1.0
C B:ILE63 4.8 18.9 1.0
CA B:ASN60 4.8 30.7 1.0
N B:GLY61 4.9 27.9 1.0
CA B:ASP58 4.9 23.9 1.0
OD1 B:ASP64 4.9 22.5 1.0
C B:ASP58 5.0 25.6 1.0

Calcium binding site 6 out of 6 in 6dae

Go back to Calcium Binding Sites List in 6dae
Calcium binding site 6 out of 6 in the 2.0 Angstrom Crystal Structure of the D95V Ca/Cam:CAV1.2 Iq Domain Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of 2.0 Angstrom Crystal Structure of the D95V Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:25.4
occ:1.00
 O B:GLN135 2.3 25.5 1.0
OD1 B:ASP129 2.4 30.1 1.0
OD1 B:ASP133 2.4 28.3 1.0
OD1 B:ASP131 2.4 35.5 1.0
O B:HOH621 2.5 28.0 1.0
OE1 B:GLU140 2.5 22.0 1.0
OE2 B:GLU140 2.6 26.9 1.0
CD B:GLU140 2.9 24.4 1.0
CG B:ASP133 3.2 31.6 1.0
CG B:ASP131 3.4 33.5 1.0
C B:GLN135 3.5 22.3 1.0
CG B:ASP129 3.5 30.5 1.0
OD2 B:ASP133 3.6 34.5 1.0
OD2 B:ASP131 3.8 36.5 1.0
N B:ASP133 4.2 32.4 1.0
N B:GLN135 4.2 27.5 1.0
OD2 B:ASP129 4.2 33.6 1.0
CA B:ASP129 4.3 22.6 1.0
CA B:GLN135 4.3 22.3 1.0
N B:VAL136 4.4 17.3 1.0
CB B:ASP129 4.4 25.6 1.0
N B:ASP131 4.4 28.3 1.0
CB B:ASP133 4.4 26.7 1.0
CG B:GLU140 4.4 18.1 1.0
CA B:VAL136 4.4 20.6 1.0
C B:ASP129 4.5 26.2 1.0
N B:GLY132 4.5 29.4 1.0
N B:ILE130 4.6 24.4 1.0
O B:HOH629 4.6 33.6 1.0
N B:ASN137 4.6 19.3 1.0
CB B:GLN135 4.7 28.8 1.0
CB B:ASP131 4.7 31.0 1.0
CA B:ASP133 4.7 30.8 1.0
N B:GLY134 4.9 23.4 1.0
CA B:ASP131 4.9 35.1 1.0
ND2 B:ASN137 4.9 19.1 1.0
C B:ASP131 4.9 36.7 1.0

Reference:

K.Wang, C.Holt, J.Lu, M.Brohus, K.T.Larsen, M.T.Overgaard, R.Wimmer, F.Van Petegem. Arrhythmia Mutations in Calmodulin Cause Conformational Changes That Affect Interactions with the Cardiac Voltage-Gated Calcium Channel. Proc. Natl. Acad. Sci. V. 115 10556 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30348784
DOI: 10.1073/PNAS.1808733115
Page generated: Wed Jul 9 13:18:21 2025

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