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Calcium in PDB 6dad: 1.65 Angstrom Crystal Structure of the N97I Ca/Cam:CAV1.2 Iq Domain Complex

Protein crystallography data

The structure of 1.65 Angstrom Crystal Structure of the N97I Ca/Cam:CAV1.2 Iq Domain Complex, PDB code: 6dad was solved by K.Wang, F.Van Petegem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.51 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.273, 69.045, 85.792, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 20.8

Calcium Binding Sites:

The binding sites of Calcium atom in the 1.65 Angstrom Crystal Structure of the N97I Ca/Cam:CAV1.2 Iq Domain Complex (pdb code 6dad). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the 1.65 Angstrom Crystal Structure of the N97I Ca/Cam:CAV1.2 Iq Domain Complex, PDB code: 6dad:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6dad

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Calcium binding site 1 out of 6 in the 1.65 Angstrom Crystal Structure of the N97I 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 1.65 Angstrom Crystal Structure of the N97I Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:18.6
occ:1.00
 O A:THR26 2.3 20.8 1.0
OD1 A:ASP20 2.3 20.4 1.0
O A:HOH634 2.4 21.5 1.0
OD1 A:ASP22 2.4 20.5 1.0
OD1 A:ASP24 2.4 20.7 1.0
OE2 A:GLU31 2.5 19.0 1.0
OE1 A:GLU31 2.5 20.5 1.0
CD A:GLU31 2.8 19.6 1.0
CG A:ASP24 3.3 24.7 1.0
CG A:ASP22 3.3 25.3 1.0
CG A:ASP20 3.4 23.1 1.0
C A:THR26 3.5 20.2 1.0
OD2 A:ASP22 3.7 25.0 1.0
OD2 A:ASP24 3.9 26.1 1.0
OG1 A:THR26 4.0 22.7 1.0
CA A:ASP20 4.0 16.2 1.0
CB A:ASP20 4.1 18.4 1.0
N A:THR26 4.1 16.6 1.0
N A:ASP24 4.2 23.4 1.0
CG A:GLU31 4.3 16.9 1.0
OD2 A:ASP20 4.3 19.4 1.0
CB A:ASP24 4.3 23.8 1.0
CA A:THR26 4.4 17.1 1.0
C A:ASP20 4.4 15.7 1.0
N A:ILE27 4.5 16.0 1.0
N A:ASP22 4.5 19.9 1.0
CA A:ILE27 4.6 16.9 1.0
CB A:ASP22 4.6 21.6 1.0
CA A:ASP24 4.7 22.6 1.0
N A:LYS21 4.7 18.3 1.0
O A:HOH615 4.7 31.9 1.0
N A:GLY23 4.8 21.4 1.0
CG2 A:THR28 4.8 18.4 1.0
O A:HOH636 4.8 23.8 1.0
CB A:THR26 4.8 19.3 1.0
N A:GLY25 4.8 18.2 1.0
C A:ASP24 4.9 21.5 1.0
N A:THR28 4.9 15.6 1.0
O A:ASP20 5.0 19.6 1.0
CA A:ASP22 5.0 21.1 1.0
O A:HOH657 5.0 30.8 1.0

Calcium binding site 2 out of 6 in 6dad

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Calcium binding site 2 out of 6 in the 1.65 Angstrom Crystal Structure of the N97I 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 1.65 Angstrom Crystal Structure of the N97I Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:19.7
occ:1.00
 OD1 A:ASP56 2.4 21.4 1.0
OD1 A:ASN60 2.4 20.0 1.0
OE1 A:GLU67 2.5 18.9 1.0
OD1 A:ASP58 2.5 21.6 1.0
O A:HOH622 2.5 22.6 1.0
O A:THR62 2.5 19.1 1.0
O A:HOH639 2.6 21.4 1.0
OE2 A:GLU67 2.6 21.3 1.0
CD A:GLU67 2.9 19.0 1.0
CG A:ASN60 3.3 22.7 1.0
CG A:ASP56 3.4 22.2 1.0
CG A:ASP58 3.5 23.6 1.0
C A:THR62 3.6 16.9 1.0
ND2 A:ASN60 3.7 23.9 1.0
OD2 A:ASP58 3.9 24.9 1.0
OD2 A:ASP56 4.2 22.6 1.0
CB A:ASP56 4.2 18.0 1.0
N A:ASN60 4.3 21.4 1.0
CA A:ASP56 4.3 20.0 1.0
N A:ASP64 4.4 17.8 1.0
N A:ASP58 4.4 23.9 1.0
CG A:GLU67 4.4 17.4 1.0
OG1 A:THR62 4.4 20.7 1.0
N A:THR62 4.4 16.9 1.0
CA A:ILE63 4.4 16.7 1.0
N A:ILE63 4.5 18.4 1.0
CB A:ASN60 4.5 20.6 1.0
OD2 A:ASP64 4.6 21.6 1.0
CA A:THR62 4.6 17.4 1.0
C A:ASP56 4.6 24.4 1.0
O A:HOH678 4.6 26.2 1.0
CB A:ASP58 4.6 23.7 1.0
CG A:ASP64 4.6 21.7 1.0
N A:GLY59 4.7 22.6 1.0
N A:ALA57 4.7 21.5 1.0
C A:ILE63 4.8 16.8 1.0
CA A:ASN60 4.8 18.7 1.0
CA A:ASP58 4.9 22.3 1.0
OD1 A:ASP64 4.9 21.7 1.0
C A:ASP58 5.0 25.0 1.0
N A:GLY61 5.0 19.8 1.0

Calcium binding site 3 out of 6 in 6dad

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Calcium binding site 3 out of 6 in the 1.65 Angstrom Crystal Structure of the N97I 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 1.65 Angstrom Crystal Structure of the N97I Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:44.6
occ:1.00
 O A:GLN135 2.3 46.5 1.0
OD1 A:ASP129 2.3 46.8 1.0
OD1 A:ASP131 2.3 51.7 1.0
OE1 A:GLU140 2.4 44.9 1.0
OD1 A:ASP133 2.5 50.0 1.0
O A:HOH666 2.5 44.2 1.0
OE2 A:GLU140 2.6 45.4 1.0
CD A:GLU140 2.8 47.5 1.0
CG A:ASP131 3.4 57.5 1.0
CG A:ASP133 3.4 55.1 1.0
CG A:ASP129 3.4 45.8 1.0
C A:GLN135 3.4 43.8 1.0
OD2 A:ASP131 3.8 57.0 1.0
OD2 A:ASP133 3.8 51.8 1.0
N A:ASP133 4.1 51.6 1.0
N A:GLN135 4.1 45.8 1.0
OD2 A:ASP129 4.2 43.8 1.0
N A:ASP131 4.2 58.2 1.0
CA A:ASP129 4.2 41.9 1.0
CA A:GLN135 4.3 43.0 1.0
N A:GLY132 4.3 56.7 1.0
N A:ILE130 4.3 47.5 1.0
CG A:GLU140 4.3 45.1 1.0
CB A:ASP129 4.4 43.5 1.0
N A:VAL136 4.4 37.3 1.0
C A:ASP129 4.4 50.0 1.0
CA A:VAL136 4.5 43.0 1.0
CB A:ASP133 4.5 54.2 1.0
CB A:ASP131 4.6 58.2 1.0
CB A:GLN135 4.6 52.3 1.0
CA A:ASP131 4.7 57.9 1.0
C A:ASP131 4.7 57.6 1.0
CA A:ASP133 4.7 52.9 1.0
N A:ASN137 4.8 46.5 1.0
N A:GLY134 4.9 43.6 1.0
ND2 A:ASN137 5.0 51.2 1.0

Calcium binding site 4 out of 6 in 6dad

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Calcium binding site 4 out of 6 in the 1.65 Angstrom Crystal Structure of the N97I 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 1.65 Angstrom Crystal Structure of the N97I Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:22.8
occ:1.00
 OD1 B:ASP20 2.3 24.3 1.0
O B:THR26 2.3 24.3 1.0
OD1 B:ASP22 2.4 28.1 1.0
O B:HOH665 2.4 29.2 1.0
OD1 B:ASP24 2.4 27.5 1.0
OE2 B:GLU31 2.5 26.1 1.0
OE1 B:GLU31 2.5 24.9 1.0
CD B:GLU31 2.8 25.1 1.0
CG B:ASP22 3.3 38.3 1.0
CG B:ASP24 3.4 34.8 1.0
CG B:ASP20 3.4 23.7 1.0
C B:THR26 3.5 24.1 1.0
OD2 B:ASP22 3.7 38.4 1.0
OG1 B:THR26 3.9 31.8 1.0
OD2 B:ASP24 4.0 37.1 1.0
CA B:ASP20 4.0 21.9 1.0
CB B:ASP20 4.2 21.9 1.0
N B:THR26 4.2 23.8 1.0
N B:ASP24 4.2 25.8 1.0
CG B:GLU31 4.3 22.4 1.0
OD2 B:ASP20 4.3 22.8 1.0
CA B:THR26 4.3 20.7 1.0
C B:ASP20 4.4 22.4 1.0
CB B:ASP24 4.4 35.3 1.0
N B:ASP22 4.4 23.3 1.0
N B:ILE27 4.5 20.1 1.0
CA B:ILE27 4.6 21.6 1.0
CB B:ASP22 4.6 31.7 1.0
N B:LYS21 4.7 23.7 1.0
N B:GLY23 4.7 28.3 1.0
CA B:ASP24 4.7 29.8 1.0
CB B:THR26 4.7 29.4 1.0
CG2 B:THR28 4.8 25.5 1.0
N B:GLY25 4.8 26.7 1.0
CA B:ASP22 4.9 27.3 1.0
N B:THR28 4.9 23.5 1.0
O B:ASP20 4.9 23.4 1.0
O B:HOH623 4.9 30.3 1.0
C B:ASP22 5.0 30.3 1.0
C B:ASP24 5.0 29.2 1.0

Calcium binding site 5 out of 6 in 6dad

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Calcium binding site 5 out of 6 in the 1.65 Angstrom Crystal Structure of the N97I 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 1.65 Angstrom Crystal Structure of the N97I Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:26.8
occ:1.00
 OD1 B:ASP56 2.3 29.0 1.0
OD1 B:ASN60 2.4 29.4 1.0
O B:HOH619 2.4 27.0 1.0
O B:HOH644 2.5 26.9 1.0
OE1 B:GLU67 2.5 22.7 1.0
O B:THR62 2.5 24.7 1.0
OD1 B:ASP58 2.5 29.9 1.0
OE2 B:GLU67 2.6 24.4 1.0
CD B:GLU67 2.9 24.3 1.0
CG B:ASN60 3.3 35.9 1.0
CG B:ASP56 3.4 30.2 1.0
CG B:ASP58 3.5 34.5 1.0
C B:THR62 3.6 22.8 1.0
ND2 B:ASN60 3.7 36.3 1.0
OD2 B:ASP58 3.9 31.9 1.0
OD2 B:ASP56 4.1 33.3 1.0
CB B:ASP56 4.3 26.4 1.0
N B:ASN60 4.3 31.6 1.0
CA B:ASP56 4.4 24.1 1.0
N B:ASP64 4.4 22.5 1.0
N B:THR62 4.4 29.9 1.0
CG B:GLU67 4.4 21.6 1.0
OG1 B:THR62 4.4 26.0 1.0
CA B:ILE63 4.4 19.9 1.0
N B:ILE63 4.5 20.5 1.0
N B:ASP58 4.5 26.1 1.0
OD2 B:ASP64 4.5 25.7 1.0
CB B:ASN60 4.5 37.3 1.0
CA B:THR62 4.6 25.2 1.0
CG B:ASP64 4.6 25.2 1.0
C B:ASP56 4.6 29.4 1.0
O B:HOH691 4.7 34.3 1.0
CB B:ASP58 4.7 31.8 1.0
N B:ALA57 4.7 27.4 1.0
N B:GLY59 4.7 33.5 1.0
C B:ILE63 4.8 22.8 1.0
CA B:ASN60 4.8 34.3 1.0
OD1 B:ASP64 4.9 23.7 1.0
N B:GLY61 4.9 33.8 1.0
CA B:ASP58 4.9 29.9 1.0
C B:ASP58 5.0 33.2 1.0

Calcium binding site 6 out of 6 in 6dad

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Calcium binding site 6 out of 6 in the 1.65 Angstrom Crystal Structure of the N97I 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 1.65 Angstrom Crystal Structure of the N97I Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:25.8
occ:1.00
 O B:GLN135 2.3 28.8 1.0
OD1 B:ASP129 2.3 30.2 1.0
OD1 B:ASP133 2.4 29.5 1.0
OD1 B:ASP131 2.4 33.0 1.0
O B:HOH655 2.5 39.0 1.0
OE2 B:GLU140 2.5 28.1 1.0
OE1 B:GLU140 2.5 25.4 1.0
CD B:GLU140 2.8 26.4 1.0
CG B:ASP133 3.3 38.5 1.0
CG B:ASP131 3.4 37.2 1.0
CG B:ASP129 3.5 33.7 1.0
C B:GLN135 3.5 25.2 1.0
OD2 B:ASP133 3.7 36.9 1.0
OD2 B:ASP131 3.9 40.1 1.0
OD2 B:ASP129 4.2 34.5 1.0
N B:GLN135 4.2 28.9 1.0
CA B:ASP129 4.3 31.0 1.0
N B:ASP133 4.3 35.5 1.0
CG B:GLU140 4.3 22.9 1.0
N B:ASP131 4.3 37.3 1.0
CA B:GLN135 4.4 23.1 1.0
CB B:ASP129 4.4 26.5 1.0
N B:VAL136 4.4 23.1 1.0
CB B:ASP133 4.4 39.1 1.0
N B:ILE130 4.5 28.5 1.0
C B:ASP129 4.5 34.2 1.0
CA B:VAL136 4.5 19.7 1.0
N B:GLY132 4.5 37.4 1.0
N B:ASN137 4.7 20.8 1.0
CB B:ASP131 4.7 38.5 1.0
O B:HOH614 4.7 34.7 1.0
CB B:GLN135 4.7 33.4 1.0
CA B:ASP133 4.8 38.1 1.0
CA B:ASP131 4.9 37.6 1.0
ND2 B:ASN137 4.9 26.6 1.0
C B:ASP131 4.9 40.0 1.0
N B:GLY134 4.9 30.9 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: Mon Jul 15 17:44:59 2024

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