Calcium in PDB 6daf: 2.4 Angstrom Crystal Structure of the F141L Ca/Cam:CAV1.2 Iq Domain Complex

Protein crystallography data

The structure of 2.4 Angstrom Crystal Structure of the F141L Ca/Cam:CAV1.2 Iq Domain Complex, PDB code: 6daf 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) 43.68 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.355, 121.309, 125.897, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 24.3

Calcium Binding Sites:

The binding sites of Calcium atom in the 2.4 Angstrom Crystal Structure of the F141L Ca/Cam:CAV1.2 Iq Domain Complex (pdb code 6daf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the 2.4 Angstrom Crystal Structure of the F141L Ca/Cam:CAV1.2 Iq Domain Complex, PDB code: 6daf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6daf

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Calcium binding site 1 out of 8 in the 2.4 Angstrom Crystal Structure of the F141L 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 2.4 Angstrom Crystal Structure of the F141L Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:87.9
occ:1.00
OD2 A:ASP20 2.3 82.1 1.0
OD1 A:ASP22 2.3 0.1 1.0
O A:THR26 2.3 75.8 1.0
OE1 A:GLU31 2.4 84.0 1.0
OD1 A:ASP24 2.5 80.1 1.0
OE2 A:GLU31 2.7 84.8 1.0
CD A:GLU31 2.8 85.4 1.0
CG A:ASP22 2.9 0.8 1.0
OD2 A:ASP22 2.9 0.4 1.0
CG A:ASP24 3.2 87.6 1.0
CG A:ASP20 3.4 82.2 1.0
OG1 A:THR26 3.5 80.6 1.0
OD2 A:ASP24 3.5 87.7 1.0
C A:THR26 3.5 79.7 1.0
CB A:ASP20 4.2 73.3 1.0
CG A:GLU31 4.3 89.3 1.0
OD1 A:ASP20 4.3 81.0 1.0
N A:THR26 4.3 77.7 1.0
CB A:ASP22 4.3 1.0 1.0
CA A:ASP20 4.3 72.0 1.0
CA A:THR26 4.3 78.0 1.0
CB A:ASP24 4.4 89.9 1.0
N A:ASP22 4.5 0.9 1.0
N A:ILE27 4.5 79.8 1.0
N A:ASP24 4.5 92.9 1.0
CB A:THR26 4.5 80.4 1.0
C A:ASP20 4.6 78.4 1.0
CA A:ILE27 4.6 78.3 1.0
N A:GLY23 4.8 97.6 1.0
N A:THR28 4.8 79.7 1.0
N A:LYS21 4.8 83.7 1.0
CA A:ASP22 4.8 0.7 1.0
CG2 A:THR28 4.9 87.6 1.0
CA A:ASP24 4.9 88.9 1.0
C A:ASP22 5.0 0.3 1.0

Calcium binding site 2 out of 8 in 6daf

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Calcium binding site 2 out of 8 in the 2.4 Angstrom Crystal Structure of the F141L 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 2.4 Angstrom Crystal Structure of the F141L Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:87.6
occ:1.00
OD1 A:ASN60 2.3 96.9 1.0
O A:THR62 2.4 98.8 1.0
OE2 A:GLU67 2.6 77.8 1.0
OD1 A:ASP58 2.7 0.9 1.0
OE1 A:GLU67 2.7 74.6 1.0
OD1 A:ASP56 2.8 94.9 1.0
CD A:GLU67 3.0 75.7 1.0
CG A:ASN60 3.1 96.6 1.0
C A:THR62 3.4 94.6 1.0
ND2 A:ASN60 3.4 86.8 1.0
CG A:ASP58 3.5 0.4 1.0
OD2 A:ASP58 3.6 0.6 1.0
CG A:ASP56 3.7 97.0 1.0
OD2 A:ASP64 4.0 83.4 1.0
N A:ASP64 4.2 74.3 1.0
N A:ILE63 4.2 84.6 1.0
N A:ASN60 4.3 0.4 1.0
CA A:ILE63 4.3 74.3 1.0
CA A:THR62 4.3 97.8 1.0
N A:THR62 4.3 0.8 1.0
CB A:ASN60 4.4 0.5 1.0
CG A:ASP64 4.4 75.7 1.0
OD2 A:ASP56 4.5 0.8 1.0
CB A:ASP56 4.5 94.1 1.0
CG A:GLU67 4.5 67.7 1.0
CB A:THR62 4.6 95.6 1.0
C A:ILE63 4.6 74.4 1.0
CA A:ASP56 4.7 91.1 1.0
CA A:ASN60 4.8 0.8 1.0
CG2 A:THR62 4.8 96.4 1.0
N A:GLY59 4.8 92.8 1.0
CB A:ASP58 4.8 91.2 1.0
N A:ASP58 4.9 97.2 1.0
CB A:ASP64 4.9 69.0 1.0
OD1 A:ASP64 5.0 74.2 1.0
C A:ASN60 5.0 0.9 1.0

Calcium binding site 3 out of 8 in 6daf

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Calcium binding site 3 out of 8 in the 2.4 Angstrom Crystal Structure of the F141L 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 2.4 Angstrom Crystal Structure of the F141L Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:50.2
occ:1.00
OD1 A:ASN97 2.3 50.1 1.0
O A:TYR99 2.3 55.4 1.0
OE2 A:GLU104 2.3 50.5 1.0
OD1 A:ASP93 2.3 63.4 1.0
O A:HOH608 2.4 66.7 1.0
OD1 A:ASP95 2.5 64.5 1.0
OE1 A:GLU104 2.6 49.5 1.0
CD A:GLU104 2.8 53.2 1.0
CG A:ASN97 3.3 52.6 1.0
CG A:ASP93 3.4 60.9 1.0
CG A:ASP95 3.4 64.0 1.0
C A:TYR99 3.5 49.3 1.0
OD2 A:ASP95 3.9 65.6 1.0
ND2 A:ASN97 4.0 49.5 1.0
OD2 A:ASP93 4.1 64.6 1.0
CA A:ASP93 4.1 58.3 1.0
N A:TYR99 4.2 44.9 1.0
N A:ASN97 4.2 52.0 1.0
CB A:ASP93 4.3 56.6 1.0
N A:ASP95 4.3 58.6 1.0
CA A:TYR99 4.3 51.1 1.0
CG A:GLU104 4.3 42.3 1.0
CB A:ASN97 4.4 50.2 1.0
C A:ASP93 4.4 56.2 1.0
N A:ILE100 4.5 51.5 1.0
N A:LYS94 4.5 60.2 1.0
CB A:TYR99 4.6 50.2 1.0
CB A:ASP95 4.6 58.8 1.0
CA A:ILE100 4.6 50.1 1.0
N A:GLY96 4.7 53.5 1.0
CA A:ASN97 4.7 47.2 1.0
CA A:ASP95 4.8 55.7 1.0
N A:SER101 4.8 51.8 1.0
C A:ASP95 4.9 52.3 1.0
O A:ASP93 4.9 54.1 1.0
N A:GLY98 4.9 51.2 1.0

Calcium binding site 4 out of 8 in 6daf

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Calcium binding site 4 out of 8 in the 2.4 Angstrom Crystal Structure of the F141L 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 2.4 Angstrom Crystal Structure of the F141L Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:58.1
occ:1.00
OD1 A:ASP131 2.3 76.9 1.0
O A:GLN135 2.3 53.1 1.0
OD1 A:ASP129 2.4 57.0 1.0
OD1 A:ASP133 2.4 62.4 1.0
OE1 A:GLU140 2.5 71.7 1.0
O A:HOH601 2.5 69.2 1.0
OE2 A:GLU140 2.7 75.7 1.0
CD A:GLU140 2.9 73.1 1.0
CG A:ASP133 3.2 59.5 1.0
CG A:ASP131 3.3 77.4 1.0
C A:GLN135 3.4 49.5 1.0
OD2 A:ASP133 3.5 64.0 1.0
CG A:ASP129 3.5 60.2 1.0
OD2 A:ASP131 3.7 80.7 1.0
N A:VAL136 4.2 48.5 1.0
N A:GLN135 4.2 51.9 1.0
CA A:VAL136 4.2 48.7 1.0
CA A:ASP129 4.3 68.1 1.0
OD2 A:ASP129 4.3 61.5 1.0
CB A:ASP129 4.4 60.9 1.0
N A:ASP133 4.4 60.9 1.0
N A:ASP131 4.4 69.5 1.0
N A:ASN137 4.4 57.7 1.0
CA A:GLN135 4.4 44.8 1.0
CG A:GLU140 4.4 74.7 1.0
N A:ILE130 4.5 75.0 1.0
CB A:ASP133 4.5 50.2 1.0
CB A:ASP131 4.6 71.4 1.0
N A:GLY132 4.7 75.0 1.0
CG A:GLN135 4.8 50.3 1.0
C A:VAL136 4.8 55.7 1.0
C A:ASP129 4.8 73.8 1.0
CA A:ASP133 4.9 54.5 1.0
CA A:ASP131 4.9 74.9 1.0
N A:GLY134 4.9 62.2 1.0

Calcium binding site 5 out of 8 in 6daf

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Calcium binding site 5 out of 8 in the 2.4 Angstrom Crystal Structure of the F141L 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 2.4 Angstrom Crystal Structure of the F141L Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:84.6
occ:1.00
O B:THR26 2.1 83.7 1.0
OE1 B:GLU31 2.2 83.7 1.0
OD1 B:ASP22 2.2 87.7 1.0
OD1 B:ASP24 2.4 92.1 1.0
OD1 B:ASP20 2.5 75.7 1.0
CD B:GLU31 2.9 88.5 1.0
OE2 B:GLU31 3.0 87.2 1.0
CG B:ASP22 3.1 89.9 1.0
C B:THR26 3.2 85.5 1.0
OD2 B:ASP22 3.3 94.1 1.0
CG B:ASP24 3.3 92.3 1.0
CG B:ASP20 3.5 81.7 1.0
CG2 B:THR26 3.7 97.7 1.0
OD2 B:ASP24 3.7 92.8 1.0
N B:THR26 4.0 83.7 1.0
CA B:THR26 4.1 86.5 1.0
CA B:ASP20 4.1 76.4 1.0
CB B:ASP20 4.1 75.2 1.0
N B:ILE27 4.2 77.5 1.0
CG B:GLU31 4.3 94.5 1.0
CA B:ILE27 4.3 69.9 1.0
N B:ASP24 4.4 92.9 1.0
CB B:ASP24 4.5 94.0 1.0
C B:ASP20 4.5 80.5 1.0
OD2 B:ASP20 4.5 77.0 1.0
N B:ASP22 4.5 93.3 1.0
CB B:ASP22 4.5 96.1 1.0
CB B:THR26 4.5 98.7 1.0
N B:THR28 4.6 77.5 1.0
N B:LYS21 4.7 81.0 1.0
N B:GLY23 4.7 96.0 1.0
CA B:ASP24 4.8 90.6 1.0
N B:GLY25 4.9 83.1 1.0
CA B:ASP22 4.9 97.3 1.0
C B:ASP24 4.9 85.7 1.0
C B:ILE27 4.9 74.1 1.0
C B:ASP22 5.0 98.6 1.0

Calcium binding site 6 out of 8 in 6daf

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Calcium binding site 6 out of 8 in the 2.4 Angstrom Crystal Structure of the F141L 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 2.4 Angstrom Crystal Structure of the F141L Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:87.0
occ:1.00
OD1 B:ASN60 2.2 95.8 1.0
O B:THR62 2.4 80.5 1.0
OE2 B:GLU67 2.5 73.3 1.0
OE1 B:GLU67 2.6 80.5 1.0
OD1 B:ASP56 2.9 95.1 1.0
CD B:GLU67 2.9 76.3 1.0
OD1 B:ASP58 2.9 0.1 1.0
CG B:ASN60 3.2 0.9 1.0
C B:THR62 3.3 79.3 1.0
ND2 B:ASN60 3.5 100.0 1.0
CG B:ASP56 3.8 97.0 1.0
OG1 B:THR62 3.8 89.5 1.0
CG B:ASP58 3.9 0.6 1.0
OD2 B:ASP58 4.0 0.6 1.0
N B:ILE63 4.1 75.4 1.0
N B:THR62 4.2 95.7 1.0
CA B:ILE63 4.2 70.0 1.0
N B:ASP64 4.2 72.0 1.0
CA B:THR62 4.2 84.6 1.0
OD2 B:ASP64 4.3 81.4 1.0
CG B:GLU67 4.4 65.3 1.0
OD2 B:ASP56 4.5 98.9 1.0
C B:ILE63 4.5 73.1 1.0
CB B:ASN60 4.5 0.6 1.0
CB B:ASP56 4.6 94.4 1.0
CG B:ASP64 4.6 74.2 1.0
CB B:THR62 4.6 87.9 1.0
CA B:ASP56 4.6 92.2 1.0
N B:ASN60 4.6 0.4 1.0
OD1 B:ASP64 5.0 73.3 1.0
CA B:ASN60 5.0 0.1 1.0
N B:ALA57 5.0 96.3 1.0

Calcium binding site 7 out of 8 in 6daf

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Calcium binding site 7 out of 8 in the 2.4 Angstrom Crystal Structure of the F141L 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 7 of 2.4 Angstrom Crystal Structure of the F141L Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:49.3
occ:1.00
O B:TYR99 2.2 53.6 1.0
O B:HOH608 2.4 61.4 1.0
OD1 B:ASP93 2.4 47.5 1.0
OD1 B:ASP95 2.4 71.1 1.0
OD1 B:ASN97 2.4 44.0 1.0
OE2 B:GLU104 2.5 53.9 1.0
OE1 B:GLU104 2.6 50.7 1.0
CD B:GLU104 2.9 49.5 1.0
CG B:ASP95 3.3 69.1 1.0
CG B:ASN97 3.4 46.3 1.0
C B:TYR99 3.5 48.2 1.0
CG B:ASP93 3.5 56.4 1.0
OD2 B:ASP95 3.6 76.8 1.0
ND2 B:ASN97 4.1 52.6 1.0
N B:TYR99 4.2 49.0 1.0
N B:ASN97 4.2 55.9 1.0
CA B:ASP93 4.2 51.1 1.0
N B:ASP95 4.3 59.8 1.0
CA B:TYR99 4.3 47.7 1.0
OD2 B:ASP93 4.4 56.9 1.0
CB B:ASP93 4.4 47.0 1.0
N B:ILE100 4.4 48.2 1.0
C B:ASP93 4.5 56.7 1.0
CG B:GLU104 4.5 45.5 1.0
CA B:ILE100 4.5 48.0 1.0
CB B:ASN97 4.5 49.3 1.0
N B:SER101 4.5 52.7 1.0
N B:GLY96 4.5 55.7 1.0
CB B:ASP95 4.6 66.6 1.0
N B:LYS94 4.6 50.2 1.0
CA B:ASN97 4.8 64.2 1.0
CB B:TYR99 4.8 48.8 1.0
CA B:ASP95 4.8 64.5 1.0
C B:ASP95 4.8 55.4 1.0
N B:GLY98 4.8 55.4 1.0
C B:ILE100 5.0 53.5 1.0
C B:ASN97 5.0 60.7 1.0
O B:ASP93 5.0 54.7 1.0

Calcium binding site 8 out of 8 in 6daf

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Calcium binding site 8 out of 8 in the 2.4 Angstrom Crystal Structure of the F141L 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 8 of 2.4 Angstrom Crystal Structure of the F141L Ca/Cam:CAV1.2 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:61.7
occ:1.00
O B:GLN135 2.3 59.5 1.0
OE1 B:GLU140 2.3 54.9 1.0
OD1 B:ASP133 2.4 60.8 1.0
OD1 B:ASP129 2.4 72.3 1.0
OE2 B:GLU140 2.4 48.6 1.0
OD1 B:ASP131 2.5 72.3 1.0
O B:HOH606 2.6 57.1 1.0
CD B:GLU140 2.7 47.9 1.0
CG B:ASP133 3.3 63.2 1.0
CG B:ASP131 3.3 71.3 1.0
CG B:ASP129 3.5 68.3 1.0
C B:GLN135 3.5 53.3 1.0
OD2 B:ASP131 3.5 75.7 1.0
OD2 B:ASP133 3.6 65.8 1.0
CA B:ASP129 4.1 62.6 1.0
CB B:ASP129 4.2 58.8 1.0
N B:ASP133 4.2 72.9 1.0
N B:GLN135 4.3 64.7 1.0
CG B:GLU140 4.3 52.7 1.0
N B:ASN137 4.3 45.7 1.0
OD2 B:ASP129 4.3 73.3 1.0
CA B:VAL136 4.3 47.0 1.0
N B:VAL136 4.3 50.5 1.0
N B:ASP131 4.4 69.5 1.0
CB B:ASP133 4.4 64.4 1.0
C B:ASP129 4.5 69.9 1.0
N B:GLY132 4.5 72.3 1.0
CA B:GLN135 4.5 55.1 1.0
N B:ILE130 4.6 68.3 1.0
CB B:ASP131 4.6 66.0 1.0
C B:VAL136 4.8 47.9 1.0
CA B:ASP133 4.8 68.0 1.0
CA B:ASP131 4.8 71.7 1.0
N B:GLY134 4.9 67.8 1.0
CG B:ASN137 4.9 55.2 1.0
C B:ASP131 4.9 73.8 1.0
OD1 B:ASN137 5.0 61.2 1.0
O B:HOH605 5.0 61.9 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: Sat Dec 12 06:02:48 2020

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