Calcium in PDB 6u39: 2.4 Angstrom Crystal Structure of the D129G Ca-Cam:CAV1.2 Iq Domain Complex

The structure of 2.4 Angstrom Crystal Structure of the D129G Ca-Cam:CAV1.2 Iq Domain Complex, PDB code: 6u39 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)	49.04 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	121.795, 161.656, 96.277, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 28.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Calcium atom in the 2.4 Angstrom Crystal Structure of the D129G Ca-Cam:CAV1.2 Iq Domain Complex (pdb code 6u39). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 29 binding sites of Calcium where determined in the 2.4 Angstrom Crystal Structure of the D129G Ca-Cam:CAV1.2 Iq Domain Complex, PDB code: 6u39:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 29 in the 2.4 Angstrom Crystal Structure of the D129G 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 D129G Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:0.2 occ:1.00 OE1 A:GLU31 2.4 0.8 1.0 OD1 A:ASP24 2.4 0.2 1.0 OD1 A:ASP22 2.4 0.0 1.0 O A:THR26 2.4 0.2 1.0 OD1 A:ASP20 2.8 0.1 1.0 OD2 A:ASP24 2.8 0.7 1.0 CG A:ASP24 2.8 0.9 1.0 OE2 A:GLU31 2.9 0.5 1.0 CD A:GLU31 3.0 1.0 1.0 CG A:ASP22 3.1 0.3 1.0 OD2 A:ASP22 3.2 0.2 1.0 C A:THR26 3.6 0.6 1.0 CG A:ASP20 3.9 0.2 1.0 CG2 A:THR28 4.1 0.2 1.0 CB A:ASP24 4.2 0.6 1.0 N A:THR26 4.3 0.5 1.0 N A:ASP24 4.3 0.7 1.0 CA A:THR26 4.4 0.9 1.0 CG A:GLU31 4.4 92.3 1.0 N A:ILE27 4.6 0.2 1.0 N A:THR28 4.6 0.1 1.0 CB A:ASP22 4.6 0.2 1.0 OD2 A:ASP20 4.7 0.5 1.0 CA A:ASP20 4.7 0.8 1.0 CB A:THR26 4.7 0.6 1.0 CB A:ASP20 4.7 98.3 1.0 CA A:ILE27 4.7 96.7 1.0 CA A:ASP24 4.8 0.6 1.0 N A:GLY23 4.8 0.1 1.0 N A:ASP22 4.8 0.5 1.0

Calcium binding site 2 out of 29 in the 2.4 Angstrom Crystal Structure of the D129G 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 D129G Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:0.7 occ:1.00 OD1 A:ASN60 2.5 0.2 1.0 OD1 A:ASP56 2.5 0.7 1.0 O A:THR62 2.8 0.8 1.0 OE1 A:GLU67 2.8 0.2 1.0 OE2 A:GLU67 2.8 0.0 1.0 CD A:GLU67 3.2 0.1 1.0 ND2 A:ASN60 3.2 1.0 1.0 CG A:ASN60 3.2 0.3 1.0 CG A:ASP56 3.5 0.0 1.0 OD1 A:ASP64 3.9 0.9 1.0 CB A:ASP58 3.9 1.0 1.0 OD2 A:ASP56 3.9 0.2 1.0 C A:THR62 3.9 0.9 1.0 N A:ASP64 4.2 0.2 1.0 CG A:ASP64 4.3 0.3 1.0 N A:ASP58 4.4 0.8 1.0 CA A:ILE63 4.5 99.9 1.0 N A:ASN60 4.6 0.8 1.0 CG A:GLU67 4.6 0.9 1.0 CA A:ASP58 4.6 0.2 1.0 CB A:ASN60 4.6 0.7 1.0 CB A:ASP56 4.6 0.1 1.0 N A:ILE63 4.7 1.0 1.0 N A:GLY59 4.7 0.9 1.0 CB A:ASP64 4.7 0.6 1.0 OG1 A:THR62 4.7 0.6 1.0 CA A:ASP56 4.8 0.3 1.0 C A:ILE63 4.8 0.1 1.0 N A:THR62 4.9 0.7 1.0 OD2 A:ASP64 4.9 0.7 1.0 C A:ASP58 5.0 0.1 1.0 N A:ALA57 5.0 0.5 1.0 CA A:THR62 5.0 0.2 1.0

Calcium binding site 3 out of 29 in the 2.4 Angstrom Crystal Structure of the D129G 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 D129G Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:62.3 occ:1.00 O A:TYR99 2.3 64.2 1.0 OD1 A:ASP95 2.3 88.2 1.0 OD1 A:ASN97 2.4 63.0 1.0 OD1 A:ASP93 2.5 62.1 1.0 O A:HOH603 2.5 74.0 1.0 OE2 A:GLU104 2.5 75.8 1.0 OE1 A:GLU104 3.1 81.0 1.0 CD A:GLU104 3.1 76.9 1.0 CG A:ASN97 3.2 64.9 1.0 CG A:ASP95 3.3 82.3 1.0 C A:TYR99 3.4 62.1 1.0 OD2 A:ASP95 3.5 83.0 1.0 CG A:ASP93 3.6 64.6 1.0 ND2 A:ASN97 3.6 65.5 1.0 N A:ASN97 4.2 66.8 1.0 N A:TYR99 4.2 69.7 1.0 CB A:ASN97 4.3 67.3 1.0 CA A:TYR99 4.3 70.2 1.0 N A:SER101 4.3 60.8 1.0 OD2 A:ASP93 4.4 67.7 1.0 N A:ILE100 4.4 62.0 1.0 CA A:ILE100 4.4 56.7 1.0 CA A:ASP93 4.4 68.5 1.0 CB A:ASP93 4.5 61.6 1.0 N A:ASP95 4.6 69.7 1.0 CG A:GLU104 4.6 64.1 1.0 CB A:TYR99 4.6 71.4 1.0 N A:GLY96 4.6 76.4 1.0 CB A:ASP95 4.6 76.2 1.0 CA A:ASN97 4.7 66.8 1.0 N A:LYS94 4.7 76.3 1.0 C A:ASP93 4.8 74.3 1.0 C A:ILE100 4.9 58.3 1.0 CA A:ASP95 5.0 74.1 1.0 CB A:SER101 5.0 60.4 1.0 OG A:SER101 5.0 60.8 1.0

Calcium binding site 4 out of 29 in the 2.4 Angstrom Crystal Structure of the D129G 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 D129G Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:88.9 occ:1.00 O C:THR26 2.4 88.7 1.0 OD1 C:ASP24 2.4 86.3 1.0 OE2 C:GLU31 2.5 91.8 1.0 OE1 C:GLU31 2.5 86.4 1.0 OD1 C:ASP22 2.5 0.1 1.0 OD2 C:ASP20 2.7 75.5 1.0 CD C:GLU31 2.8 87.3 1.0 OD2 C:ASP22 3.2 0.1 1.0 CG C:ASP22 3.2 0.9 1.0 CG C:ASP24 3.3 88.6 1.0 OD2 C:ASP24 3.5 88.1 1.0 C C:THR26 3.5 80.1 1.0 OG1 C:THR26 3.6 94.6 1.0 CG C:ASP20 3.7 68.1 1.0 N C:THR26 4.2 76.0 1.0 CA C:THR26 4.2 76.4 1.0 CG C:GLU31 4.3 82.0 1.0 CA C:ASP20 4.4 76.5 1.0 CG2 C:THR28 4.4 73.1 1.0 CB C:THR26 4.4 86.4 1.0 CB C:ASP20 4.4 69.2 1.0 OD1 C:ASP20 4.5 69.7 1.0 N C:ILE27 4.6 68.7 1.0 N C:ASP24 4.6 86.1 1.0 CB C:ASP24 4.6 90.5 1.0 CB C:ASP22 4.6 0.5 1.0 N C:THR28 4.7 71.6 1.0 N C:ASP22 4.7 92.4 1.0 CA C:ILE27 4.7 64.8 1.0 C C:ASP20 4.8 81.3 1.0 N C:GLY23 4.9 99.9 1.0 N C:LYS21 4.9 84.2 1.0 OG1 C:THR28 5.0 73.5 1.0

Calcium binding site 5 out of 29 in the 2.4 Angstrom Crystal Structure of the D129G 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 D129G Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:80.8 occ:1.00 OD1 C:ASN60 2.4 89.3 1.0 OE1 C:GLU67 2.4 63.0 1.0 OD1 C:ASP58 2.4 97.6 1.0 O C:THR62 2.5 71.8 1.0 OD1 C:ASP56 2.5 81.3 1.0 OE2 C:GLU67 2.6 67.2 1.0 CD C:GLU67 2.8 64.1 1.0 CG C:ASP58 3.2 98.4 1.0 CG C:ASN60 3.2 94.2 1.0 OD2 C:ASP58 3.3 98.6 1.0 CG C:ASP56 3.6 88.8 1.0 C C:THR62 3.6 72.1 1.0 ND2 C:ASN60 3.7 90.6 1.0 OD1 C:ASP64 3.8 0.7 1.0 OD2 C:ASP56 4.2 91.6 1.0 OG1 C:THR62 4.3 89.4 1.0 N C:ASP64 4.3 68.1 1.0 CG C:GLU67 4.3 62.1 1.0 CB C:ASN60 4.4 92.7 1.0 N C:ASN60 4.4 87.3 1.0 N C:THR62 4.4 79.4 1.0 N C:ILE63 4.4 66.2 1.0 CA C:ILE63 4.4 65.6 1.0 N C:ASP58 4.5 91.1 1.0 CB C:ASP58 4.5 0.1 1.0 CA C:ASP56 4.5 83.0 1.0 CA C:THR62 4.6 79.8 1.0 CB C:ASP56 4.6 86.9 1.0 N C:ALA57 4.6 90.2 1.0 CG C:ASP64 4.8 0.3 1.0 N C:GLY59 4.8 92.8 1.0 C C:ILE63 4.8 68.3 1.0 CA C:ASN60 4.9 92.4 1.0 CA C:ASP58 4.9 0.4 1.0 C C:ASP56 5.0 88.6 1.0 CB C:ASP64 5.0 82.9 1.0

Calcium binding site 6 out of 29 in the 2.4 Angstrom Crystal Structure of the D129G 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 D129G Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:59.8 occ:1.00 OD1 C:ASN97 2.4 71.7 1.0 OD1 C:ASP95 2.4 71.6 1.0 O C:TYR99 2.4 60.3 1.0 OE1 C:GLU104 2.4 50.3 1.0 OD1 C:ASP93 2.5 60.8 1.0 OE2 C:GLU104 2.7 52.9 1.0 CD C:GLU104 2.9 51.0 1.0 CG C:ASP95 3.1 73.4 1.0 OD2 C:ASP95 3.1 79.4 1.0 CG C:ASN97 3.3 67.5 1.0 C C:TYR99 3.5 54.3 1.0 CG C:ASP93 3.6 62.7 1.0 ND2 C:ASN97 3.9 61.2 1.0 N C:ASN97 4.3 67.1 1.0 N C:SER101 4.3 60.5 1.0 OD2 C:ASP93 4.4 72.0 1.0 CA C:ASP93 4.4 66.6 1.0 N C:TYR99 4.4 58.4 1.0 N C:ILE100 4.4 50.9 1.0 CG C:GLU104 4.4 50.0 1.0 CB C:ASN97 4.4 60.4 1.0 CA C:ILE100 4.4 49.3 1.0 N C:ASP95 4.4 69.6 1.0 CA C:TYR99 4.4 59.4 1.0 CB C:ASP95 4.5 73.5 1.0 CB C:ASP93 4.5 62.0 1.0 N C:GLY96 4.6 72.8 1.0 C C:ASP93 4.6 69.1 1.0 N C:LYS94 4.6 60.7 1.0 CB C:TYR99 4.8 65.0 1.0 OG C:SER101 4.8 57.1 1.0 CA C:ASN97 4.8 66.3 1.0 C C:ILE100 4.9 52.6 1.0 CA C:ASP95 4.9 76.3 1.0 CB C:SER101 4.9 54.1 1.0

Calcium binding site 7 out of 29 in the 2.4 Angstrom Crystal Structure of the D129G 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 D129G Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca501 b:65.6 occ:1.00 OD1 E:ASP24 2.4 83.9 1.0 O E:THR26 2.4 61.3 1.0 OE1 E:GLU31 2.4 69.0 1.0 OE2 E:GLU31 2.4 75.1 1.0 OD1 E:ASP22 2.5 80.5 1.0 OD1 E:ASP20 2.5 68.4 1.0 CD E:GLU31 2.7 67.9 1.0 CG E:ASP24 3.1 85.1 1.0 CG E:ASP22 3.3 85.0 1.0 OD2 E:ASP22 3.4 85.7 1.0 OD2 E:ASP24 3.6 92.1 1.0 C E:THR26 3.6 61.5 1.0 CG E:ASP20 3.7 70.5 1.0 OG1 E:THR26 4.1 79.0 1.0 CG E:GLU31 4.1 61.5 1.0 CB E:ASP24 4.2 74.1 1.0 N E:THR26 4.3 53.9 1.0 CA E:ASP20 4.3 70.8 1.0 N E:ASP24 4.4 74.9 1.0 CA E:THR26 4.5 60.5 1.0 CG2 E:THR28 4.5 59.7 1.0 CB E:ASP20 4.5 69.8 1.0 OD2 E:ASP20 4.6 66.6 1.0 N E:ILE27 4.6 54.4 1.0 CA E:ILE27 4.7 56.2 1.0 CB E:ASP22 4.7 88.4 1.0 CA E:ASP24 4.7 70.2 1.0 N E:ASP22 4.8 81.6 1.0 N E:THR28 4.8 58.8 1.0 C E:ASP20 4.8 77.1 1.0 CB E:THR26 4.9 65.3 1.0 N E:LYS21 4.9 85.7 1.0 N E:GLY25 4.9 66.3 1.0 N E:GLY23 4.9 76.2 1.0

Calcium binding site 8 out of 29 in the 2.4 Angstrom Crystal Structure of the D129G 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 D129G Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca502 b:53.1 occ:1.00 OD1 E:ASN60 2.4 57.2 1.0 OD1 E:ASP56 2.4 61.7 1.0 O E:HOH601 2.4 64.9 1.0 O E:THR62 2.5 62.0 1.0 OD1 E:ASP58 2.5 81.3 1.0 OE1 E:GLU67 2.5 54.6 1.0 OE2 E:GLU67 2.6 64.2 1.0 O E:HOH602 2.7 76.2 1.0 CD E:GLU67 2.9 57.1 1.0 CG E:ASN60 3.2 62.2 1.0 CG E:ASP58 3.2 74.2 1.0 OD2 E:ASP58 3.3 87.6 1.0 CG E:ASP56 3.4 67.1 1.0 C E:THR62 3.6 56.3 1.0 ND2 E:ASN60 3.6 63.9 1.0 OD2 E:ASP56 4.1 67.4 1.0 N E:THR62 4.4 58.5 1.0 CB E:ASN60 4.4 63.3 1.0 N E:ILE63 4.4 52.3 1.0 N E:ASN60 4.4 63.4 1.0 N E:ASP64 4.4 44.8 1.0 CG E:GLU67 4.4 48.1 1.0 OG1 E:THR62 4.4 59.8 1.0 CA E:ILE63 4.4 51.9 1.0 CA E:ASP56 4.4 58.5 1.0 CB E:ASP56 4.4 69.5 1.0 N E:ASP58 4.5 58.3 1.0 CA E:THR62 4.5 56.5 1.0 N E:ALA57 4.6 69.0 1.0 CB E:ASP58 4.6 67.2 1.0 CG E:ASP64 4.7 67.3 1.0 N E:GLY59 4.7 58.6 1.0 OD1 E:ASP64 4.8 74.3 1.0 OD2 E:ASP64 4.8 76.9 1.0 C E:ILE63 4.8 51.5 1.0 CA E:ASN60 4.9 68.6 1.0 C E:ASP56 4.9 68.5 1.0 CA E:ASP58 5.0 56.3 1.0 N E:GLY61 5.0 55.8 1.0

Calcium binding site 9 out of 29 in the 2.4 Angstrom Crystal Structure of the D129G 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 9 of 2.4 Angstrom Crystal Structure of the D129G Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca503 b:77.2 occ:1.00 OD1 E:ASP95 2.4 88.1 1.0 O E:TYR99 2.4 67.9 1.0 OD1 E:ASN97 2.5 92.9 1.0 OD1 E:ASP93 2.5 78.5 1.0 OE1 E:GLU104 2.5 79.3 1.0 OE2 E:GLU104 2.7 80.1 1.0 CD E:GLU104 3.0 80.4 1.0 CG E:ASN97 3.1 87.7 1.0 ND2 E:ASN97 3.1 84.2 1.0 CG E:ASP95 3.1 88.0 1.0 OD2 E:ASP95 3.3 83.3 1.0 C E:TYR99 3.5 64.9 1.0 CG E:ASP93 3.6 77.5 1.0 N E:SER101 4.2 61.1 1.0 CA E:ASP93 4.3 72.7 1.0 N E:TYR99 4.3 62.4 1.0 N E:ILE100 4.4 63.5 1.0 N E:ASN97 4.4 80.8 1.0 CA E:TYR99 4.4 63.8 1.0 CA E:ILE100 4.4 63.9 1.0 CB E:ASN97 4.4 84.3 1.0 CG E:GLU104 4.4 71.2 1.0 OD2 E:ASP93 4.4 80.2 1.0 N E:ASP95 4.5 94.8 1.0 CB E:ASP93 4.5 71.5 1.0 CB E:ASP95 4.5 93.7 1.0 N E:GLY96 4.6 94.3 1.0 NE2 G:GLN135 4.7 0.4 1.0 OG E:SER101 4.7 73.4 1.0 N E:LYS94 4.7 85.3 1.0 C E:ASP93 4.7 77.7 1.0 CB E:TYR99 4.7 65.2 1.0 C E:ILE100 4.8 59.8 1.0 CB E:SER101 4.9 64.6 1.0 CA E:ASN97 4.9 80.8 1.0 CA E:ASP95 4.9 92.2 1.0

Calcium binding site 10 out of 29 in the 2.4 Angstrom Crystal Structure of the D129G 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 10 of 2.4 Angstrom Crystal Structure of the D129G Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca501 b:82.1 occ:1.00 OD1 G:ASP24 2.4 0.5 1.0 O G:THR26 2.4 74.5 1.0 OE2 G:GLU31 2.4 96.3 1.0 OD1 G:ASP22 2.5 0.2 1.0 OD1 G:ASP20 2.5 74.4 1.0 OE1 G:GLU31 2.6 88.2 1.0 CD G:GLU31 2.8 91.0 1.0 CG G:ASP24 3.1 1.0 1.0 CG G:ASP22 3.3 0.4 1.0 OD2 G:ASP24 3.3 0.4 1.0 OD2 G:ASP22 3.3 0.8 1.0 C G:THR26 3.5 66.3 1.0 CG G:ASP20 3.7 73.1 1.0 CG2 G:THR26 3.8 85.0 1.0 CG2 G:THR28 3.8 82.8 1.0 CG G:GLU31 4.2 92.5 1.0 N G:THR26 4.3 70.8 1.0 CA G:ASP20 4.3 68.5 1.0 CA G:THR26 4.4 64.8 1.0 CB G:ASP20 4.5 70.6 1.0 N G:ILE27 4.5 61.6 1.0 OD2 G:ASP20 4.5 74.3 1.0 N G:ASP24 4.5 83.2 1.0 CB G:ASP24 4.5 1.0 1.0 N G:THR28 4.6 68.6 1.0 CA G:ILE27 4.6 59.0 1.0 CB G:ASP22 4.7 0.1 1.0 CB G:THR26 4.7 81.3 1.0 N G:ASP22 4.7 99.7 1.0 C G:ASP20 4.8 80.1 1.0 N G:GLY23 4.9 85.0 1.0 N G:LYS21 4.9 89.4 1.0 CA G:ASP24 5.0 93.1 1.0

K.Wang, M.Brohus, C.Holt, M.T.Overgaard, R.Wimmer, F.Van Petegem. Arrhythmia Mutations in Calmodulin Can Disrupt Cooperativity of CA2+Binding and Cause Misfolding. J. Physiol. (Lond.) 2020.
ISSN: ISSN 1469-7793
PubMed: 32012279
DOI: 10.1113/JP279307