Calcium in PDB 6dah: 2.5 Angstrom Crystal Structure of the N97S Cam Mutant

The structure of 2.5 Angstrom Crystal Structure of the N97S Cam Mutant, PDB code: 6dah 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)	47.21 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.117, 94.414, 60.977, 90.00, 94.42, 90.00
R / Rfree (%)	21.8 / 27.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the 2.5 Angstrom Crystal Structure of the N97S Cam Mutant (pdb code 6dah). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the 2.5 Angstrom Crystal Structure of the N97S Cam Mutant, PDB code: 6dah:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in the 2.5 Angstrom Crystal Structure of the N97S Cam Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 2.5 Angstrom Crystal Structure of the N97S Cam Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:40.3 occ:1.00 O A:THR26 2.2 44.3 1.0 OD1 A:ASP20 2.3 34.2 1.0 OD1 A:ASP24 2.3 46.5 1.0 OE2 A:GLU31 2.3 54.9 1.0 OD1 A:ASP22 2.4 55.7 1.0 OE1 A:GLU31 2.7 61.9 1.0 O A:HOH604 2.8 38.0 1.0 CD A:GLU31 2.9 49.8 1.0 CG A:ASP24 3.3 39.8 1.0 CG A:ASP22 3.4 55.1 1.0 C A:THR26 3.5 42.7 1.0 CG A:ASP20 3.5 42.2 1.0 OD2 A:ASP22 3.6 59.7 1.0 OD2 A:ASP24 3.9 49.0 1.0 N A:THR26 4.1 27.1 1.0 N A:ASP24 4.1 34.9 1.0 CA A:ASP20 4.1 38.1 1.0 CB A:ASP20 4.2 38.1 1.0 CB A:ASP24 4.3 33.4 1.0 OG1 A:THR26 4.3 50.0 1.0 CG A:GLU31 4.4 45.4 1.0 CA A:THR26 4.4 37.4 1.0 N A:ILE27 4.4 46.6 1.0 C A:ASP20 4.4 43.9 1.0 OD2 A:ASP20 4.5 41.3 1.0 CA A:ILE27 4.5 33.5 1.0 N A:GLY25 4.5 28.9 1.0 N A:ASP22 4.5 39.0 1.0 N A:GLY23 4.6 38.9 1.0 N A:LYS21 4.6 43.1 1.0 CA A:ASP24 4.6 34.4 1.0 CB A:ASP22 4.7 32.8 1.0 N A:THR28 4.8 25.7 1.0 C A:ASP24 4.8 44.0 1.0 CG2 A:THR28 4.9 29.1 1.0 O A:ASP20 4.9 47.6 1.0 CA A:ASP22 5.0 48.6 1.0 CB A:THR26 5.0 46.0 1.0

Calcium binding site 2 out of 16 in the 2.5 Angstrom Crystal Structure of the N97S Cam Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 2.5 Angstrom Crystal Structure of the N97S Cam Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:39.0 occ:1.00 OD1 A:ASP56 2.3 48.3 1.0 OD1 A:ASP58 2.4 57.8 1.0 O A:THR62 2.4 28.5 1.0 OD1 A:ASN60 2.4 38.0 1.0 OE1 A:GLU67 2.5 39.6 1.0 OE2 A:GLU67 2.6 40.0 1.0 CD A:GLU67 2.9 38.4 1.0 CG A:ASP58 3.0 58.5 1.0 OD2 A:ASP58 3.1 60.8 1.0 CG A:ASN60 3.5 45.7 1.0 CG A:ASP56 3.5 55.3 1.0 C A:THR62 3.6 34.8 1.0 ND2 A:ASN60 4.1 45.7 1.0 N A:THR62 4.2 37.8 1.0 N A:ASP58 4.3 58.7 1.0 OD2 A:ASP56 4.4 63.5 1.0 CB A:ASP58 4.4 53.1 1.0 N A:ASN60 4.4 41.9 1.0 CA A:ASP56 4.4 44.6 1.0 CG A:GLU67 4.4 35.9 1.0 CB A:ASP56 4.4 48.0 1.0 N A:ILE63 4.4 29.8 1.0 N A:ASP64 4.4 31.1 1.0 CA A:ILE63 4.5 31.0 1.0 OG1 A:THR62 4.5 34.6 1.0 C A:ASP56 4.5 46.5 1.0 N A:ALA57 4.5 40.4 1.0 CA A:THR62 4.5 34.7 1.0 OD2 A:ASP64 4.5 51.1 1.0 CB A:ASN60 4.5 38.7 1.0 N A:GLY59 4.7 48.8 1.0 CA A:ASP58 4.8 55.1 1.0 N A:GLY61 4.8 53.3 1.0 CA A:ASN60 4.9 49.7 1.0 CG A:ASP64 4.9 44.0 1.0 C A:ILE63 4.9 34.4 1.0 O A:HOH607 5.0 45.5 1.0 C A:ASN60 5.0 58.5 1.0

Calcium binding site 3 out of 16 in the 2.5 Angstrom Crystal Structure of the N97S Cam Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 2.5 Angstrom Crystal Structure of the N97S Cam Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:49.0 occ:1.00 OD1 A:ASP95 2.2 53.7 1.0 OD1 A:ASP93 2.2 54.5 1.0 O A:TYR99 2.2 50.5 1.0 OE2 A:GLU104 2.4 36.4 1.0 OG A:SER97 2.6 48.3 1.0 OE1 A:GLU104 2.6 40.2 1.0 CD A:GLU104 2.8 36.0 1.0 CG A:ASP95 3.0 54.8 1.0 OD2 A:ASP95 3.3 46.0 1.0 C A:TYR99 3.4 52.1 1.0 CG A:ASP93 3.4 47.8 1.0 CB A:SER97 3.8 49.0 1.0 OD2 A:ASP93 4.2 47.0 1.0 N A:SER97 4.2 44.8 1.0 N A:TYR99 4.3 58.1 1.0 N A:ILE100 4.3 50.9 1.0 CA A:ILE100 4.3 41.4 1.0 CG A:GLU104 4.3 32.3 1.0 CB A:ASP95 4.3 52.7 1.0 CA A:ASP93 4.3 37.8 1.0 CA A:TYR99 4.4 56.1 1.0 CB A:ASP93 4.4 46.3 1.0 N A:SER101 4.5 35.5 1.0 N A:ASP95 4.5 43.9 1.0 CA A:SER97 4.5 50.0 1.0 O A:HOH601 4.6 55.1 1.0 C A:ASP93 4.6 41.2 1.0 NE2 A:GLN135 4.7 92.2 1.0 CA A:ASP95 4.8 49.1 1.0 C A:ILE100 4.8 44.8 1.0 O A:ASP93 4.9 37.2 1.0 CB A:TYR99 4.9 53.1 1.0 C A:ASP95 4.9 58.9 1.0 N A:GLY96 4.9 52.1 1.0 N A:GLY98 4.9 55.4 1.0 C A:SER97 5.0 54.1 1.0 N A:LYS94 5.0 43.5 1.0

Calcium binding site 4 out of 16 in the 2.5 Angstrom Crystal Structure of the N97S Cam Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 2.5 Angstrom Crystal Structure of the N97S Cam Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:78.6 occ:1.00 OD1 A:ASP131 2.2 80.1 1.0 OE1 A:GLU140 2.2 95.6 1.0 OD1 A:ASP133 2.3 77.9 1.0 OE2 A:GLU140 2.5 99.3 1.0 OD1 A:ASP129 2.5 75.4 1.0 O A:GLN135 2.5 65.9 1.0 CD A:GLU140 2.6 95.8 1.0 CG A:ASP133 3.0 81.5 1.0 CG A:ASP131 3.2 81.8 1.0 OD2 A:ASP133 3.3 83.0 1.0 OD2 A:ASP131 3.5 80.7 1.0 C A:GLN135 3.5 59.7 1.0 CG A:ASP129 3.7 79.1 1.0 ND2 A:ASN137 3.9 70.0 1.0 N A:ASN137 3.9 61.6 1.0 CG A:GLU140 4.1 85.9 1.0 CA A:VAL136 4.1 42.7 1.0 N A:VAL136 4.2 47.4 1.0 CB A:ASP133 4.3 82.6 1.0 OD2 A:ASP129 4.3 74.8 1.0 N A:ASP131 4.4 81.0 1.0 CG A:ASN137 4.5 69.4 1.0 CB A:ASP131 4.5 81.5 1.0 N A:ASP133 4.5 72.3 1.0 N A:GLN135 4.5 79.1 1.0 C A:VAL136 4.6 42.9 1.0 CA A:GLN135 4.6 69.0 1.0 N A:ILE130 4.7 86.0 1.0 CA A:ASP129 4.7 76.3 1.0 CA A:ASP131 4.8 83.5 1.0 CB A:ASN137 4.8 68.5 1.0 CB A:ASP129 4.8 80.6 1.0 N A:GLY132 4.8 76.5 1.0 C A:ASP131 4.9 85.5 1.0 CA A:ASP133 4.9 79.6 1.0

Calcium binding site 5 out of 16 in the 2.5 Angstrom Crystal Structure of the N97S Cam Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 2.5 Angstrom Crystal Structure of the N97S Cam Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:49.5 occ:1.00 OD1 B:ASP20 2.4 58.9 1.0 OE2 B:GLU31 2.4 48.8 1.0 OD1 B:ASP24 2.4 49.6 1.0 OD1 B:ASP22 2.4 82.7 1.0 O B:THR26 2.5 50.8 1.0 OE1 B:GLU31 2.7 61.1 1.0 CD B:GLU31 2.8 57.6 1.0 CG B:ASP22 3.1 82.2 1.0 OD2 B:ASP22 3.2 83.3 1.0 CG B:ASP24 3.2 54.5 1.0 CG B:ASP20 3.6 56.6 1.0 OD2 B:ASP24 3.6 52.4 1.0 C B:THR26 3.7 45.5 1.0 CG B:GLU31 4.2 52.1 1.0 N B:ASP24 4.3 55.0 1.0 OG1 B:THR26 4.3 65.3 1.0 OD2 B:ASP20 4.4 56.4 1.0 N B:THR26 4.4 49.6 1.0 CG2 B:THR28 4.4 55.3 1.0 CB B:ASP24 4.4 56.9 1.0 CA B:ASP20 4.5 48.0 1.0 CB B:ASP20 4.5 52.0 1.0 CB B:ASP22 4.5 77.5 1.0 CA B:THR26 4.6 46.2 1.0 N B:ILE27 4.6 43.1 1.0 N B:GLY23 4.7 64.9 1.0 N B:ASP22 4.7 63.0 1.0 CA B:ILE27 4.7 35.1 1.0 C B:ASP20 4.8 53.1 1.0 CA B:ASP24 4.8 57.1 1.0 N B:THR28 4.8 52.3 1.0 N B:LYS21 5.0 54.0 1.0

Calcium binding site 6 out of 16 in the 2.5 Angstrom Crystal Structure of the N97S Cam Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of 2.5 Angstrom Crystal Structure of the N97S Cam Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:42.5 occ:1.00 OD1 B:ASN60 2.4 40.9 1.0 O B:THR62 2.4 39.5 1.0 OD1 B:ASP58 2.5 57.3 1.0 OD1 B:ASP56 2.5 54.6 1.0 OE2 B:GLU67 2.6 40.1 1.0 OE1 B:GLU67 2.6 39.2 1.0 OD2 B:ASP58 2.9 53.3 1.0 CD B:GLU67 2.9 42.4 1.0 CG B:ASP58 3.0 59.2 1.0 CG B:ASN60 3.0 52.4 1.0 ND2 B:ASN60 3.4 51.8 1.0 C B:THR62 3.5 43.7 1.0 CG B:ASP56 3.6 52.7 1.0 OD2 B:ASP56 4.2 61.3 1.0 CA B:ILE63 4.2 42.3 1.0 N B:ILE63 4.2 44.4 1.0 CB B:ASN60 4.2 52.8 1.0 N B:ASN60 4.3 46.9 1.0 N B:ASP64 4.3 38.0 1.0 N B:THR62 4.3 44.6 1.0 OD2 B:ASP64 4.4 57.1 1.0 OG1 B:THR62 4.4 38.0 1.0 CB B:ASP58 4.4 56.3 1.0 CG B:GLU67 4.4 40.0 1.0 CA B:THR62 4.5 46.8 1.0 N B:ASP58 4.6 49.5 1.0 CB B:ASP56 4.6 51.1 1.0 CA B:ASP56 4.6 51.3 1.0 N B:GLY61 4.6 54.0 1.0 CA B:ASN60 4.7 53.9 1.0 C B:ILE63 4.7 36.6 1.0 CD1 B:ILE63 4.7 35.7 1.0 N B:GLY59 4.7 47.0 1.0 CG B:ASP64 4.8 54.8 1.0 C B:ASN60 4.8 53.5 1.0 CA B:ASP58 5.0 56.2 1.0 C B:ASP56 5.0 49.9 1.0

Calcium binding site 7 out of 16 in the 2.5 Angstrom Crystal Structure of the N97S Cam Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of 2.5 Angstrom Crystal Structure of the N97S Cam Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:66.6 occ:1.00 OD1 B:ASP93 2.2 76.9 1.0 OG B:SER97 2.3 71.1 1.0 O B:TYR99 2.3 69.2 1.0 OE1 B:GLU104 2.4 58.4 1.0 OE2 B:GLU104 2.5 60.3 1.0 OD1 B:ASP95 2.5 84.3 1.0 CD B:GLU104 2.7 58.9 1.0 CG B:ASP95 3.3 84.6 1.0 CB B:SER97 3.3 79.6 1.0 OD2 B:ASP95 3.3 82.9 1.0 CG B:ASP93 3.5 69.8 1.0 C B:TYR99 3.5 69.3 1.0 N B:SER97 4.0 81.4 1.0 CA B:SER97 4.1 81.9 1.0 CA B:ASP93 4.1 54.3 1.0 CG B:GLU104 4.2 58.0 1.0 N B:TYR99 4.2 80.7 1.0 CB B:ASP93 4.2 57.6 1.0 CA B:ILE100 4.4 67.3 1.0 OD2 B:ASP93 4.4 75.4 1.0 N B:ILE100 4.4 66.7 1.0 C B:SER97 4.4 85.7 1.0 CA B:TYR99 4.4 77.2 1.0 C B:ASP93 4.5 60.5 1.0 N B:SER101 4.5 59.4 1.0 N B:GLY98 4.7 79.9 1.0 N B:GLY96 4.7 97.9 1.0 N B:ASP95 4.7 74.9 1.0 CB B:ASP95 4.7 90.8 1.0 OG B:SER101 4.7 64.3 1.0 N B:LYS94 4.7 57.7 1.0 C B:ILE100 4.9 66.3 1.0 O B:ASP93 5.0 63.0 1.0 CB B:TYR99 5.0 85.0 1.0

Calcium binding site 8 out of 16 in the 2.5 Angstrom Crystal Structure of the N97S Cam Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of 2.5 Angstrom Crystal Structure of the N97S Cam Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:78.9 occ:1.00 OE2 B:GLU140 2.4 80.6 1.0 O B:GLN135 2.5 73.3 1.0 OD1 B:ASP133 2.6 0.5 1.0 OD1 B:ASP129 2.7 82.7 1.0 OE1 B:GLU140 2.9 77.8 1.0 CD B:GLU140 3.0 78.4 1.0 CB B:ASP131 3.3 96.5 1.0 CG B:ASP133 3.5 0.4 1.0 N B:GLY132 3.7 97.1 1.0 CG B:ASP129 3.7 82.6 1.0 C B:GLN135 3.7 77.6 1.0 N B:ASP131 3.7 0.3 1.0 OD2 B:ASP133 3.8 0.1 1.0 CA B:ASP131 3.8 0.5 1.0 N B:ASP133 4.0 0.3 1.0 C B:ASP131 4.0 0.4 1.0 ND2 B:ASN137 4.1 77.0 1.0 OD2 B:ASP129 4.1 86.1 1.0 N B:GLN135 4.3 88.2 1.0 N B:ASN137 4.4 63.3 1.0 N B:ILE130 4.4 75.7 1.0 CG B:GLU140 4.5 67.3 1.0 CA B:VAL136 4.6 67.8 1.0 N B:VAL136 4.6 69.7 1.0 CA B:GLN135 4.6 84.2 1.0 CA B:GLY132 4.7 96.9 1.0 C B:ILE130 4.7 96.0 1.0 N B:GLY134 4.7 0.3 1.0 CB B:ASP133 4.7 0.0 1.0 C B:GLY132 4.8 0.9 1.0 CA B:ASP133 4.8 0.0 1.0 CA B:ASP129 4.8 82.1 1.0 CB B:ASP129 4.8 81.7 1.0 O B:ASP131 4.9 0.5 1.0 CE2 B:TYR99 4.9 100.0 1.0 CD2 B:TYR99 5.0 98.3 1.0 C B:VAL136 5.0 63.8 1.0

Calcium binding site 9 out of 16 in the 2.5 Angstrom Crystal Structure of the N97S Cam Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of 2.5 Angstrom Crystal Structure of the N97S Cam Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:57.4 occ:1.00 OD1 C:ASP20 2.3 47.7 1.0 OE1 C:GLU31 2.4 69.3 1.0 O C:THR26 2.4 60.6 1.0 OE2 C:GLU31 2.4 69.5 1.0 OD1 C:ASP24 2.5 61.0 1.0 CD C:GLU31 2.7 68.9 1.0 OD1 C:ASP22 2.7 51.4 1.0 CG C:ASP20 3.3 46.2 1.0 CG C:ASP24 3.5 58.5 1.0 C C:THR26 3.6 63.0 1.0 CG C:ASP22 3.8 59.5 1.0 CA C:ASP20 3.8 55.7 1.0 CB C:ASP20 3.9 57.1 1.0 OD2 C:ASP24 3.9 62.6 1.0 OG1 C:THR26 4.1 52.0 1.0 CG C:GLU31 4.2 58.3 1.0 OD2 C:ASP22 4.2 54.8 1.0 OD2 C:ASP20 4.3 46.0 1.0 N C:THR26 4.4 48.1 1.0 C C:ASP20 4.4 51.7 1.0 N C:LYS21 4.5 47.9 1.0 N C:ILE27 4.5 61.4 1.0 CA C:ILE27 4.5 60.5 1.0 CA C:THR26 4.5 60.9 1.0 N C:ASP24 4.6 56.7 1.0 N C:GLY23 4.7 49.9 1.0 CG2 C:THR28 4.7 53.9 1.0 N C:ASP22 4.7 62.4 1.0 CB C:ASP24 4.8 53.2 1.0 N C:THR28 4.8 53.8 1.0 CB C:THR26 5.0 50.7 1.0 O C:PHE19 5.0 46.2 1.0

Calcium binding site 10 out of 16 in the 2.5 Angstrom Crystal Structure of the N97S Cam Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of 2.5 Angstrom Crystal Structure of the N97S Cam Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:57.1 occ:1.00 OD1 C:ASP56 2.3 51.9 1.0 OD1 C:ASP58 2.4 88.2 1.0 OD2 C:ASP58 2.4 81.5 1.0 O C:THR62 2.5 49.9 1.0 OE2 C:GLU67 2.5 47.9 1.0 OD1 C:ASN60 2.5 54.4 1.0 OE1 C:GLU67 2.5 66.8 1.0 CG C:ASP58 2.7 84.2 1.0 CD C:GLU67 2.9 60.3 1.0 CG C:ASN60 3.5 61.0 1.0 CG C:ASP56 3.5 66.0 1.0 C C:THR62 3.7 49.7 1.0 ND2 C:ASN60 4.0 55.6 1.0 O C:HOH607 4.0 46.0 1.0 CB C:ASP58 4.0 73.3 1.0 N C:ASP58 4.2 51.9 1.0 OD2 C:ASP56 4.2 55.1 1.0 CA C:ILE63 4.3 51.9 1.0 N C:ASP64 4.3 45.1 1.0 N C:ASN60 4.4 75.7 1.0 CG C:GLU67 4.4 58.6 1.0 CA C:ASP56 4.4 58.5 1.0 N C:GLY59 4.4 68.1 1.0 N C:ILE63 4.4 47.8 1.0 N C:THR62 4.5 61.3 1.0 CB C:ASP56 4.5 53.6 1.0 CD1 C:ILE63 4.5 46.4 1.0 CA C:ASP58 4.6 65.4 1.0 C C:ASP56 4.6 61.7 1.0 CA C:THR62 4.7 62.3 1.0 CB C:ASN60 4.7 63.0 1.0 N C:ALA57 4.8 53.4 1.0 C C:ILE63 4.8 50.8 1.0 C C:ASP58 4.8 63.9 1.0 N C:GLY61 4.9 62.0 1.0 OG1 C:THR62 4.9 53.1 1.0 CG C:ASP64 4.9 55.1 1.0 CA C:ASN60 5.0 59.6 1.0

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