Calcium in PDB 3dvm: Crystal Structure of CA2+/Cam-CAV2.1 Iq Domain Complex

The structure of Crystal Structure of CA2+/Cam-CAV2.1 Iq Domain Complex, PDB code: 3dvm was solved by E.Y.Kim, C.H.Rumpf, Y.Fujiwara, E.S.Cooley, F.Van Petegem, D.L.Minor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.60
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	43.956, 43.956, 337.870, 90.00, 90.00, 120.00
R / Rfree (%)	27.6 / 32

The binding sites of Calcium atom in the Crystal Structure of CA2+/Cam-CAV2.1 Iq Domain Complex (pdb code 3dvm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of CA2+/Cam-CAV2.1 Iq Domain Complex, PDB code: 3dvm:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of CA2+/Cam-CAV2.1 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 Crystal Structure of CA2+/Cam-CAV2.1 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:64.8 occ:1.00 O A:THR26 2.3 51.0 1.0 OD1 A:ASP22 2.4 55.5 1.0 OE2 A:GLU31 2.4 52.5 1.0 OD1 A:ASP20 2.5 60.5 1.0 OD2 A:ASP24 2.7 55.4 1.0 OE1 A:GLU31 2.8 51.7 1.0 CD A:GLU31 3.0 50.7 1.0 CG A:ASP22 3.3 54.1 1.0 CG A:ASP24 3.4 54.6 1.0 C A:THR26 3.5 53.4 1.0 CG A:ASP20 3.5 61.4 1.0 OD2 A:ASP22 3.6 50.4 1.0 OD1 A:ASP24 3.7 55.6 1.0 N A:THR26 4.1 51.6 1.0 CA A:ASP20 4.1 58.4 1.0 N A:ASP24 4.2 54.8 1.0 CB A:ASP20 4.3 59.6 1.0 OD2 A:ASP20 4.4 61.1 1.0 N A:GLY23 4.4 59.3 1.0 C A:ASP20 4.4 60.2 1.0 CA A:THR26 4.4 52.2 1.0 N A:ILE27 4.4 50.7 1.0 CG A:GLU31 4.4 51.0 1.0 CA A:ILE27 4.5 47.2 1.0 CB A:ASP24 4.5 54.6 1.0 N A:ASP22 4.5 61.9 1.0 N A:LYS21 4.6 62.2 1.0 N A:GLY25 4.6 51.5 1.0 OG1 A:THR26 4.7 56.2 1.0 CB A:ASP22 4.7 55.1 1.0 CA A:ASP24 4.8 55.3 1.0 O A:ASP20 4.9 59.1 1.0 CA A:ASP22 5.0 59.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of CA2+/Cam-CAV2.1 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 Crystal Structure of CA2+/Cam-CAV2.1 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:76.1 occ:1.00 OD1 A:ASN60 2.3 58.3 1.0 OE1 A:GLU67 2.3 65.0 1.0 OD2 A:ASP56 2.5 31.5 1.0 OD1 A:ASP58 2.6 72.1 1.0 O A:THR62 2.7 66.4 1.0 OE2 A:GLU67 2.8 65.9 1.0 CD A:GLU67 2.9 65.0 1.0 CG A:ASN60 3.3 61.5 1.0 CG A:ASP58 3.4 67.4 1.0 OD2 A:ASP58 3.4 68.6 1.0 C A:THR62 3.5 63.1 1.0 CG A:ASP56 3.7 41.1 1.0 ND2 A:ASN60 3.8 61.0 1.0 CG2 A:THR62 4.0 67.8 1.0 CA A:ILE63 4.0 62.3 1.0 N A:ILE63 4.1 62.5 1.0 OD2 A:ASP64 4.1 68.1 1.0 N A:ASP64 4.1 64.4 1.0 CG A:GLU67 4.3 63.9 1.0 OD1 A:ASP56 4.4 43.6 1.0 CG A:ASP64 4.5 66.1 1.0 CA A:THR62 4.5 64.1 1.0 N A:THR62 4.5 60.1 1.0 CB A:ASN60 4.6 59.8 1.0 C A:ILE63 4.6 64.2 1.0 CA A:ASP56 4.6 48.6 1.0 N A:ASN60 4.7 64.0 1.0 CB A:ASP56 4.7 42.7 1.0 CB A:ASP58 4.8 64.1 1.0 N A:ASP58 4.8 61.1 1.0 OD1 A:ASP64 4.8 65.3 1.0 CB A:THR62 4.8 64.9 1.0 CA A:ASN60 4.9 61.4 1.0 C A:ASN60 5.0 59.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of CA2+/Cam-CAV2.1 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 Crystal Structure of CA2+/Cam-CAV2.1 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:50.3 occ:1.00 O A:TYR99 2.1 37.1 1.0 OD1 A:ASP93 2.4 32.1 1.0 OD1 A:ASP95 2.5 37.8 1.0 OD1 A:ASN97 2.6 29.2 1.0 OE1 A:GLU104 2.7 49.3 1.0 OE2 A:GLU104 2.7 52.0 1.0 CD A:GLU104 3.0 48.4 1.0 C A:TYR99 3.3 41.5 1.0 CG A:ASN97 3.5 27.5 1.0 CG A:ASP93 3.5 36.8 1.0 CG A:ASP95 3.5 34.4 1.0 OD2 A:ASP95 3.9 33.1 1.0 N A:ASN97 4.0 37.2 1.0 ND2 A:ASN97 4.1 20.1 1.0 OD2 A:ASP93 4.1 40.6 1.0 N A:ILE100 4.2 37.5 1.0 N A:TYR99 4.2 42.4 1.0 O A:HOH510 4.2 43.9 1.0 CA A:ILE100 4.3 34.6 1.0 CA A:TYR99 4.3 40.7 1.0 N A:GLY96 4.4 37.1 1.0 CG A:GLU104 4.4 47.3 1.0 CB A:ASN97 4.5 27.9 1.0 CA A:ASP93 4.5 38.5 1.0 N A:ASP95 4.5 36.6 1.0 CB A:ASP93 4.6 35.1 1.0 N A:SER101 4.6 33.3 1.0 C A:ASP93 4.6 40.1 1.0 CA A:ASN97 4.7 34.0 1.0 C A:ASP95 4.8 35.6 1.0 CB A:ASP95 4.8 32.1 1.0 CB A:TYR99 4.8 43.5 1.0 C A:ILE100 4.9 35.6 1.0 N A:GLY98 4.9 33.7 1.0 N A:LYS94 5.0 40.5 1.0 CA A:ASP95 5.0 33.5 1.0 O A:ASP93 5.0 36.8 1.0 CA A:GLY96 5.0 38.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of CA2+/Cam-CAV2.1 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 Crystal Structure of CA2+/Cam-CAV2.1 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:39.1 occ:1.00 OD1 A:ASP131 2.3 39.2 1.0 O A:HOH513 2.3 38.2 1.0 OD1 A:ASP129 2.3 33.0 1.0 OE1 A:GLU140 2.4 36.1 1.0 O A:GLN135 2.4 39.8 1.0 OD1 A:ASP133 2.4 34.4 1.0 OE2 A:GLU140 2.5 35.8 1.0 CD A:GLU140 2.8 36.6 1.0 CG A:ASP131 3.1 38.5 1.0 OD2 A:ASP131 3.3 38.3 1.0 CG A:ASP133 3.3 34.3 1.0 CG A:ASP129 3.4 32.4 1.0 C A:GLN135 3.5 38.3 1.0 OD2 A:ASP133 3.7 32.3 1.0 N A:ASP133 4.0 40.0 1.0 OD2 A:ASP129 4.2 29.6 1.0 N A:GLN135 4.2 33.3 1.0 N A:ASP131 4.3 36.2 1.0 N A:GLY132 4.3 42.2 1.0 CG A:GLU140 4.3 35.0 1.0 CB A:ASP129 4.3 33.2 1.0 CA A:VAL136 4.4 36.3 1.0 CA A:ASP129 4.4 35.2 1.0 N A:VAL136 4.4 39.1 1.0 CB A:ASP133 4.4 31.6 1.0 CB A:ASP131 4.4 33.1 1.0 CA A:GLN135 4.4 35.9 1.0 N A:ASN137 4.5 38.4 1.0 N A:ILE130 4.5 38.8 1.0 CA A:ASP133 4.6 37.9 1.0 N A:GLY134 4.7 39.0 1.0 C A:ASP129 4.7 37.3 1.0 CA A:ASP131 4.7 34.5 1.0 C A:ASP131 4.7 39.1 1.0 C A:VAL136 4.9 40.3 1.0 C A:ASP133 4.9 40.6 1.0 CB A:GLN135 4.9 38.5 1.0 CG A:ASN137 5.0 38.2 1.0

E.Y.Kim, C.H.Rumpf, Y.Fujiwara, E.S.Cooley, F.Van Petegem, D.L.Minor. Structures of Ca(V)2 Ca(2+)/Cam-Iq Domain Complexes Reveal Binding Modes That Underlie Calcium-Dependent Inactivation and Facilitation. Structure V. 16 1455 2008.
ISSN: ISSN 0969-2126
PubMed: 18940602
DOI: 10.1016/J.STR.2008.07.010