Calcium in PDB 3dve: Crystal Structure of CA2+/Cam-CAV2.2 Iq Domain Complex

The structure of Crystal Structure of CA2+/Cam-CAV2.2 Iq Domain Complex, PDB code: 3dve 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 / 2.35
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	40.303, 40.303, 344.652, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 27.1

The structure of Crystal Structure of CA2+/Cam-CAV2.2 Iq Domain Complex also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Calcium atom in the Crystal Structure of CA2+/Cam-CAV2.2 Iq Domain Complex (pdb code 3dve). 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-CAV2.2 Iq Domain Complex, PDB code: 3dve:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of CA2+/Cam-CAV2.2 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 Crystal Structure of CA2+/Cam-CAV2.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:26.1 occ:1.00 OD1 A:ASP20 2.2 23.2 1.0 O A:THR26 2.3 25.2 1.0 O A:HOH524 2.4 21.9 1.0 OD1 A:ASP22 2.4 27.4 1.0 OD2 A:ASP24 2.4 22.5 1.0 OE2 A:GLU31 2.5 21.6 1.0 OE1 A:GLU31 2.6 22.0 1.0 CD A:GLU31 2.9 20.8 1.0 CG A:ASP22 3.3 28.9 1.0 CG A:ASP20 3.4 25.9 1.0 CG A:ASP24 3.4 24.4 1.0 C A:THR26 3.5 24.9 1.0 OD2 A:ASP22 3.6 28.9 1.0 OD1 A:ASP24 4.0 20.8 1.0 N A:ASP24 4.1 26.6 1.0 CA A:ASP20 4.1 25.7 1.0 N A:THR26 4.1 26.5 1.0 OD2 A:ASP20 4.2 26.4 1.0 CB A:ASP20 4.3 24.6 1.0 O A:HOH538 4.3 32.0 1.0 C A:ASP20 4.4 26.2 1.0 CG A:GLU31 4.4 19.4 1.0 N A:ILE27 4.4 23.3 1.0 CA A:ILE27 4.4 21.2 1.0 OG1 A:THR26 4.4 29.8 1.0 N A:ASP22 4.4 28.2 1.0 CA A:THR26 4.4 25.9 1.0 CB A:ASP24 4.5 24.7 1.0 N A:GLY23 4.6 28.4 1.0 CB A:ASP22 4.6 27.8 1.0 CA A:ASP24 4.7 25.8 1.0 O A:ASP20 4.7 26.5 1.0 N A:LYS21 4.7 27.4 1.0 N A:GLY25 4.8 25.8 1.0 CA A:ASP22 4.8 28.4 1.0 O A:HOH508 4.8 23.1 1.0 C A:ASP22 4.9 28.4 1.0 N A:THR28 4.9 19.4 1.0 C A:ASP24 4.9 25.9 1.0 CG2 A:THR28 5.0 18.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of CA2+/Cam-CAV2.2 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 Crystal Structure of CA2+/Cam-CAV2.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:30.3 occ:1.00 OD2 A:ASP56 2.2 26.5 1.0 O A:HOH543 2.2 31.2 1.0 OD1 A:ASN60 2.3 26.9 1.0 OD2 A:ASP58 2.4 29.6 1.0 OE1 A:GLU67 2.5 28.3 1.0 O A:THR62 2.5 25.9 1.0 OE2 A:GLU67 2.5 31.5 1.0 CD A:GLU67 2.9 28.4 1.0 CG A:ASP58 3.3 30.4 1.0 CG A:ASN60 3.4 28.1 1.0 CG A:ASP56 3.5 30.2 1.0 OD1 A:ASP58 3.5 31.7 1.0 C A:THR62 3.7 26.4 1.0 O A:HOH514 4.0 26.6 1.0 ND2 A:ASN60 4.0 28.9 1.0 CA A:ASP56 4.2 32.5 1.0 N A:THR62 4.2 26.9 1.0 N A:ASN60 4.2 29.3 1.0 OD1 A:ASP56 4.2 31.6 1.0 CG A:GLU67 4.4 26.1 1.0 CB A:ASP56 4.4 32.2 1.0 N A:GLY61 4.5 28.1 1.0 O A:HOH559 4.5 46.5 1.0 CB A:ASN60 4.5 27.9 1.0 N A:ASP58 4.5 31.5 1.0 N A:ILE63 4.6 26.5 1.0 CA A:ILE63 4.6 26.4 1.0 CA A:THR62 4.6 26.4 1.0 C A:ASP56 4.6 32.5 1.0 CB A:ASP58 4.6 31.1 1.0 N A:ASP64 4.6 27.1 1.0 OG1 A:THR62 4.6 28.4 1.0 CA A:ASN60 4.7 28.3 1.0 N A:GLY59 4.7 31.0 1.0 N A:ALA57 4.8 32.1 1.0 C A:ASN60 4.9 28.3 1.0 OD2 A:ASP64 4.9 32.6 1.0 CA A:ASP58 4.9 31.1 1.0 C A:ASP58 5.0 31.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of CA2+/Cam-CAV2.2 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 Crystal Structure of CA2+/Cam-CAV2.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:21.6 occ:1.00 OD2 A:ASP93 2.1 21.9 1.0 O A:TYR99 2.3 18.8 1.0 OD1 A:ASP95 2.4 22.2 1.0 OD1 A:ASN97 2.4 17.8 1.0 OE1 A:GLU104 2.4 25.1 1.0 O A:HOH535 2.5 26.8 1.0 OE2 A:GLU104 2.7 26.8 1.0 CD A:GLU104 2.9 25.0 1.0 CG A:ASP95 3.3 22.1 1.0 CG A:ASN97 3.3 19.0 1.0 CG A:ASP93 3.3 24.7 1.0 C A:TYR99 3.5 19.2 1.0 OD2 A:ASP95 3.6 22.8 1.0 ND2 A:ASN97 4.0 15.9 1.0 N A:TYR99 4.1 18.4 1.0 N A:ASN97 4.1 19.3 1.0 OD1 A:ASP93 4.1 24.1 1.0 CA A:ASP93 4.2 24.7 1.0 O A:HOH511 4.3 20.3 1.0 CB A:ASP93 4.3 23.9 1.0 N A:ASP95 4.3 23.5 1.0 CB A:ASN97 4.3 18.7 1.0 CA A:TYR99 4.3 17.7 1.0 C A:ASP93 4.4 25.2 1.0 CG A:GLU104 4.4 22.0 1.0 N A:ILE100 4.5 19.6 1.0 N A:LYS94 4.5 25.4 1.0 CB A:ASP95 4.5 22.4 1.0 CA A:ILE100 4.6 19.5 1.0 CA A:ASN97 4.6 19.2 1.0 O A:HOH567 4.7 26.7 1.0 N A:GLY96 4.7 21.4 1.0 N A:GLY98 4.7 18.9 1.0 N A:SER101 4.7 21.0 1.0 CA A:ASP95 4.8 22.5 1.0 CB A:TYR99 4.8 17.4 1.0 C A:ASP95 4.9 22.2 1.0 O A:ASP93 4.9 25.4 1.0 C A:ASN97 4.9 19.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of CA2+/Cam-CAV2.2 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 Crystal Structure of CA2+/Cam-CAV2.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:20.7 occ:1.00 OD2 A:ASP133 2.4 19.1 1.0 OD1 A:ASP131 2.4 18.2 1.0 OD2 A:ASP129 2.4 19.4 1.0 O A:HOH509 2.4 17.4 1.0 O A:GLN135 2.4 17.5 1.0 OE2 A:GLU140 2.5 19.1 1.0 OE1 A:GLU140 2.5 20.0 1.0 CD A:GLU140 2.8 19.7 1.0 CG A:ASP131 3.3 17.9 1.0 CG A:ASP133 3.3 19.3 1.0 CG A:ASP129 3.4 21.7 1.0 OD2 A:ASP131 3.6 17.2 1.0 C A:GLN135 3.6 17.6 1.0 OD1 A:ASP133 3.8 20.6 1.0 N A:ASP133 4.1 18.1 1.0 N A:GLN135 4.1 17.9 1.0 N A:ASP131 4.2 18.3 1.0 OD1 A:ASP129 4.2 22.6 1.0 N A:ILE130 4.2 20.7 1.0 CA A:ASP129 4.3 20.9 1.0 CB A:ASP129 4.3 20.2 1.0 CB A:ASP133 4.4 16.7 1.0 CG A:GLU140 4.4 18.1 1.0 N A:GLY132 4.4 18.7 1.0 CA A:VAL136 4.4 17.7 1.0 N A:ASN137 4.5 18.5 1.0 CA A:GLN135 4.5 17.2 1.0 N A:VAL136 4.5 17.9 1.0 CB A:ASP131 4.5 17.1 1.0 N A:GLY134 4.6 16.5 1.0 CA A:ASP133 4.6 17.5 1.0 CA A:ASP131 4.7 18.2 1.0 C A:ASP129 4.7 20.8 1.0 C A:ASP133 4.9 17.2 1.0 C A:ASP131 4.9 18.3 1.0 C A:VAL136 4.9 18.6 1.0 CB A:GLN135 5.0 17.0 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