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

Protein crystallography data

The structure of Crystal Structure of CA2+/Cam-CAV2.3 Iq Domain Complex, PDB code: 3dvk 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 / 2.30
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 44.262, 44.262, 337.941, 90.00, 90.00, 120.00
R / Rfree (%) 25.6 / 29.1

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 3dvk

Go back to Calcium Binding Sites List in 3dvk
Calcium binding site 1 out of 4 in the Crystal Structure of CA2+/Cam-CAV2.3 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-CAV2.3 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:61.1
occ:1.00
OD1 A:ASP22 2.3 71.0 1.0
O A:THR26 2.4 67.2 1.0
OD1 A:ASP20 2.4 75.9 1.0
OE2 A:GLU31 2.4 71.6 1.0
OD2 A:ASP24 2.5 76.0 1.0
OE1 A:GLU31 2.7 70.7 1.0
CD A:GLU31 2.9 70.6 1.0
CG A:ASP22 3.2 71.8 1.0
CG A:ASP24 3.3 75.6 1.0
OD2 A:ASP22 3.4 67.7 1.0
CG A:ASP20 3.6 78.7 1.0
C A:THR26 3.6 71.0 1.0
OD1 A:ASP24 3.8 75.0 1.0
N A:ASP24 4.1 78.0 1.0
N A:THR26 4.1 72.9 1.0
CA A:ASP20 4.2 76.2 1.0
OG1 A:THR26 4.3 79.8 1.0
CB A:ASP24 4.4 74.8 1.0
OD2 A:ASP20 4.4 78.3 1.0
CB A:ASP20 4.4 76.5 1.0
CG A:GLU31 4.4 67.7 1.0
C A:ASP20 4.4 79.3 1.0
CA A:THR26 4.4 73.6 1.0
N A:GLY23 4.4 77.7 1.0
N A:ASP22 4.5 78.5 1.0
N A:ILE27 4.5 68.6 1.0
N A:LYS21 4.6 76.8 1.0
CB A:ASP22 4.6 74.3 1.0
N A:GLY25 4.6 78.5 1.0
CA A:ILE27 4.6 68.0 1.0
CA A:ASP24 4.7 77.2 1.0
O A:HOH521 4.8 47.2 1.0
N A:THR28 4.9 66.7 1.0
CA A:ASP22 4.9 77.7 1.0
C A:ASP22 5.0 79.7 1.0
O A:ASP20 5.0 77.7 1.0

Calcium binding site 2 out of 4 in 3dvk

Go back to Calcium Binding Sites List in 3dvk
Calcium binding site 2 out of 4 in the Crystal Structure of CA2+/Cam-CAV2.3 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-CAV2.3 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:73.4
occ:1.00
OD2 A:ASP56 2.1 62.5 1.0
O A:THR62 2.5 66.3 1.0
OE1 A:GLU67 2.5 80.0 1.0
OD1 A:ASN60 2.6 70.5 1.0
OD2 A:ASP58 2.7 81.0 1.0
OE2 A:GLU67 2.9 77.6 1.0
CD A:GLU67 3.1 78.3 1.0
CG A:ASP56 3.3 70.9 1.0
CG A:ASP58 3.3 77.5 1.0
CG A:ASN60 3.4 69.2 1.0
OD1 A:ASP58 3.4 77.1 1.0
C A:THR62 3.5 68.9 1.0
ND2 A:ASN60 3.8 69.3 1.0
OD1 A:ASP56 4.0 66.8 1.0
CB A:ASP56 4.3 70.9 1.0
N A:ILE63 4.3 72.2 1.0
CA A:ILE63 4.3 71.6 1.0
CA A:ASP56 4.3 75.4 1.0
N A:THR62 4.3 69.0 1.0
N A:ASN60 4.3 71.1 1.0
OG1 A:THR62 4.4 72.1 1.0
CA A:THR62 4.5 68.0 1.0
N A:ASP64 4.5 70.4 1.0
CG A:GLU67 4.5 75.7 1.0
N A:ASP58 4.5 75.2 1.0
CB A:ASN60 4.6 68.2 1.0
CB A:ASP58 4.7 75.7 1.0
C A:ASP56 4.7 76.6 1.0
CA A:ASN60 4.8 70.8 1.0
C A:ILE63 4.8 72.9 1.0
N A:GLY59 4.8 70.5 1.0
N A:GLY61 4.9 70.2 1.0
N A:ALA57 4.9 75.4 1.0
C A:ASN60 4.9 70.8 1.0
CA A:ASP58 4.9 75.2 1.0

Calcium binding site 3 out of 4 in 3dvk

Go back to Calcium Binding Sites List in 3dvk
Calcium binding site 3 out of 4 in the Crystal Structure of CA2+/Cam-CAV2.3 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-CAV2.3 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:48.6
occ:1.00
O A:TYR99 2.3 60.5 1.0
OD2 A:ASP93 2.3 64.3 1.0
OE1 A:GLU104 2.4 64.2 1.0
OD1 A:ASP95 2.4 64.7 1.0
OD1 A:ASN97 2.5 50.2 1.0
O A:HOH535 2.5 49.0 1.0
OE2 A:GLU104 2.6 61.2 1.0
CD A:GLU104 2.8 64.2 1.0
CG A:ASP95 3.3 64.0 1.0
CG A:ASP93 3.4 63.5 1.0
C A:TYR99 3.4 61.0 1.0
CG A:ASN97 3.5 53.5 1.0
OD2 A:ASP95 3.6 63.2 1.0
N A:TYR99 4.1 60.0 1.0
N A:ASN97 4.1 60.0 1.0
ND2 A:ASN97 4.1 51.1 1.0
OD1 A:ASP93 4.2 66.3 1.0
O A:HOH536 4.3 42.9 1.0
CA A:TYR99 4.3 61.5 1.0
CA A:ASP93 4.3 60.6 1.0
CG A:GLU104 4.4 59.8 1.0
CB A:ASP93 4.4 62.0 1.0
N A:GLY96 4.4 60.8 1.0
N A:ILE100 4.4 62.8 1.0
N A:ASP95 4.4 61.0 1.0
CA A:ILE100 4.5 60.9 1.0
C A:ASP93 4.5 60.7 1.0
CB A:ASN97 4.5 52.5 1.0
CB A:ASP95 4.6 61.0 1.0
C A:ASP95 4.7 62.1 1.0
N A:SER101 4.7 60.2 1.0
N A:GLY98 4.7 57.5 1.0
CA A:ASN97 4.7 57.4 1.0
N A:LYS94 4.7 60.0 1.0
CB A:TYR99 4.7 64.3 1.0
CA A:ASP95 4.8 60.6 1.0
O A:HOH509 4.8 49.7 1.0
O A:ASP93 4.9 61.2 1.0
C A:ASN97 5.0 57.8 1.0

Calcium binding site 4 out of 4 in 3dvk

Go back to Calcium Binding Sites List in 3dvk
Calcium binding site 4 out of 4 in the Crystal Structure of CA2+/Cam-CAV2.3 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-CAV2.3 Iq Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:50.2
occ:1.00
OD2 A:ASP129 2.3 59.1 1.0
OE1 A:GLU140 2.4 58.7 1.0
O A:GLN135 2.4 63.8 1.0
OD1 A:ASP131 2.4 70.3 1.0
O A:HOH520 2.6 45.2 1.0
OD2 A:ASP133 2.6 60.2 1.0
OE2 A:GLU140 2.6 63.8 1.0
CD A:GLU140 2.8 62.9 1.0
CG A:ASP131 3.2 63.0 1.0
CG A:ASP133 3.3 59.1 1.0
CG A:ASP129 3.4 58.7 1.0
OD2 A:ASP131 3.5 59.6 1.0
C A:GLN135 3.5 61.7 1.0
OD1 A:ASP133 3.7 56.2 1.0
N A:ASP133 4.2 58.5 1.0
N A:GLN135 4.2 61.6 1.0
OD1 A:ASP129 4.2 57.9 1.0
N A:ASP131 4.3 61.6 1.0
CB A:ASP129 4.3 61.6 1.0
CA A:ASP129 4.3 65.8 1.0
CG A:GLU140 4.3 63.6 1.0
N A:VAL136 4.4 62.5 1.0
CA A:VAL136 4.4 61.2 1.0
CB A:ASP133 4.4 56.3 1.0
N A:GLY132 4.4 62.4 1.0
N A:ASN137 4.4 63.4 1.0
CA A:GLN135 4.5 61.1 1.0
CB A:ASP131 4.5 62.2 1.0
N A:ILE130 4.6 70.1 1.0
C A:ASP129 4.7 68.8 1.0
CA A:ASP131 4.7 59.4 1.0
CA A:ASP133 4.7 59.3 1.0
N A:GLY134 4.7 61.1 1.0
C A:ASP131 4.9 59.7 1.0
C A:VAL136 4.9 58.5 1.0
C A:ASP133 5.0 58.2 1.0

Reference:

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
Page generated: Sat Dec 12 04:09:22 2020

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