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Calcium in PDB 1xa5: Structure of Calmodulin in Complex with Kar-2, A Bis-Indol Alkaloid

Protein crystallography data

The structure of Structure of Calmodulin in Complex with Kar-2, A Bis-Indol Alkaloid, PDB code: 1xa5 was solved by I.Horvath, V.Harmat, E.Hlavanda, G.Naray-Szabo, J.Ovadi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.12
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 37.573, 37.573, 356.662, 90.00, 90.00, 120.00
R / Rfree (%) 21.8 / 26.1

Other elements in 1xa5:

The structure of Structure of Calmodulin in Complex with Kar-2, A Bis-Indol Alkaloid also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Calmodulin in Complex with Kar-2, A Bis-Indol Alkaloid (pdb code 1xa5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Calmodulin in Complex with Kar-2, A Bis-Indol Alkaloid, PDB code: 1xa5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1xa5

Go back to Calcium Binding Sites List in 1xa5
Calcium binding site 1 out of 4 in the Structure of Calmodulin in Complex with Kar-2, A Bis-Indol Alkaloid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Calmodulin in Complex with Kar-2, A Bis-Indol Alkaloid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca149

b:36.6
occ:1.00
OD1 A:ASP20 2.2 16.1 1.0
O A:THR26 2.2 20.2 1.0
OD1 A:ASP24 2.3 16.4 1.0
OE2 A:GLU31 2.4 14.6 1.0
OD1 A:ASP22 2.5 20.4 1.0
O A:HOH188 2.6 35.0 1.0
OE1 A:GLU31 2.7 13.0 1.0
CD A:GLU31 2.9 13.6 1.0
CG A:ASP22 3.3 21.1 1.0
CG A:ASP24 3.3 17.9 1.0
CG A:ASP20 3.4 16.1 1.0
C A:THR26 3.5 19.1 1.0
OD2 A:ASP22 3.5 19.6 1.0
OD2 A:ASP24 3.9 17.4 1.0
N A:THR26 4.1 19.7 1.0
N A:ASP24 4.1 21.3 1.0
OG1 A:THR26 4.2 21.7 1.0
OD2 A:ASP20 4.2 15.1 1.0
CA A:ASP20 4.3 16.9 1.0
CA A:THR26 4.3 19.8 1.0
CB A:ASP24 4.3 19.1 1.0
CB A:ASP20 4.4 16.3 1.0
CG A:GLU31 4.4 12.7 1.0
N A:ILE27 4.4 16.7 1.0
N A:GLY23 4.5 22.8 1.0
CA A:ILE27 4.5 15.2 1.0
N A:ASP22 4.5 22.0 1.0
CB A:ASP22 4.6 21.8 1.0
N A:GLY25 4.6 20.4 1.0
CA A:ASP24 4.6 20.2 1.0
C A:ASP20 4.7 18.8 1.0
C A:ASP24 4.8 20.4 1.0
CG2 A:THR28 4.8 13.5 1.0
N A:LYS21 4.8 20.8 1.0
N A:THR28 4.9 13.9 1.0
CB A:THR26 4.9 20.6 1.0
C A:ASP22 4.9 22.3 1.0
CA A:ASP22 4.9 22.3 1.0

Calcium binding site 2 out of 4 in 1xa5

Go back to Calcium Binding Sites List in 1xa5
Calcium binding site 2 out of 4 in the Structure of Calmodulin in Complex with Kar-2, A Bis-Indol Alkaloid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Calmodulin in Complex with Kar-2, A Bis-Indol Alkaloid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca151

b:28.8
occ:1.00
OD1 A:ASN97 2.2 13.0 1.0
O A:TYR99 2.3 18.8 1.0
OD1 A:ASP95 2.3 11.9 1.0
OE2 A:GLU104 2.4 14.1 1.0
OD1 A:ASP93 2.4 13.7 1.0
OE1 A:GLU104 2.6 15.7 1.0
O A:HOH196 2.6 31.2 1.0
CD A:GLU104 2.8 14.9 1.0
CG A:ASN97 3.2 14.1 1.0
CG A:ASP95 3.4 11.5 1.0
C A:TYR99 3.5 16.0 1.0
CG A:ASP93 3.6 13.4 1.0
OD2 A:ASP95 3.8 11.8 1.0
ND2 A:ASN97 3.9 11.7 1.0
N A:TYR99 4.1 14.1 1.0
N A:ASN97 4.1 12.8 1.0
CA A:ASP93 4.2 13.0 1.0
C A:ASP93 4.2 13.2 1.0
N A:ASP95 4.3 10.9 1.0
CA A:TYR99 4.3 15.9 1.0
CG A:GLU104 4.3 15.7 1.0
CB A:ASN97 4.3 12.8 1.0
CB A:ASP93 4.3 12.6 1.0
N A:LYS94 4.4 12.4 1.0
OD2 A:ASP93 4.4 12.2 1.0
N A:ILE100 4.4 15.6 1.0
N A:GLY96 4.5 9.1 1.0
CA A:ILE100 4.5 16.0 1.0
CB A:ASP95 4.5 10.6 1.0
N A:SER101 4.6 16.7 1.0
CA A:ASN97 4.6 13.5 1.0
CB A:TYR99 4.7 17.6 1.0
O A:HOH189 4.7 33.3 1.0
N A:GLY98 4.7 12.7 1.0
O A:ASP93 4.7 11.0 1.0
CA A:ASP95 4.8 10.7 1.0
C A:ASP95 4.8 9.9 1.0
C A:ASN97 4.9 12.9 1.0

Calcium binding site 3 out of 4 in 1xa5

Go back to Calcium Binding Sites List in 1xa5
Calcium binding site 3 out of 4 in the Structure of Calmodulin in Complex with Kar-2, A Bis-Indol Alkaloid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Calmodulin in Complex with Kar-2, A Bis-Indol Alkaloid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca152

b:31.6
occ:1.00
OD1 A:ASP129 2.2 19.4 1.0
O A:GLN135 2.3 16.6 1.0
OD1 A:ASP133 2.5 14.7 1.0
O A:HOH168 2.5 29.7 1.0
OE2 A:GLU140 2.5 14.3 1.0
OE1 A:GLU140 2.6 14.1 1.0
OD1 A:ASP131 2.6 19.3 1.0
CD A:GLU140 2.9 13.0 1.0
CG A:ASP129 3.3 19.6 1.0
CG A:ASP133 3.4 14.1 1.0
C A:GLN135 3.4 15.5 1.0
CG A:ASP131 3.6 18.2 1.0
OD2 A:ASP133 3.7 13.4 1.0
OD2 A:ASP131 3.9 17.5 1.0
OD2 A:ASP129 4.0 17.0 1.0
N A:GLN135 4.1 15.2 1.0
N A:ASP133 4.2 14.2 1.0
CA A:ASP129 4.2 19.7 1.0
CB A:ASP129 4.3 19.6 1.0
CA A:GLN135 4.3 16.8 1.0
N A:VAL136 4.3 15.6 1.0
N A:ASP131 4.3 18.0 1.0
N A:GLY132 4.3 17.2 1.0
CA A:VAL136 4.4 14.9 1.0
CG A:GLU140 4.4 12.8 1.0
N A:ASN137 4.5 14.0 1.0
N A:ILE130 4.5 20.4 1.0
CB A:ASP133 4.6 14.2 1.0
C A:ASP129 4.6 19.9 1.0
CB A:GLN135 4.8 19.4 1.0
CB A:ASP131 4.8 18.2 1.0
N A:GLY134 4.8 12.4 1.0
CA A:ASP133 4.8 14.2 1.0
ND2 A:ASN137 4.8 13.9 1.0
CA A:ASP131 4.9 17.7 1.0
C A:ASP131 4.9 17.1 1.0
C A:VAL136 5.0 14.1 1.0

Calcium binding site 4 out of 4 in 1xa5

Go back to Calcium Binding Sites List in 1xa5
Calcium binding site 4 out of 4 in the Structure of Calmodulin in Complex with Kar-2, A Bis-Indol Alkaloid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Calmodulin in Complex with Kar-2, A Bis-Indol Alkaloid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca150

b:36.1
occ:1.00
OD1 A:ASP56 2.3 13.4 1.0
O A:THR62 2.3 15.5 1.0
O A:HOH159 2.4 35.6 1.0
OD1 A:ASP58 2.4 23.0 1.0
OD1 A:ASN60 2.4 17.8 1.0
OE1 A:GLU67 2.4 16.4 1.0
OE2 A:GLU67 2.6 13.2 1.0
CD A:GLU67 2.9 14.2 1.0
CG A:ASN60 3.2 18.4 1.0
CG A:ASP58 3.3 23.2 1.0
OD2 A:ASP58 3.5 24.1 1.0
CG A:ASP56 3.5 15.7 1.0
C A:THR62 3.5 16.9 1.0
O A:HOH183 3.6 52.2 1.0
ND2 A:ASN60 3.7 19.4 1.0
OD2 A:ASP56 4.1 15.0 1.0
N A:ASN60 4.2 20.9 1.0
N A:THR62 4.2 17.5 1.0
N A:ASP64 4.2 15.4 1.0
CA A:ASP56 4.4 18.7 1.0
N A:ILE63 4.4 15.2 1.0
CG A:GLU67 4.4 13.5 1.0
CA A:ILE63 4.4 14.7 1.0
CB A:ASN60 4.4 18.7 1.0
CB A:ASP56 4.5 17.4 1.0
CA A:THR62 4.5 17.1 1.0
N A:GLY59 4.5 22.4 1.0
N A:ASP58 4.5 22.3 1.0
OD2 A:ASP64 4.6 21.7 1.0
OG1 A:THR62 4.6 19.8 1.0
CB A:ASP58 4.6 23.0 1.0
CG A:ASP64 4.6 19.3 1.0
CA A:ASN60 4.7 19.2 1.0
C A:ILE63 4.7 15.5 1.0
N A:ALA57 4.7 19.9 1.0
N A:GLY61 4.7 17.8 1.0
C A:ASP56 4.8 19.1 1.0
O A:HOH177 4.8 38.1 1.0
CB A:ASP64 4.9 17.0 1.0
C A:ASP58 4.9 22.8 1.0
CA A:ASP58 4.9 22.6 1.0
C A:ASN60 4.9 18.1 1.0
OD1 A:ASP64 5.0 21.5 1.0

Reference:

I.Horvath, V.Harmat, A.Perczel, V.Palfi, L.Nyitrai, A.Nagy, E.Hlavanda, G.Naray-Szabo, J.Ovadi. The Structure of the Complex of Calmodulin with Kar-2: A Novel Mode of Binding Explains the Unique Pharmacology of the Drug J.Biol.Chem. V. 280 8266 2005.
ISSN: ISSN 0021-9258
PubMed: 15596444
DOI: 10.1074/JBC.M410353200
Page generated: Sat Dec 12 03:26:41 2020

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