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Calcium in PDB 3if7: Structure of Calmodulin Complexed with Its First Endogenous Inhibitor, Sphingosylphosphorylcholine

Protein crystallography data

The structure of Structure of Calmodulin Complexed with Its First Endogenous Inhibitor, Sphingosylphosphorylcholine, PDB code: 3if7 was solved by E.Kovacs, V.Harmat, J.Toth, B.G.Vertessy, K.Modos, J.Kardos, K.Liliom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.39 / 1.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 39.669, 39.669, 170.340, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 23.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Calmodulin Complexed with Its First Endogenous Inhibitor, Sphingosylphosphorylcholine (pdb code 3if7). 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 Complexed with Its First Endogenous Inhibitor, Sphingosylphosphorylcholine, PDB code: 3if7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3if7

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Calcium binding site 1 out of 4 in the Structure of Calmodulin Complexed with Its First Endogenous Inhibitor, Sphingosylphosphorylcholine


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 Complexed with Its First Endogenous Inhibitor, Sphingosylphosphorylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca149

b:23.2
occ:1.00
 O A:THR26 2.3 26.8 1.0
OD1 A:ASP20 2.3 29.5 1.0
OD1 A:ASP22 2.4 30.5 1.0
OD1 A:ASP24 2.4 32.4 1.0
O A:HOH160 2.4 26.5 1.0
OE1 A:GLU31 2.5 21.8 1.0
OE2 A:GLU31 2.5 27.2 1.0
CD A:GLU31 2.8 28.1 1.0
CG A:ASP24 3.3 34.3 1.0
CG A:ASP22 3.3 34.3 1.0
C A:THR26 3.5 24.7 1.0
CG A:ASP20 3.5 27.9 1.0
OD2 A:ASP22 3.7 38.2 1.0
OD2 A:ASP24 3.9 43.8 1.0
N A:THR26 4.1 25.8 1.0
OG1 A:THR26 4.2 34.4 1.0
N A:ASP24 4.2 34.3 1.0
CA A:ASP20 4.2 25.3 1.0
CG A:GLU31 4.3 22.4 1.0
CB A:ASP24 4.3 34.3 1.0
CB A:ASP20 4.3 24.8 1.0
CA A:THR26 4.4 26.7 1.0
N A:ASP22 4.4 34.9 1.0
OD2 A:ASP20 4.4 27.8 1.0
N A:ILE27 4.4 19.7 1.0
C A:ASP20 4.5 26.6 1.0
CA A:ILE27 4.5 18.0 1.0
CB A:ASP22 4.6 35.7 1.0
O A:HOH171 4.6 28.0 1.0
N A:GLY23 4.6 34.5 1.0
CA A:ASP24 4.7 34.8 1.0
N A:LYS21 4.7 30.1 1.0
CG2 A:THR28 4.8 24.3 1.0
CA A:ASP22 4.8 35.1 1.0
N A:THR28 4.8 20.2 1.0
N A:GLY25 4.8 30.9 1.0
O A:ASP20 4.9 31.5 1.0
C A:ASP22 4.9 35.8 1.0
O A:HOH198 4.9 35.2 1.0
CB A:THR26 4.9 29.0 1.0
C A:ASP24 5.0 33.7 1.0

Calcium binding site 2 out of 4 in 3if7

Go back to Calcium Binding Sites List in 3if7
Calcium binding site 2 out of 4 in the Structure of Calmodulin Complexed with Its First Endogenous Inhibitor, Sphingosylphosphorylcholine


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 Complexed with Its First Endogenous Inhibitor, Sphingosylphosphorylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca150

b:27.3
occ:1.00
 OD1 A:ASP56 2.2 33.0 1.0
O A:THR62 2.2 25.1 1.0
O A:HOH157 2.3 34.8 1.0
OD1 A:ASN60 2.4 35.6 1.0
OD1 A:ASP58 2.4 33.0 1.0
OE1 A:GLU67 2.4 26.1 1.0
OE2 A:GLU67 2.5 28.2 1.0
CD A:GLU67 2.8 30.6 1.0
CG A:ASP58 3.3 42.8 1.0
CG A:ASN60 3.3 35.1 1.0
O A:HOH185 3.4 39.1 1.0
CG A:ASP56 3.4 31.9 1.0
C A:THR62 3.5 24.6 1.0
OD2 A:ASP58 3.6 44.6 1.0
ND2 A:ASN60 3.8 39.7 1.0
OD2 A:ASP56 4.2 34.2 1.0
N A:THR62 4.2 28.2 1.0
N A:ASN60 4.3 37.4 1.0
CG A:GLU67 4.3 26.8 1.0
N A:ILE63 4.4 22.5 1.0
CA A:ILE63 4.4 21.0 1.0
N A:ASP58 4.4 36.2 1.0
CB A:ASP56 4.4 33.1 1.0
N A:ASP64 4.5 23.2 1.0
CB A:ASN60 4.5 36.9 1.0
CA A:ASP56 4.5 31.8 1.0
CA A:THR62 4.5 23.6 1.0
CB A:ASP58 4.5 39.6 1.0
OG1 A:THR62 4.6 29.9 1.0
OD2 A:ASP64 4.6 40.5 1.0
N A:GLY59 4.7 40.6 1.0
CA A:ASN60 4.7 36.8 1.0
C A:ASP56 4.7 34.4 1.0
CA A:ASP58 4.8 38.0 1.0
N A:GLY61 4.8 34.0 1.0
CG A:ASP64 4.8 30.3 1.0
C A:ILE63 4.9 22.8 1.0
N A:ALA57 4.9 33.2 1.0
C A:ASP58 4.9 40.4 1.0
CD1 A:ILE63 4.9 32.2 1.0
C A:ASN60 5.0 36.0 1.0

Calcium binding site 3 out of 4 in 3if7

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Calcium binding site 3 out of 4 in the Structure of Calmodulin Complexed with Its First Endogenous Inhibitor, Sphingosylphosphorylcholine


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 Complexed with Its First Endogenous Inhibitor, Sphingosylphosphorylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca151

b:19.6
occ:1.00
 O A:HOH180 2.2 28.5 1.0
O A:TYR99 2.2 19.1 1.0
OD1 A:ASP93 2.3 23.8 1.0
OD1 A:ASP95 2.4 27.1 1.0
OD1 A:ASN97 2.4 20.3 1.0
OE1 A:GLU104 2.4 22.4 1.0
OE2 A:GLU104 2.5 25.9 1.0
CD A:GLU104 2.8 27.3 1.0
CG A:ASP95 3.3 35.4 1.0
CG A:ASN97 3.4 19.9 1.0
CG A:ASP93 3.5 22.6 1.0
C A:TYR99 3.5 16.5 1.0
OD2 A:ASP95 3.7 36.6 1.0
ND2 A:ASN97 4.0 23.0 1.0
N A:TYR99 4.2 16.8 1.0
N A:ASN97 4.2 21.9 1.0
CA A:ASP93 4.3 22.7 1.0
CG A:GLU104 4.3 20.0 1.0
CA A:TYR99 4.3 17.1 1.0
CB A:ASP93 4.3 22.7 1.0
N A:ILE100 4.4 15.5 1.0
OD2 A:ASP93 4.4 22.2 1.0
N A:ASP95 4.4 30.8 1.0
CB A:ASN97 4.5 20.8 1.0
CA A:ILE100 4.5 16.8 1.0
C A:ASP93 4.5 23.5 1.0
CB A:ASP95 4.5 31.2 1.0
N A:SER101 4.6 18.6 1.0
CB A:TYR99 4.7 15.6 1.0
N A:GLY96 4.7 23.9 1.0
CA A:ASN97 4.8 19.4 1.0
O A:HOH182 4.8 29.5 1.0
N A:LYS94 4.8 26.9 1.0
CA A:ASP95 4.8 30.2 1.0
N A:GLY98 4.8 19.5 1.0
C A:ASP95 5.0 28.1 1.0
C A:ASN97 5.0 18.7 1.0

Calcium binding site 4 out of 4 in 3if7

Go back to Calcium Binding Sites List in 3if7
Calcium binding site 4 out of 4 in the Structure of Calmodulin Complexed with Its First Endogenous Inhibitor, Sphingosylphosphorylcholine


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 Complexed with Its First Endogenous Inhibitor, Sphingosylphosphorylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca152

b:16.1
occ:1.00
 O A:GLN135 2.3 17.2 1.0
OD1 A:ASP131 2.3 20.5 1.0
OD1 A:ASP133 2.3 20.2 1.0
O A:HOH158 2.3 21.0 1.0
OD1 A:ASP129 2.4 18.5 1.0
OE1 A:GLU140 2.4 17.8 1.0
OE2 A:GLU140 2.5 18.1 1.0
CD A:GLU140 2.9 20.2 1.0
CG A:ASP131 3.2 23.8 1.0
CG A:ASP133 3.2 20.4 1.0
CG A:ASP129 3.4 18.2 1.0
OD2 A:ASP131 3.4 26.5 1.0
C A:GLN135 3.5 16.4 1.0
OD2 A:ASP133 3.7 21.9 1.0
OD2 A:ASP129 4.1 20.1 1.0
N A:ASP133 4.2 17.6 1.0
N A:GLN135 4.2 17.4 1.0
N A:ASP131 4.2 18.6 1.0
N A:VAL136 4.3 16.9 1.0
CA A:ASP129 4.3 21.0 1.0
CB A:ASP133 4.3 18.4 1.0
CG A:GLU140 4.3 19.9 1.0
CA A:VAL136 4.3 17.2 1.0
CB A:ASP129 4.3 18.4 1.0
N A:ILE130 4.4 18.1 1.0
N A:GLY132 4.4 18.5 1.0
CA A:GLN135 4.4 15.6 1.0
N A:ASN137 4.5 16.6 1.0
CB A:ASP131 4.5 19.9 1.0
CA A:ASP133 4.6 17.2 1.0
N A:GLY134 4.7 17.3 1.0
CA A:ASP131 4.7 18.8 1.0
C A:VAL136 4.9 18.8 1.0
C A:ASP129 4.9 20.2 1.0
C A:ASP131 4.9 19.1 1.0
C A:ASP133 4.9 18.4 1.0
CB A:GLN135 5.0 17.2 1.0
ND2 A:ASN137 5.0 23.6 1.0

Reference:

E.Kovacs, V.Harmat, J.Toth, B.G.Vertessy, K.Modos, J.Kardos, K.Liliom. Structure and Mechanism of Calmodulin Binding to A Signaling Sphingolipid Reveal New Aspects of Lipid-Protein Interactions Faseb J. V. 24 3829 2010.
ISSN: ISSN 0892-6638
PubMed: 20522785
DOI: 10.1096/FJ.10-155614
Page generated: Sat Jul 13 11:30:36 2024

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