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Calcium in PDB 2bcx: Crystal Structure of Calmodulin in Complex with A Ryanodine Receptor Peptide

Protein crystallography data

The structure of Crystal Structure of Calmodulin in Complex with A Ryanodine Receptor Peptide, PDB code: 2bcx was solved by A.A.Maximciuc, Y.Shamoo, K.R.Mackenzie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.99 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.100, 44.100, 90.300, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 24.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Calmodulin in Complex with A Ryanodine Receptor Peptide (pdb code 2bcx). 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 Calmodulin in Complex with A Ryanodine Receptor Peptide, PDB code: 2bcx:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2bcx

Go back to Calcium Binding Sites List in 2bcx
Calcium binding site 1 out of 4 in the Crystal Structure of Calmodulin in Complex with A Ryanodine Receptor Peptide


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 Calmodulin in Complex with A Ryanodine Receptor Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca149

b:15.9
occ:1.00
 OD1 A:ASP20 2.2 14.1 1.0
OD1 A:ASP22 2.3 15.4 1.0
O A:THR26 2.4 15.0 1.0
OD1 A:ASP24 2.4 18.3 1.0
OE2 A:GLU31 2.5 17.9 1.0
O A:HOH171 2.5 20.4 1.0
OE1 A:GLU31 2.6 20.3 1.0
CD A:GLU31 2.9 17.8 1.0
CG A:ASP22 3.2 18.2 1.0
CG A:ASP24 3.4 21.6 1.0
CG A:ASP20 3.4 16.2 1.0
C A:THR26 3.5 15.8 1.0
OD2 A:ASP22 3.5 17.9 1.0
OG1 A:THR26 3.7 21.0 1.0
OD2 A:ASP24 4.0 21.2 1.0
N A:THR26 4.1 16.3 1.0
OD2 A:ASP20 4.2 13.5 1.0
N A:ASP24 4.2 20.1 1.0
N A:ASP22 4.3 17.9 1.0
CA A:ASP20 4.3 16.6 1.0
CA A:THR26 4.3 17.4 1.0
CB A:ASP24 4.3 21.5 1.0
CG A:GLU31 4.4 17.4 1.0
CB A:ASP20 4.4 17.4 1.0
N A:ILE27 4.5 14.7 1.0
CB A:ASP22 4.5 17.1 1.0
C A:ASP20 4.6 17.1 1.0
N A:LYS21 4.6 16.3 1.0
CA A:ILE27 4.6 14.5 1.0
N A:GLY23 4.6 18.7 1.0
CB A:THR26 4.6 19.6 1.0
CA A:ASP24 4.6 20.8 1.0
O A:HOH180 4.7 32.2 1.0
N A:GLY25 4.8 19.9 1.0
O A:HOH199 4.8 23.7 1.0
CA A:ASP22 4.8 19.7 1.0
N A:THR28 4.9 15.8 1.0
O A:HOH223 4.9 39.1 1.0
C A:ASP24 4.9 20.6 1.0
CG2 A:THR28 5.0 15.7 1.0
C A:ASP22 5.0 20.2 1.0

Calcium binding site 2 out of 4 in 2bcx

Go back to Calcium Binding Sites List in 2bcx
Calcium binding site 2 out of 4 in the Crystal Structure of Calmodulin in Complex with A Ryanodine Receptor Peptide


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 Calmodulin in Complex with A Ryanodine Receptor Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca150

b:19.2
occ:1.00
 OD1 A:ASP56 2.1 22.3 1.0
OD1 A:ASN60 2.3 26.0 1.0
O A:THR62 2.4 18.4 1.0
OD1 A:ASP58 2.4 24.5 1.0
OE2 A:GLU67 2.5 16.6 1.0
OE1 A:GLU67 2.5 17.7 1.0
CD A:GLU67 2.8 18.1 1.0
CG A:ASP58 3.3 26.8 1.0
CG A:ASP56 3.3 23.1 1.0
CG A:ASN60 3.3 27.3 1.0
OD2 A:ASP58 3.6 24.1 1.0
C A:THR62 3.6 21.0 1.0
ND2 A:ASN60 4.0 27.0 1.0
OD2 A:ASP56 4.0 25.5 1.0
N A:ASN60 4.0 27.1 1.0
N A:THR62 4.3 23.3 1.0
CA A:ASP56 4.3 22.8 1.0
OD2 A:ASP64 4.3 22.0 1.0
CB A:ASP56 4.3 23.9 1.0
CG A:GLU67 4.3 16.9 1.0
N A:GLY59 4.3 28.5 1.0
CA A:ILE63 4.4 17.2 1.0
N A:ASP58 4.4 27.0 1.0
CB A:ASN60 4.4 27.0 1.0
N A:ILE63 4.5 17.5 1.0
N A:ASP64 4.5 20.3 1.0
C A:ASP56 4.5 24.4 1.0
CB A:ASP58 4.5 26.8 1.0
CA A:THR62 4.6 21.5 1.0
N A:GLY61 4.6 26.7 1.0
CA A:ASN60 4.7 27.2 1.0
OG1 A:THR62 4.7 21.4 1.0
CG A:ASP64 4.7 21.6 1.0
N A:ALA57 4.8 24.4 1.0
CA A:ASP58 4.8 27.8 1.0
C A:ASP58 4.9 28.0 1.0
C A:ASN60 4.9 27.1 1.0
C A:ILE63 4.9 17.6 1.0
C A:GLY59 5.0 28.1 1.0

Calcium binding site 3 out of 4 in 2bcx

Go back to Calcium Binding Sites List in 2bcx
Calcium binding site 3 out of 4 in the Crystal Structure of Calmodulin in Complex with A Ryanodine Receptor Peptide


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 Calmodulin in Complex with A Ryanodine Receptor Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca151

b:15.6
occ:1.00
 OD1 A:ASP93 2.2 18.2 1.0
O A:TYR99 2.3 16.6 1.0
OD1 A:ASP95 2.3 16.8 1.0
O A:HOH160 2.4 16.1 1.0
OE2 A:GLU104 2.4 12.2 1.0
OE1 A:GLU104 2.5 14.7 1.0
OD1 A:ASN97 2.6 15.1 1.0
CD A:GLU104 2.8 13.1 1.0
CG A:ASP95 3.3 18.6 1.0
CG A:ASP93 3.4 16.5 1.0
CG A:ASN97 3.4 13.9 1.0
C A:TYR99 3.5 14.0 1.0
OD2 A:ASP95 3.7 18.3 1.0
ND2 A:ASN97 3.9 12.3 1.0
CA A:ASP93 4.1 15.6 1.0
N A:TYR99 4.2 14.7 1.0
CB A:ASP93 4.2 15.5 1.0
O A:HOH193 4.2 27.4 1.0
CG A:GLU104 4.3 12.8 1.0
N A:ASP95 4.3 19.9 1.0
OD2 A:ASP93 4.3 15.6 1.0
N A:ASN97 4.3 19.7 1.0
CA A:TYR99 4.4 15.0 1.0
C A:ASP93 4.4 16.0 1.0
N A:ILE100 4.4 13.0 1.0
CA A:ILE100 4.5 12.8 1.0
CB A:ASP95 4.5 18.8 1.0
N A:GLY96 4.5 19.5 1.0
CB A:ASN97 4.6 16.9 1.0
N A:SER101 4.6 13.4 1.0
OE1 A:GLN135 4.6 15.8 1.0
CA A:ASP95 4.7 20.3 1.0
CB A:TYR99 4.8 14.8 1.0
N A:LYS94 4.8 18.0 1.0
C A:ASP95 4.8 20.1 1.0
O A:ASP93 4.9 16.0 1.0
CA A:ASN97 4.9 18.0 1.0
N A:GLY98 4.9 17.5 1.0

Calcium binding site 4 out of 4 in 2bcx

Go back to Calcium Binding Sites List in 2bcx
Calcium binding site 4 out of 4 in the Crystal Structure of Calmodulin in Complex with A Ryanodine Receptor Peptide


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 Calmodulin in Complex with A Ryanodine Receptor Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca152

b:15.8
occ:1.00
 OD1 A:ASP129 2.2 15.2 1.0
OD1 A:ASP131 2.4 15.8 1.0
O A:GLN135 2.4 13.5 1.0
O A:HOH154 2.4 11.0 1.0
OD1 A:ASP133 2.4 14.1 1.0
OE1 A:GLU140 2.5 17.2 1.0
OE2 A:GLU140 2.6 14.1 1.0
CD A:GLU140 2.9 15.3 1.0
CG A:ASP133 3.2 16.7 1.0
CG A:ASP131 3.2 18.8 1.0
CG A:ASP129 3.3 16.6 1.0
OD2 A:ASP131 3.6 19.6 1.0
C A:GLN135 3.6 12.7 1.0
OD2 A:ASP133 3.6 17.9 1.0
N A:ASP133 4.0 20.5 1.0
OD2 A:ASP129 4.1 14.9 1.0
CA A:ASP129 4.1 16.9 1.0
CB A:ASP129 4.2 16.5 1.0
N A:GLN135 4.2 12.4 1.0
CB A:ASP133 4.3 16.2 1.0
N A:ASP131 4.3 20.2 1.0
N A:GLY132 4.4 22.5 1.0
CA A:VAL136 4.4 10.0 1.0
N A:ASN137 4.4 11.6 1.0
CG A:GLU140 4.4 15.0 1.0
N A:VAL136 4.4 12.2 1.0
C A:ASP129 4.4 19.5 1.0
CB A:ASP131 4.5 20.0 1.0
N A:ILE130 4.5 20.2 1.0
CA A:GLN135 4.5 13.2 1.0
CA A:ASP133 4.6 18.1 1.0
N A:GLY134 4.6 15.5 1.0
CA A:ASP131 4.7 22.2 1.0
C A:ASP131 4.8 22.8 1.0
C A:VAL136 4.9 10.2 1.0
C A:ASP133 4.9 17.7 1.0
CG A:ASN137 4.9 13.7 1.0
ND2 A:ASN137 5.0 15.0 1.0

Reference:

A.A.Maximciuc, J.A.Putkey, Y.Shamoo, K.R.Mackenzie. Complex of Calmodulin with A Ryanodine Receptor Target Reveals A Novel, Flexible Binding Mode. Structure V. 14 1547 2006.
ISSN: ISSN 0969-2126
PubMed: 17027503
DOI: 10.1016/J.STR.2006.08.011
Page generated: Fri Jul 12 08:58:52 2024

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