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Calcium in PDB 2aao: Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana

Protein crystallography data

The structure of Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana, PDB code: 2aao was solved by V.Chandran, E.J.Stollar, K.Lindorff-Larsen, J.F.Harper, W.J.Chazin, C.M.Dobson, B.F.Luisi, J.Christodoulou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.70 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 35.968, 88.154, 117.552, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 25.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana (pdb code 2aao). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana, PDB code: 2aao:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 2aao

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Calcium binding site 1 out of 9 in the Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca293

b:26.1
occ:1.00
 O A:GLN43 2.2 5.5 1.0
O A:HOH298 2.3 36.8 1.0
OD1 A:ASP37 2.3 6.7 1.0
OD1 A:ASP39 2.4 13.3 1.0
OE2 A:GLU48 2.5 3.9 1.0
OG A:SER41 2.5 4.4 1.0
OE1 A:GLU48 2.6 6.6 1.0
CD A:GLU48 2.9 4.3 1.0
CG A:ASP39 3.3 13.4 1.0
C A:GLN43 3.4 5.5 1.0
CG A:ASP37 3.5 7.5 1.0
OD2 A:ASP39 3.5 12.1 1.0
CB A:SER41 3.6 5.0 1.0
N A:SER41 4.1 6.3 1.0
O A:HOH300 4.1 29.1 1.0
N A:GLN43 4.2 4.4 1.0
CA A:ASP37 4.3 5.1 1.0
OD2 A:ASP37 4.3 5.9 1.0
N A:ILE44 4.3 3.3 1.0
CA A:ILE44 4.3 4.4 1.0
CA A:SER41 4.4 5.2 1.0
CB A:ASP37 4.4 6.0 1.0
CG A:GLU48 4.4 3.2 1.0
CA A:GLN43 4.4 5.6 1.0
C A:ASP37 4.5 6.9 1.0
N A:ASP39 4.6 10.4 1.0
CB A:ASP39 4.7 12.7 1.0
N A:THR45 4.7 4.1 1.0
N A:GLY42 4.8 3.8 1.0
C A:SER41 4.8 3.7 1.0
N A:ALA38 4.8 9.0 1.0
N A:LYS40 4.8 10.1 1.0
O A:HOH346 4.9 48.8 1.0
CG2 A:THR45 4.9 5.9 1.0
O A:ASP37 5.0 5.3 1.0
CA A:ASP39 5.0 11.0 1.0
C A:ILE44 5.0 2.9 1.0
CB A:GLN43 5.0 6.3 1.0

Calcium binding site 2 out of 9 in 2aao

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Calcium binding site 2 out of 9 in the Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca294

b:31.3
occ:1.00
 OD2 A:ASP75 2.2 15.0 1.0
OD2 A:ASP73 2.3 12.0 1.0
O A:THR79 2.3 9.4 1.0
OE2 A:GLU84 2.4 10.8 1.0
OG A:SER77 2.4 9.9 1.0
OE1 A:GLU84 2.4 9.6 1.0
O A:HOH305 2.5 43.4 1.0
CD A:GLU84 2.8 8.7 1.0
CG A:ASP75 3.2 16.5 1.0
CB A:SER77 3.3 11.8 1.0
CG A:ASP73 3.4 15.0 1.0
C A:THR79 3.5 10.2 1.0
OD1 A:ASP75 3.6 18.7 1.0
N A:SER77 3.9 12.3 1.0
CA A:ASP73 4.0 15.0 1.0
CB A:ASP73 4.1 14.3 1.0
CA A:SER77 4.2 11.7 1.0
OG1 A:THR79 4.2 13.3 1.0
OD1 A:ASP73 4.3 12.3 1.0
N A:THR79 4.3 10.3 1.0
CG A:GLU84 4.3 8.5 1.0
CA A:ILE80 4.4 9.2 1.0
N A:ILE80 4.4 9.7 1.0
C A:ASP73 4.4 16.0 1.0
N A:ASP81 4.4 8.4 1.0
CA A:THR79 4.5 12.1 1.0
N A:ASP75 4.5 16.3 1.0
CB A:ASP75 4.5 16.9 1.0
N A:VAL74 4.7 16.7 1.0
N A:ASN76 4.7 16.4 1.0
N A:GLY78 4.8 10.9 1.0
C A:ASP75 4.8 15.5 1.0
CA A:ASP75 4.9 16.6 1.0
C A:SER77 4.9 11.6 1.0
C A:ILE80 4.9 8.5 1.0
OD2 A:ASP81 4.9 15.5 1.0
O A:ASP73 4.9 14.0 1.0
CB A:THR79 5.0 13.1 1.0
CG A:ASP81 5.0 11.4 1.0

Calcium binding site 3 out of 9 in 2aao

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Calcium binding site 3 out of 9 in the Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca295

b:40.5
occ:1.00
 OG A:SER113 2.1 18.9 1.0
O A:TYR115 2.3 17.2 1.0
OE2 A:GLU120 2.4 16.9 1.0
OD1 A:ASP111 2.4 22.2 1.0
OD2 A:ASP109 2.4 17.6 1.0
O A:HOH309 2.4 40.5 1.0
OE1 A:GLU120 2.6 16.7 1.0
CD A:GLU120 2.8 17.9 1.0
CG A:ASP111 3.3 22.6 1.0
CB A:SER113 3.3 19.6 1.0
C A:TYR115 3.5 17.1 1.0
OD2 A:ASP111 3.5 23.1 1.0
CG A:ASP109 3.5 18.3 1.0
N A:SER113 3.9 20.7 1.0
N A:TYR115 4.2 15.5 1.0
CA A:SER113 4.2 19.7 1.0
CA A:ASP109 4.2 18.5 1.0
CG A:GLU120 4.3 18.8 1.0
OD1 A:ASP109 4.4 17.5 1.0
N A:ASP111 4.4 23.6 1.0
N A:ILE116 4.4 15.2 1.0
CA A:ILE116 4.4 16.0 1.0
CB A:ASP109 4.4 17.4 1.0
CA A:TYR115 4.4 16.9 1.0
C A:ASP109 4.4 19.4 1.0
O A:HOH314 4.5 32.3 1.0
CB A:ASP111 4.6 23.2 1.0
N A:THR117 4.6 15.8 1.0
N A:GLY114 4.6 16.1 1.0
CG2 A:THR117 4.7 18.0 1.0
N A:LYS110 4.7 21.6 1.0
C A:SER113 4.7 18.3 1.0
N A:GLY112 4.8 22.4 1.0
O A:ASP109 4.8 18.3 1.0
CA A:ASP111 4.8 23.1 1.0
OG1 A:THR117 4.9 16.4 1.0
C A:ILE116 4.9 15.8 1.0
C A:ASP111 5.0 23.5 1.0
CB A:TYR115 5.0 16.9 1.0

Calcium binding site 4 out of 9 in 2aao

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Calcium binding site 4 out of 9 in the Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca296

b:40.7
occ:1.00
 O A:ARG149 2.2 20.2 1.0
OD1 A:ASP147 2.3 18.5 1.0
OD2 A:ASP143 2.3 26.3 1.0
OD1 A:ASP145 2.4 27.5 1.0
O A:HOH310 2.4 45.1 1.0
OE2 A:GLU154 2.5 17.5 1.0
OE1 A:GLU154 2.6 17.4 1.0
CD A:GLU154 2.9 18.1 1.0
CG A:ASP143 3.3 27.1 1.0
CG A:ASP147 3.3 19.1 1.0
C A:ARG149 3.4 22.4 1.0
CG A:ASP145 3.4 28.4 1.0
OD2 A:ASP145 3.7 30.4 1.0
OD2 A:ASP147 3.7 18.7 1.0
OD1 A:ASP143 3.9 24.7 1.0
CB A:ASP143 4.1 27.3 1.0
N A:ARG149 4.2 22.9 1.0
CA A:ASP143 4.2 28.0 1.0
N A:ASP147 4.2 19.8 1.0
N A:ILE150 4.2 20.2 1.0
CA A:ARG149 4.3 23.7 1.0
CA A:ILE150 4.3 19.5 1.0
N A:ASP145 4.3 26.4 1.0
CG A:GLU154 4.4 17.7 1.0
N A:ASP151 4.4 18.9 1.0
CB A:ASP147 4.5 19.4 1.0
C A:ASP143 4.5 28.1 1.0
N A:ASN146 4.6 24.1 1.0
CB A:ASP145 4.6 27.4 1.0
CB A:ARG149 4.6 25.1 1.0
N A:GLN144 4.7 28.0 1.0
CA A:ASP147 4.8 19.9 1.0
CA A:ASP145 4.8 26.4 1.0
C A:ILE150 4.8 19.9 1.0
C A:ASP145 4.8 25.4 1.0
N A:GLY148 4.9 20.3 1.0
OD1 A:ASP151 4.9 24.9 1.0

Calcium binding site 5 out of 9 in 2aao

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Calcium binding site 5 out of 9 in the Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca297

b:29.8
occ:1.00
 OD2 B:ASP37 2.3 7.3 1.0
O B:GLN43 2.3 7.2 1.0
O B:HOH305 2.3 30.4 1.0
OD1 B:ASP39 2.3 9.8 1.0
OE2 B:GLU48 2.5 9.8 1.0
OG B:SER41 2.5 8.6 1.0
OE1 B:GLU48 2.6 7.5 1.0
CD B:GLU48 2.9 8.7 1.0
CG B:ASP39 3.3 12.0 1.0
CG B:ASP37 3.5 7.3 1.0
OD2 B:ASP39 3.5 12.1 1.0
CB B:SER41 3.5 10.1 1.0
C B:GLN43 3.6 7.5 1.0
N B:SER41 3.9 9.4 1.0
OD1 B:ASP37 4.2 6.2 1.0
CA B:SER41 4.2 9.6 1.0
N B:GLN43 4.2 5.2 1.0
N B:ILE44 4.4 5.7 1.0
CA B:ILE44 4.4 5.6 1.0
CG B:GLU48 4.4 6.9 1.0
CA B:ASP37 4.4 7.4 1.0
CB B:ASP37 4.5 7.2 1.0
CA B:GLN43 4.5 6.4 1.0
N B:ASP39 4.5 11.5 1.0
CB B:ASP39 4.6 12.0 1.0
C B:ASP37 4.6 8.0 1.0
N B:GLY42 4.7 9.1 1.0
N B:LYS40 4.7 13.5 1.0
N B:THR45 4.7 5.8 1.0
C B:SER41 4.8 8.5 1.0
N B:ALA38 4.9 11.1 1.0
CG2 B:THR45 4.9 9.0 1.0
CA B:ASP39 4.9 11.6 1.0
C B:ASP39 5.0 11.9 1.0
O B:HOH356 5.0 48.2 1.0

Calcium binding site 6 out of 9 in 2aao

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Calcium binding site 6 out of 9 in the Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca298

b:26.9
occ:1.00
 OD2 B:ASP75 2.3 5.1 1.0
OD2 B:ASP73 2.3 2.9 1.0
O B:HOH312 2.3 32.6 1.0
O B:THR79 2.4 8.9 1.0
OE1 B:GLU84 2.4 7.2 1.0
OG B:SER77 2.5 11.8 1.0
OE2 B:GLU84 2.5 4.3 1.0
CD B:GLU84 2.8 5.7 1.0
CG B:ASP75 3.2 7.0 1.0
CG B:ASP73 3.4 8.4 1.0
CB B:SER77 3.5 10.8 1.0
C B:THR79 3.6 9.7 1.0
OD1 B:ASP75 3.6 8.3 1.0
N B:SER77 3.9 7.8 1.0
CA B:ASP73 4.1 7.8 1.0
OG1 B:THR79 4.2 9.4 1.0
CB B:ASP73 4.2 8.5 1.0
CA B:SER77 4.2 8.7 1.0
N B:THR79 4.3 10.9 1.0
OD1 B:ASP73 4.3 5.0 1.0
N B:ASP75 4.3 6.9 1.0
CG B:GLU84 4.3 6.2 1.0
C B:ASP73 4.4 8.9 1.0
CA B:ILE80 4.4 6.0 1.0
N B:ILE80 4.5 6.4 1.0
CB B:ASP75 4.5 8.0 1.0
CA B:THR79 4.5 11.3 1.0
OE1 B:GLN43 4.5 14.8 1.0
N B:ASP81 4.6 5.5 1.0
OD2 B:ASP81 4.6 10.7 1.0
N B:VAL74 4.6 9.0 1.0
N B:ASN76 4.6 5.5 1.0
O B:HOH303 4.7 29.6 1.0
CA B:ASP75 4.8 7.4 1.0
C B:SER77 4.8 10.0 1.0
N B:GLY78 4.8 8.7 1.0
C B:ASP75 4.8 6.9 1.0
O B:ASP73 4.9 9.1 1.0
CB B:THR79 5.0 10.9 1.0

Calcium binding site 7 out of 9 in 2aao

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Calcium binding site 7 out of 9 in the Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca299

b:38.2
occ:1.00
 O B:TYR115 2.3 18.3 1.0
OD2 B:ASP109 2.3 11.3 1.0
OE2 B:GLU120 2.3 17.6 1.0
OG B:SER113 2.3 15.6 1.0
OE1 B:GLU120 2.5 18.7 1.0
CD B:GLU120 2.7 18.1 1.0
CB B:ASP111 3.2 27.4 1.0
C B:TYR115 3.5 17.0 1.0
CB B:SER113 3.5 17.9 1.0
CG B:ASP109 3.5 14.9 1.0
OD2 B:ASP111 3.7 29.4 1.0
CG B:ASP111 3.9 28.2 1.0
N B:SER113 4.0 18.7 1.0
N B:ASP111 4.1 24.8 1.0
CA B:ASP109 4.1 16.6 1.0
CG B:GLU120 4.2 20.2 1.0
CA B:ASP111 4.2 26.2 1.0
N B:TYR115 4.3 18.1 1.0
CA B:SER113 4.3 17.6 1.0
CB B:ASP109 4.3 14.4 1.0
OD1 B:ASP109 4.3 13.7 1.0
C B:ASP109 4.4 19.0 1.0
N B:ILE116 4.4 16.5 1.0
CA B:TYR115 4.4 17.3 1.0
CA B:ILE116 4.4 17.5 1.0
N B:GLY112 4.4 22.4 1.0
CG2 B:THR117 4.7 19.8 1.0
N B:LYS110 4.7 20.7 1.0
N B:THR117 4.7 17.6 1.0
O B:ASP109 4.8 17.5 1.0
N B:GLY114 4.8 16.7 1.0
CB B:TYR115 4.9 17.2 1.0
OG1 B:THR117 4.9 21.4 1.0
C B:ASP111 4.9 24.8 1.0
C B:SER113 4.9 17.9 1.0
C B:ILE116 5.0 16.4 1.0

Calcium binding site 8 out of 9 in 2aao

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Calcium binding site 8 out of 9 in the Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca300

b:40.2
occ:1.00
 OD1 B:ASP145 1.9 32.2 1.0
O B:ARG149 2.1 16.1 1.0
OD2 B:ASP143 2.2 21.2 1.0
O B:HOH316 2.3 43.6 1.0
OE2 B:GLU154 2.4 19.3 1.0
OD1 B:ASP147 2.5 16.5 1.0
OE1 B:GLU154 2.6 18.1 1.0
CD B:GLU154 2.8 18.5 1.0
CG B:ASP145 3.0 29.4 1.0
CG B:ASP143 3.3 22.4 1.0
C B:ARG149 3.4 17.1 1.0
CG B:ASP147 3.4 16.7 1.0
OD2 B:ASP145 3.4 32.4 1.0
OD2 B:ASP147 3.7 15.2 1.0
OD1 B:ASP143 4.1 20.7 1.0
N B:ARG149 4.2 16.3 1.0
CA B:ASP143 4.2 24.0 1.0
CB B:ASP143 4.2 23.6 1.0
N B:ILE150 4.3 15.8 1.0
CB B:ASP145 4.3 28.8 1.0
N B:ASP145 4.3 27.3 1.0
CA B:ARG149 4.3 16.7 1.0
CA B:ILE150 4.3 16.1 1.0
N B:ASP147 4.3 17.9 1.0
CG B:GLU154 4.4 17.9 1.0
O B:HOH348 4.4 50.6 1.0
N B:ASP151 4.4 16.9 1.0
CB B:ASP147 4.6 17.5 1.0
C B:ASP143 4.6 25.0 1.0
CG B:ARG149 4.6 19.1 1.0
CA B:ASP145 4.7 27.3 1.0
N B:ASN146 4.7 22.6 1.0
N B:GLN144 4.7 26.1 1.0
OD1 B:ASP151 4.8 26.0 1.0
C B:ASP145 4.9 25.4 1.0
CA B:ASP147 4.9 17.7 1.0
C B:ILE150 4.9 17.2 1.0
CB B:ARG149 5.0 18.1 1.0
N B:GLY148 5.0 15.4 1.0

Calcium binding site 9 out of 9 in 2aao

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Calcium binding site 9 out of 9 in the Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Regulatory Apparatus of Calcium Dependent Protein Kinase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:55.4
occ:1.00
 O B:HOH311 2.4 28.9 1.0
OD1 B:ASN76 2.4 7.1 1.0
O B:HOH343 3.2 44.4 1.0
CG B:ASN76 3.5 8.4 1.0
ND2 B:ASN76 4.0 10.4 1.0
O B:GLN70 4.3 9.4 1.0
O B:ASP73 4.5 9.1 1.0
CB B:ASN76 4.8 7.3 1.0
CG B:GLN70 4.8 17.9 1.0

Reference:

V.Chandran, E.J.Stollar, K.Lindorff-Larsen, J.F.Harper, W.J.Chazin, C.M.Dobson, B.F.Luisi, J.Christodoulou. Structure of the Regulatory Apparatus of A Calcium-Dependent Protein Kinase (Cdpk): A Novel Mode of Calmodulin-Target Recognition. J.Mol.Biol. V. 357 400 2006.
ISSN: ISSN 0022-2836
PubMed: 16430916
DOI: 10.1016/J.JMB.2005.11.093
Page generated: Fri Jul 12 08:38:32 2024

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