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Calcium in PDB 2wel: Crystal Structure of SU6656-Bound Calcium/Calmodulin-Dependent Protein Kinase II Delta in Complex with Calmodulin

Enzymatic activity of Crystal Structure of SU6656-Bound Calcium/Calmodulin-Dependent Protein Kinase II Delta in Complex with Calmodulin

All present enzymatic activity of Crystal Structure of SU6656-Bound Calcium/Calmodulin-Dependent Protein Kinase II Delta in Complex with Calmodulin:
2.7.11.17;

Protein crystallography data

The structure of Crystal Structure of SU6656-Bound Calcium/Calmodulin-Dependent Protein Kinase II Delta in Complex with Calmodulin, PDB code: 2wel was solved by A.C.W.Pike, P.Rellos, E.Salah, N.Burgess-Brown, T.Keates, J.Muniz, R.Sethi, A.Roos, P.Filippakopoulos, F.Von Delft, A.Edwards, J.Weigelt, C.H.Arrowsmith, C.Bountra, S.Knapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.34 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.260, 68.850, 121.980, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of SU6656-Bound Calcium/Calmodulin-Dependent Protein Kinase II Delta in Complex with Calmodulin (pdb code 2wel). 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 SU6656-Bound Calcium/Calmodulin-Dependent Protein Kinase II Delta in Complex with Calmodulin, PDB code: 2wel:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2wel

Go back to Calcium Binding Sites List in 2wel
Calcium binding site 1 out of 4 in the Crystal Structure of SU6656-Bound Calcium/Calmodulin-Dependent Protein Kinase II Delta in Complex with Calmodulin


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 SU6656-Bound Calcium/Calmodulin-Dependent Protein Kinase II Delta in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca600

b:30.7
occ:1.00
 OD1 D:ASP21 2.2 14.5 1.0
OD2 D:ASP23 2.3 18.0 1.0
O D:THR27 2.3 16.4 1.0
O D:HOH2019 2.4 16.6 1.0
OD1 D:ASP25 2.5 12.6 1.0
OE1 D:GLU32 2.6 13.7 1.0
OE2 D:GLU32 2.6 17.7 1.0
CD D:GLU32 2.9 10.7 1.0
CG D:ASP23 3.3 26.7 1.0
CG D:ASP25 3.3 29.3 1.0
CG D:ASP21 3.4 13.6 1.0
C D:THR27 3.5 16.7 1.0
OD1 D:ASP23 3.7 32.4 1.0
OD2 D:ASP25 3.7 25.1 1.0
OG1 D:THR27 4.1 24.8 1.0
CA D:ASP21 4.2 15.0 1.0
OD2 D:ASP21 4.2 23.7 1.0
CB D:ASP21 4.2 12.6 1.0
N D:THR27 4.2 15.8 1.0
N D:ASP25 4.3 18.8 1.0
N D:ASP23 4.3 18.0 1.0
CG D:GLU32 4.4 10.5 1.0
CA D:THR27 4.4 15.8 1.0
N D:ILE28 4.4 15.8 1.0
CB D:ASP25 4.4 19.1 1.0
C D:ASP21 4.5 19.5 1.0
CA D:ILE28 4.5 11.5 1.0
CB D:ASP23 4.6 18.0 1.0
O D:HOH2030 4.6 23.1 1.0
N D:LYS22 4.6 19.0 1.0
N D:GLY24 4.6 20.1 1.0
CG2 D:THR29 4.8 13.4 1.0
CA D:ASP25 4.8 18.1 1.0
CA D:ASP23 4.8 19.5 1.0
N D:THR29 4.8 12.8 1.0
N D:GLY26 4.9 14.9 1.0
C D:ASP23 4.9 19.0 1.0
CB D:THR27 4.9 22.5 1.0
O D:ASP21 5.0 20.9 1.0

Calcium binding site 2 out of 4 in 2wel

Go back to Calcium Binding Sites List in 2wel
Calcium binding site 2 out of 4 in the Crystal Structure of SU6656-Bound Calcium/Calmodulin-Dependent Protein Kinase II Delta in Complex with Calmodulin


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 SU6656-Bound Calcium/Calmodulin-Dependent Protein Kinase II Delta in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:39.0
occ:1.00
 O D:HOH2053 2.1 40.1 1.0
OD1 D:ASP57 2.2 14.0 1.0
OD1 D:ASN61 2.4 13.0 1.0
O D:THR63 2.4 13.3 1.0
OE1 D:GLU68 2.5 13.2 1.0
OD1 D:ASP59 2.5 11.1 1.0
OE2 D:GLU68 2.7 15.5 1.0
CD D:GLU68 3.0 19.7 1.0
CG D:ASN61 3.2 26.2 1.0
CG D:ASP57 3.3 20.0 1.0
CG D:ASP59 3.4 28.7 1.0
ND2 D:ASN61 3.6 12.8 1.0
C D:THR63 3.6 17.7 1.0
OD2 D:ASP59 3.7 27.2 1.0
OD2 D:ASP57 3.9 15.6 1.0
N D:THR63 4.3 16.8 1.0
CB D:ASP57 4.3 14.0 1.0
N D:ASN61 4.3 21.3 1.0
CB D:ASN61 4.4 14.6 1.0
CA D:ASP57 4.4 16.1 1.0
CA D:ILE64 4.5 9.3 1.0
CG D:GLU68 4.5 11.6 1.0
N D:ILE64 4.5 11.7 1.0
OD1 D:ASP65 4.5 33.6 1.0
CA D:THR63 4.5 18.5 1.0
N D:ASP65 4.6 13.0 1.0
N D:ASP59 4.6 25.3 1.0
OG1 D:THR63 4.7 20.3 1.0
N D:GLY60 4.7 23.0 1.0
CB D:ASP59 4.7 25.0 1.0
C D:ASP57 4.8 15.7 1.0
CA D:ASN61 4.8 17.4 1.0
N D:GLY62 4.8 22.6 1.0
CG D:ASP65 4.9 21.5 1.0
O D:HOH2056 4.9 16.6 1.0
N D:ALA58 4.9 21.2 1.0
C D:ASN61 5.0 21.2 1.0
C D:ILE64 5.0 12.1 1.0

Calcium binding site 3 out of 4 in 2wel

Go back to Calcium Binding Sites List in 2wel
Calcium binding site 3 out of 4 in the Crystal Structure of SU6656-Bound Calcium/Calmodulin-Dependent Protein Kinase II Delta in Complex with Calmodulin


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 SU6656-Bound Calcium/Calmodulin-Dependent Protein Kinase II Delta in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca602

b:18.4
occ:1.00
 O D:TYR100 2.3 11.8 1.0
OD1 D:ASP94 2.3 10.7 1.0
OD1 D:ASP96 2.4 16.4 1.0
OD1 D:ASN98 2.4 11.6 1.0
OE2 D:GLU105 2.5 16.3 1.0
OE1 D:GLU105 2.5 10.4 1.0
O D:HOH2104 2.5 9.9 1.0
CD D:GLU105 2.8 13.6 1.0
CG D:ASP96 3.3 26.8 1.0
CG D:ASN98 3.4 12.6 1.0
CG D:ASP94 3.4 11.3 1.0
C D:TYR100 3.5 11.1 1.0
OD2 D:ASP96 3.7 24.3 1.0
ND2 D:ASN98 3.9 7.0 1.0
O D:HOH2062 4.1 28.9 1.0
OD2 D:ASP94 4.2 7.9 1.0
N D:TYR100 4.2 9.2 1.0
CA D:ASP94 4.3 9.9 1.0
CA D:TYR100 4.3 11.9 1.0
N D:ASP96 4.3 14.8 1.0
CB D:ASP94 4.3 13.9 1.0
CG D:GLU105 4.3 8.7 1.0
N D:ASN98 4.4 9.7 1.0
N D:ILE101 4.4 10.4 1.0
CA D:ILE101 4.5 8.4 1.0
C D:ASP94 4.5 10.3 1.0
CB D:ASN98 4.6 9.0 1.0
CB D:ASP96 4.6 12.8 1.0
CB D:TYR100 4.6 10.6 1.0
N D:SER102 4.6 11.5 1.0
OE1 D:GLN136 4.6 13.5 1.0
N D:GLY97 4.7 18.3 1.0
N D:LYS95 4.7 16.7 1.0
CA D:ASP96 4.8 17.7 1.0
CA D:ASN98 4.9 13.0 1.0
C D:ASP96 4.9 16.6 1.0
O D:HOH2071 4.9 29.1 1.0
O D:ASP94 5.0 11.7 1.0

Calcium binding site 4 out of 4 in 2wel

Go back to Calcium Binding Sites List in 2wel
Calcium binding site 4 out of 4 in the Crystal Structure of SU6656-Bound Calcium/Calmodulin-Dependent Protein Kinase II Delta in Complex with Calmodulin


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 SU6656-Bound Calcium/Calmodulin-Dependent Protein Kinase II Delta in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca603

b:22.3
occ:1.00
 OD1 D:ASP130 2.3 11.2 1.0
O D:GLN136 2.4 12.6 1.0
OD1 D:ASP132 2.4 15.6 1.0
O D:HOH2102 2.4 15.4 1.0
OE2 D:GLU141 2.4 12.8 1.0
OD1 D:ASP134 2.4 11.2 1.0
OE1 D:GLU141 2.5 10.5 1.0
CD D:GLU141 2.9 13.5 1.0
CG D:ASP134 3.3 29.1 1.0
CG D:ASP130 3.3 14.1 1.0
CG D:ASP132 3.4 23.9 1.0
C D:GLN136 3.5 8.5 1.0
OD2 D:ASP134 3.7 23.3 1.0
OD2 D:ASP132 3.8 25.3 1.0
OD2 D:ASP130 4.1 15.1 1.0
CA D:ASP130 4.1 4.7 1.0
CB D:ASP130 4.1 14.1 1.0
N D:ASP134 4.2 15.0 1.0
N D:GLN136 4.3 11.9 1.0
CG D:GLU141 4.4 10.0 1.0
N D:ASP132 4.4 15.3 1.0
N D:GLY133 4.4 19.8 1.0
CA D:VAL137 4.4 7.4 1.0
N D:VAL137 4.4 11.1 1.0
CB D:ASP134 4.4 16.6 1.0
N D:ASN138 4.4 12.4 1.0
CA D:GLN136 4.5 11.0 1.0
C D:ASP130 4.5 12.3 1.0
O D:HOH2100 4.6 34.3 1.0
CB D:ASP132 4.6 18.1 1.0
N D:ILE131 4.6 14.7 1.0
CA D:ASP134 4.8 16.1 1.0
CA D:ASP132 4.8 19.4 1.0
C D:ASP132 4.8 21.9 1.0
C D:VAL137 4.9 12.6 1.0
N D:GLY135 4.9 9.1 1.0
CG D:ASN138 4.9 14.7 1.0
ND2 D:ASN138 4.9 17.2 1.0

Reference:

P.Rellos, A.C.W.Pike, F.H.Niesen, E.Salah, W.H.Lee, F.Von Delft, S.Knapp. Structure of the Camkiidelta/Calmodulin Complex Reveals the Molecular Mechanism of Camkii Kinase Activation. Plos Biol. V. 8 426 2010.
ISSN: ISSN 1544-9173
PubMed: 20668654
DOI: 10.1371/JOURNAL.PBIO.1000426
Page generated: Fri Jul 12 18:36:32 2024

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