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Calcium in PDB 6paw: Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex

Enzymatic activity of Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex

All present enzymatic activity of Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex, PDB code: 6paw was solved by B.Simon, M.Wilmanns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 131.65 / 2.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.440, 95.880, 263.300, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 28.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex (pdb code 6paw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex, PDB code: 6paw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 6paw

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Calcium binding site 1 out of 9 in the Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex


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 DAPK2 S308A Calcium/Calmodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:59.7
occ:1.00
 OD1 D:ASP25 2.6 53.6 1.0
OD1 D:ASP23 2.6 59.0 1.0
OE1 D:GLU32 2.7 50.8 1.0
OE2 D:GLU32 2.9 65.2 1.0
CD D:GLU32 3.0 54.8 1.0
OD1 D:ASP21 3.1 58.9 1.0
CG D:ASP25 3.1 53.9 1.0
OD2 D:ASP25 3.2 52.1 1.0
OD2 D:ASP23 3.2 59.8 1.0
CG D:ASP23 3.2 62.2 1.0
O D:THR27 3.2 45.8 1.0
C D:THR27 4.1 50.5 1.0
CG2 D:THR29 4.2 54.9 1.0
CG D:GLU32 4.2 53.2 1.0
N D:THR29 4.3 36.7 1.0
CG D:ASP21 4.3 55.4 1.0
OG1 D:THR27 4.4 54.3 1.0
CB D:ASP25 4.5 53.2 1.0
CA D:ILE28 4.5 52.1 1.0
CB D:ASP23 4.6 67.4 1.0
N D:ILE28 4.7 51.8 1.0
CB D:THR29 4.8 54.5 1.0
C D:ILE28 4.9 48.6 1.0
N D:ASP25 4.9 53.5 1.0
OD2 D:ASP21 5.0 63.7 1.0

Calcium binding site 2 out of 9 in 6paw

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Calcium binding site 2 out of 9 in the Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex


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 DAPK2 S308A Calcium/Calmodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:58.9
occ:1.00
 OE2 D:GLU68 2.4 71.2 1.0
OD1 D:ASN61 2.4 63.0 1.0
OD1 D:ASP59 2.5 73.3 1.0
O D:THR63 2.7 60.0 1.0
OE1 D:GLU68 2.7 72.3 1.0
CD D:GLU68 2.8 73.9 1.0
OD1 D:ASP57 3.0 69.3 1.0
CG D:ASN61 3.1 64.9 1.0
CG D:ASP65 3.3 79.8 1.0
ND2 D:ASN61 3.3 71.8 1.0
CG D:ASP59 3.4 62.4 1.0
N D:ASP65 3.4 69.7 1.0
OD2 D:ASP65 3.5 94.9 1.0
OD2 D:ASP59 3.5 60.8 1.0
OD1 D:ASP65 3.5 82.0 1.0
CB D:ASP65 3.7 73.6 1.0
C D:THR63 3.7 55.0 1.0
C D:ILE64 4.1 61.2 1.0
CA D:ILE64 4.1 63.9 1.0
CG D:GLU68 4.1 74.9 1.0
CG D:ASP57 4.1 65.1 1.0
CA D:ASP65 4.2 76.4 1.0
N D:ILE64 4.3 62.7 1.0
CB D:ASN61 4.5 54.8 1.0
N D:ASN61 4.7 60.8 1.0
N D:ASP59 4.8 72.2 1.0
CB D:ASP59 4.8 61.3 1.0
OG1 D:THR63 4.8 62.4 1.0
OD2 D:ASP57 4.8 61.4 1.0
CA D:ASP57 4.9 66.0 1.0
CB D:GLU68 4.9 67.6 1.0
N D:THR63 4.9 56.5 1.0
CA D:THR63 4.9 42.5 1.0
N D:ALA58 4.9 69.6 1.0

Calcium binding site 3 out of 9 in 6paw

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Calcium binding site 3 out of 9 in the Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex


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 DAPK2 S308A Calcium/Calmodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca203

b:52.9
occ:1.00
 OE2 D:GLU105 2.4 50.9 1.0
OD1 D:ASN98 2.4 43.1 1.0
OD1 D:ASP96 2.5 59.8 1.0
O D:TYR100 2.5 42.6 1.0
CD D:GLU105 2.8 59.4 1.0
CG D:ASN98 2.8 50.9 1.0
OE1 D:GLU105 2.9 59.3 1.0
ND2 D:ASN98 2.9 55.6 1.0
OD2 D:ASP96 2.9 61.0 1.0
CG D:ASP96 3.0 59.2 1.0
OD1 D:ASP94 3.2 50.2 1.0
C D:TYR100 3.7 43.5 1.0
CB D:ASN98 4.1 52.8 1.0
CG D:GLU105 4.2 61.0 1.0
N D:SER102 4.3 51.7 1.0
OG D:SER102 4.4 49.8 1.0
CG D:ASP94 4.4 47.8 1.0
N D:TYR100 4.5 46.7 1.0
CB D:ASP96 4.5 50.3 1.0
CA D:TYR100 4.6 42.6 1.0
N D:ILE101 4.6 42.5 1.0
N D:ASN98 4.7 44.0 1.0
CA D:ILE101 4.7 37.3 1.0
OE1 D:GLN136 4.7 42.8 1.0
CB D:SER102 4.7 51.7 1.0
N D:ASP96 4.9 47.2 1.0
CB D:TYR100 4.9 42.7 1.0
CA D:ASN98 5.0 49.5 1.0
C D:ILE101 5.0 39.4 1.0

Calcium binding site 4 out of 9 in 6paw

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Calcium binding site 4 out of 9 in the Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex


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 DAPK2 S308A Calcium/Calmodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca204

b:31.0
occ:1.00
 OE2 D:GLU141 2.3 45.7 1.0
OD1 D:ASP134 2.4 54.7 1.0
O D:GLN136 2.5 43.8 1.0
OD1 D:ASP130 2.6 37.6 1.0
OD2 D:ASP132 2.6 41.7 1.0
OE1 D:GLU141 2.8 52.2 1.0
OD1 D:ASP132 2.8 51.5 1.0
CD D:GLU141 2.8 46.0 1.0
CG D:ASP132 3.0 46.0 1.0
OD1 D:ASN138 3.0 55.4 1.0
CG D:ASP134 3.3 53.9 1.0
C D:GLN136 3.5 40.1 1.0
CG D:ASP130 3.7 42.0 1.0
OD2 D:ASP134 3.7 53.1 1.0
CG D:ASN138 3.7 46.1 1.0
N D:ASN138 4.0 41.5 1.0
ND2 D:ASN138 4.2 41.4 1.0
CG D:GLU141 4.3 36.7 1.0
N D:ASP134 4.3 38.4 1.0
OD2 D:ASP130 4.3 50.8 1.0
N D:VAL137 4.3 36.0 1.0
N D:GLN136 4.3 35.8 1.0
CA D:VAL137 4.4 33.9 1.0
CB D:ASP134 4.4 50.7 1.0
CB D:ASP132 4.5 41.4 1.0
N D:GLY133 4.5 39.9 1.0
N D:ASP132 4.5 31.0 1.0
CA D:GLN136 4.5 37.3 1.0
CA D:ASP130 4.5 44.1 1.0
N D:ILE131 4.6 46.5 1.0
CB D:ASP130 4.6 34.1 1.0
C D:VAL137 4.6 35.4 1.0
CB D:ASN138 4.7 33.8 1.0
CA D:ASP134 4.9 40.5 1.0
CA D:ASP132 4.9 40.8 1.0
N D:GLY135 4.9 43.5 1.0
CA D:ASN138 5.0 34.4 1.0

Calcium binding site 5 out of 9 in 6paw

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Calcium binding site 5 out of 9 in the Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca201

b:95.5
occ:1.00
 O G:TYR100 2.6 0.8 1.0
ND2 G:ASN98 2.6 99.5 1.0
OD2 G:ASP96 2.7 0.6 1.0
OD1 G:ASN98 2.8 99.9 1.0
OE2 G:GLU105 3.0 99.1 1.0
CG G:ASN98 3.0 99.7 1.0
OE1 G:GLN136 3.6 77.2 1.0
CG G:ASP96 3.6 0.9 1.0
OD1 G:ASP96 3.7 0.1 1.0
C G:TYR100 3.8 99.0 1.0
CB G:SER102 4.1 0.3 1.0
OD1 G:ASP94 4.1 94.3 1.0
CD G:GLU105 4.1 98.6 1.0
N G:SER102 4.2 0.8 1.0
CB G:TYR100 4.4 85.0 1.0
CB G:ASN98 4.4 94.8 1.0
CD G:GLN136 4.5 90.3 1.0
CA G:TYR100 4.5 92.3 1.0
N G:TYR100 4.6 93.7 1.0
CA G:SER102 4.8 0.7 1.0
N G:ILE101 4.8 93.3 1.0
CG G:GLU105 4.8 0.7 1.0
C G:ILE101 4.9 94.1 1.0
CA G:ILE101 4.9 86.1 1.0
OE1 G:GLU105 5.0 94.3 1.0

Calcium binding site 6 out of 9 in 6paw

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Calcium binding site 6 out of 9 in the Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca202

b:90.4
occ:1.00
 OE1 G:GLU141 2.5 83.7 1.0
OD1 G:ASP130 2.5 0.3 1.0
O G:GLN136 2.6 90.2 1.0
OD1 G:ASP134 2.8 0.5 1.0
OD2 G:ASP132 2.8 0.3 1.0
OD1 G:ASP132 2.9 0.4 1.0
OE2 G:GLU141 3.0 96.8 1.0
CD G:GLU141 3.0 87.1 1.0
CG G:ASP132 3.1 0.4 1.0
CG G:ASP130 3.4 0.4 1.0
C G:GLN136 3.6 87.0 1.0
ND2 G:ASN138 3.7 91.3 1.0
CG G:ASP134 3.8 0.1 1.0
CA G:VAL137 3.8 89.7 1.0
N G:ASN138 3.8 96.1 1.0
CG G:ASN138 4.0 96.8 1.0
OD2 G:ASP130 4.0 98.3 1.0
N G:VAL137 4.1 79.9 1.0
OD1 G:ASN138 4.2 0.8 1.0
C G:VAL137 4.2 95.5 1.0
OD2 G:ASP134 4.3 90.4 1.0
CA G:ASP130 4.3 0.5 1.0
N G:ASP132 4.3 0.7 1.0
N G:ILE131 4.3 99.7 1.0
CB G:ASP130 4.4 0.1 1.0
N G:GLY133 4.4 0.6 1.0
CG G:GLU141 4.4 87.5 1.0
CB G:ASP132 4.5 99.4 1.0
N G:ASP134 4.6 0.1 1.0
CB G:ASN138 4.8 76.1 1.0
CA G:GLN136 4.8 97.0 1.0
C G:ASP130 4.8 0.2 1.0
N G:GLN136 4.8 0.3 1.0
CA G:ASP132 4.9 0.7 1.0
CA G:ASN138 4.9 79.6 1.0
CB G:ASP134 4.9 0.2 1.0

Calcium binding site 7 out of 9 in 6paw

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Calcium binding site 7 out of 9 in the Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca201

b:0.1
occ:1.00
 OD1 H:ASP134 2.4 0.7 1.0
OD2 H:ASP134 2.5 0.9 1.0
OE1 H:GLU141 2.5 0.0 1.0
OE2 H:GLU141 2.5 0.2 1.0
O H:GLN136 2.5 0.8 1.0
OD1 H:ASP132 2.6 0.4 1.0
CD H:GLU141 2.7 0.3 1.0
OD1 H:ASP130 2.7 0.9 1.0
CG H:ASP134 2.8 1.0 1.0
OD1 H:ASN138 3.3 0.9 1.0
CG H:ASP132 3.4 0.3 1.0
OD2 H:ASP132 3.4 0.9 1.0
C H:GLN136 3.7 0.7 1.0
CG H:ASP130 3.8 0.1 1.0
CG H:GLU141 4.0 96.8 1.0
CG H:ASN138 4.1 0.2 1.0
CB H:ASP134 4.2 0.3 1.0
N H:ASN138 4.4 0.0 1.0
CA H:VAL137 4.4 0.7 1.0
OD2 H:ASP130 4.5 0.1 1.0
N H:GLN136 4.5 1.0 1.0
N H:VAL137 4.5 0.6 1.0
N H:ASP134 4.6 0.6 1.0
C H:VAL137 4.7 0.2 1.0
CA H:GLN136 4.8 0.6 1.0
N H:ASP132 4.8 0.8 1.0
CA H:ASP130 4.8 0.6 1.0
CB H:ASN138 4.8 0.3 1.0
CB H:ASP132 4.8 0.7 1.0
CB H:ASP130 4.8 0.9 1.0
N H:ILE131 4.8 1.0 1.0
CA H:ASP134 5.0 0.2 1.0
ND2 H:ASN138 5.0 0.1 1.0
N H:GLY135 5.0 0.4 1.0

Calcium binding site 8 out of 9 in 6paw

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Calcium binding site 8 out of 9 in the Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:0.3
occ:1.00
 OE2 C:GLU105 2.3 86.7 1.0
O C:TYR100 2.4 95.9 1.0
OD1 C:ASP96 2.4 98.5 1.0
OD1 C:ASN98 2.4 88.6 1.0
OD2 C:ASP96 2.5 0.4 1.0
OD1 C:ASP94 2.7 84.9 1.0
CG C:ASP96 2.8 0.3 1.0
CD C:GLU105 3.0 88.2 1.0
OE1 C:GLU105 3.1 91.1 1.0
CG C:ASN98 3.2 80.5 1.0
ND2 C:ASN98 3.4 82.3 1.0
C C:TYR100 3.6 91.4 1.0
CG C:ASP94 3.9 85.7 1.0
CB C:ASP96 4.2 90.8 1.0
N C:TYR100 4.3 83.7 1.0
CG C:GLU105 4.3 84.9 1.0
N C:SER102 4.4 85.1 1.0
CA C:TYR100 4.5 84.4 1.0
CB C:ASN98 4.5 82.6 1.0
N C:ILE101 4.5 89.4 1.0
OD2 C:ASP94 4.6 85.1 1.0
CA C:ILE101 4.6 88.2 1.0
OG C:SER102 4.6 93.1 1.0
N C:ASN98 4.6 93.2 1.0
N C:ASP96 4.7 95.6 1.0
CB C:TYR100 4.9 79.8 1.0
CB C:SER102 4.9 85.4 1.0
N C:GLY97 4.9 88.2 1.0
C C:ILE101 5.0 88.5 1.0
CA C:ASP96 5.0 90.9 1.0

Calcium binding site 9 out of 9 in 6paw

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Calcium binding site 9 out of 9 in the Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of DAPK2 S308A Calcium/Calmodulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:89.1
occ:1.00
 OD1 C:ASP134 2.4 90.6 1.0
OE2 C:GLU141 2.4 63.9 1.0
OD2 C:ASP132 2.5 93.1 1.0
OD1 C:ASP132 2.6 92.7 1.0
CG C:ASP134 2.9 99.3 1.0
CG C:ASP132 2.9 92.2 1.0
OD2 C:ASP134 3.0 96.5 1.0
OD1 C:ASP130 3.2 80.9 1.0
O C:GLN136 3.2 77.3 1.0
CD C:GLU141 3.5 68.2 1.0
C C:GLN136 3.9 85.7 1.0
OE1 C:GLU141 4.1 73.5 1.0
CB C:ASP134 4.1 91.6 1.0
N C:ASN138 4.1 78.7 1.0
CG C:ASP130 4.1 78.4 1.0
CE2 C:TYR100 4.2 82.6 1.0
CB C:ASP132 4.4 91.1 1.0
CD2 C:TYR100 4.4 77.0 1.0
CB C:ASN138 4.5 69.4 1.0
N C:VAL137 4.5 84.8 1.0
CG C:GLU141 4.6 73.6 1.0
N C:ASP134 4.6 88.9 1.0
CA C:VAL137 4.6 82.9 1.0
OD2 C:ASP130 4.6 78.2 1.0
N C:GLN136 4.7 93.5 1.0
C C:VAL137 4.7 77.8 1.0
CA C:GLN136 4.8 89.2 1.0
CA C:ASP134 4.9 92.0 1.0
CA C:ASN138 4.9 72.9 1.0

Reference:

B.Simon, M.Wilmanns. Crystal Structure of Death-Associated Protein Kinase 2 in Complex with Calcium Calmodulin To Be Published.
Page generated: Tue Jul 16 12:50:42 2024

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