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Calcium in PDB 4aqr: Crystal Structure of A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase

Enzymatic activity of Crystal Structure of A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase

All present enzymatic activity of Crystal Structure of A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase:
3.6.3.8;

Protein crystallography data

The structure of Crystal Structure of A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase, PDB code: 4aqr was solved by H.Tidow, L.R.Poulsen, A.Andreeva, K.L.Hein, M.G.Palmgren, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.142 / 1.95
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.251, 71.251, 163.279, 90.00, 90.00, 90.00
R / Rfree (%) 21.56 / 24.67

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase (pdb code 4aqr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase, PDB code: 4aqr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4aqr

Go back to Calcium Binding Sites List in 4aqr
Calcium binding site 1 out of 8 in the Crystal Structure of A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase


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 A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca150

b:41.3
occ:0.72
 O A:CYS27 2.3 57.5 1.0
O A:HOH2017 2.3 58.2 1.0
OD1 A:ASP21 2.3 57.8 1.0
OD1 A:ASP23 2.4 53.7 1.0
OD1 A:ASP25 2.4 49.1 1.0
OE1 A:GLU32 2.5 52.7 1.0
OE2 A:GLU32 2.5 50.8 1.0
CD A:GLU32 2.8 57.9 1.0
CG A:ASP23 3.3 52.0 1.0
CG A:ASP25 3.4 52.8 1.0
C A:CYS27 3.4 50.2 1.0
CG A:ASP21 3.5 53.0 1.0
OD2 A:ASP23 3.6 58.7 1.0
OD2 A:ASP25 3.8 59.6 1.0
N A:CYS27 4.2 46.7 1.0
CA A:ASP21 4.3 44.5 1.0
CA A:CYS27 4.3 50.0 1.0
N A:ASP25 4.3 53.8 1.0
CG A:GLU32 4.3 54.0 1.0
OD2 A:ASP21 4.3 50.3 1.0
CB A:ASP21 4.4 43.7 1.0
N A:ILE28 4.4 41.5 1.0
N A:ASP23 4.4 49.3 1.0
CA A:ILE28 4.5 42.7 1.0
C A:ASP21 4.5 57.0 1.0
CB A:ASP23 4.6 53.5 1.0
CB A:ASP25 4.6 52.4 1.0
CG2 A:THR29 4.7 50.6 1.0
N A:GLY24 4.7 54.5 1.0
CB A:CYS27 4.7 58.8 1.0
N A:LYS22 4.8 54.0 1.0
N A:THR29 4.8 44.2 1.0
CA A:ASP23 4.8 47.4 1.0
CA A:ASP25 4.9 54.4 1.0
C A:ASP23 4.9 45.0 1.0
O A:ASP21 4.9 52.8 1.0
O A:HOH2018 5.0 60.7 1.0
N A:GLY26 5.0 51.1 1.0
O A:HOH2022 5.0 50.2 1.0

Calcium binding site 2 out of 8 in 4aqr

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Calcium binding site 2 out of 8 in the Crystal Structure of A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase


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 A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca151

b:49.1
occ:0.86
 OD1 A:ASP57 2.2 54.9 1.0
OD1 A:ASN61 2.3 63.9 1.0
O A:THR63 2.4 56.7 1.0
OE2 A:GLU68 2.5 67.7 1.0
O A:HOH2050 2.5 59.7 1.0
OD1 A:ASP59 2.5 57.9 1.0
OE1 A:GLU68 2.5 53.9 1.0
CD A:GLU68 2.9 55.7 1.0
CG A:ASN61 3.2 67.8 1.0
CG A:ASP59 3.4 72.0 1.0
CG A:ASP57 3.4 55.2 1.0
C A:THR63 3.6 55.5 1.0
OD2 A:ASP59 3.7 69.7 1.0
ND2 A:ASN61 3.7 59.5 1.0
N A:ASN61 4.1 72.8 1.0
OD2 A:ASP57 4.2 60.0 1.0
CB A:ASN61 4.3 78.8 1.0
N A:THR63 4.3 63.6 1.0
CG A:GLU68 4.4 45.9 1.0
N A:ASP59 4.4 58.7 1.0
CB A:ASP57 4.4 52.8 1.0
CA A:ASP57 4.4 50.3 1.0
CA A:ILE64 4.5 46.5 1.0
N A:ASP65 4.5 56.5 1.0
N A:ILE64 4.5 59.5 1.0
CB A:ASP59 4.6 72.8 1.0
CA A:THR63 4.6 51.4 1.0
C A:ASP57 4.6 65.5 1.0
CA A:ASN61 4.6 70.4 1.0
N A:GLY60 4.6 61.3 1.0
CG A:ASP65 4.7 65.9 1.0
OD2 A:ASP65 4.7 71.0 1.0
N A:ALA58 4.7 54.3 1.0
OG1 A:THR63 4.7 55.5 1.0
N A:GLY62 4.8 78.0 1.0
OD1 A:ASP65 4.8 61.8 1.0
CA A:ASP59 4.8 70.1 1.0
C A:ASN61 4.9 70.3 1.0
C A:ASP59 4.9 71.0 1.0
C A:ILE64 4.9 57.5 1.0

Calcium binding site 3 out of 8 in 4aqr

Go back to Calcium Binding Sites List in 4aqr
Calcium binding site 3 out of 8 in the Crystal Structure of A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase


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 A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca152

b:41.0
occ:0.65
 O A:PHE100 2.3 52.6 1.0
OD1 A:ASP94 2.3 50.1 1.0
OD1 A:ASP96 2.3 57.0 1.0
OD1 A:ASN98 2.3 56.0 1.0
OE1 A:GLU105 2.5 53.6 1.0
OE2 A:GLU105 2.5 59.4 1.0
O A:HOH2064 2.5 49.1 1.0
CD A:GLU105 2.8 56.8 1.0
CG A:ASP96 3.2 65.3 1.0
CG A:ASN98 3.3 57.7 1.0
CG A:ASP94 3.4 59.1 1.0
C A:PHE100 3.5 56.1 1.0
OD2 A:ASP96 3.5 68.4 1.0
ND2 A:ASN98 3.9 53.6 1.0
N A:PHE100 4.1 57.6 1.0
CA A:ASP94 4.2 49.2 1.0
N A:ASN98 4.2 50.6 1.0
CB A:ASP94 4.3 48.9 1.0
OD2 A:ASP94 4.3 61.6 1.0
N A:ASP96 4.3 54.1 1.0
CG A:GLU105 4.3 55.8 1.0
CA A:PHE100 4.3 57.0 1.0
C A:ASP94 4.4 51.9 1.0
N A:ILE101 4.4 54.0 1.0
CB A:ASN98 4.5 54.8 1.0
CB A:ASP96 4.5 53.5 1.0
CA A:ILE101 4.5 48.6 1.0
N A:LYS95 4.6 54.5 1.0
N A:SER102 4.6 54.7 1.0
N A:GLN97 4.7 57.3 1.0
CA A:ASP96 4.7 57.5 1.0
CA A:ASN98 4.7 54.1 1.0
CB A:PHE100 4.8 46.3 1.0
N A:GLY99 4.8 51.5 1.0
C A:ASP96 4.9 57.3 1.0
O A:ASP94 4.9 55.3 1.0
C A:ASN98 4.9 63.5 1.0
C A:ILE101 5.0 49.3 1.0

Calcium binding site 4 out of 8 in 4aqr

Go back to Calcium Binding Sites List in 4aqr
Calcium binding site 4 out of 8 in the Crystal Structure of A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase


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 A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca153

b:46.9
occ:0.65
 OD1 A:ASP130 2.3 61.9 1.0
OD1 A:ASP134 2.3 68.4 1.0
O A:GLN136 2.4 62.1 1.0
OE2 A:GLU141 2.4 70.1 1.0
OD1 A:ASP132 2.4 76.1 1.0
OE1 A:GLU141 2.5 54.7 1.0
O A:HOH2087 2.5 69.4 1.0
CD A:GLU141 2.8 65.9 1.0
CG A:ASP134 3.2 66.6 1.0
CG A:ASP132 3.2 85.2 1.0
CG A:ASP130 3.4 72.4 1.0
C A:GLN136 3.5 50.1 1.0
OD2 A:ASP132 3.6 76.3 1.0
OD2 A:ASP134 3.6 67.6 1.0
N A:ASP134 4.2 85.7 1.0
N A:GLN136 4.2 72.4 1.0
N A:ASP132 4.2 64.4 1.0
OD2 A:ASP130 4.2 78.0 1.0
CG A:GLU141 4.3 67.5 1.0
CB A:ASP130 4.4 61.3 1.0
CB A:ASP134 4.4 76.5 1.0
CA A:GLN136 4.4 57.5 1.0
CA A:ASP130 4.4 58.8 1.0
CA A:ILE137 4.4 57.5 1.0
N A:ILE137 4.4 60.5 1.0
CB A:ASP132 4.5 89.7 1.0
N A:GLY133 4.5 81.8 1.0
N A:ASN138 4.5 55.3 1.0
N A:VAL131 4.6 74.8 1.0
CA A:ASP132 4.6 81.9 1.0
CA A:ASP134 4.7 77.1 1.0
C A:ASP132 4.7 89.8 1.0
N A:GLY135 4.8 79.1 1.0
CB A:GLN136 4.8 75.6 1.0
C A:ASP130 4.8 85.9 1.0
C A:ILE137 5.0 52.0 1.0
CG A:ASN138 5.0 67.5 1.0
CD1 A:ILE137 5.0 69.9 1.0
C A:ASP134 5.0 68.0 1.0

Calcium binding site 5 out of 8 in 4aqr

Go back to Calcium Binding Sites List in 4aqr
Calcium binding site 5 out of 8 in the Crystal Structure of A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase


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 A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca150

b:39.8
occ:0.70
 OD1 B:ASP21 2.3 51.0 1.0
O B:HOH2020 2.3 46.6 1.0
OD1 B:ASP25 2.3 52.4 1.0
O B:CYS27 2.3 49.8 1.0
OD1 B:ASP23 2.4 53.2 1.0
OE1 B:GLU32 2.4 46.7 1.0
OE2 B:GLU32 2.5 50.5 1.0
CD B:GLU32 2.8 56.9 1.0
CG B:ASP23 3.3 60.4 1.0
CG B:ASP25 3.3 57.7 1.0
C B:CYS27 3.4 51.7 1.0
CG B:ASP21 3.5 50.5 1.0
OD2 B:ASP23 3.6 52.9 1.0
OD2 B:ASP25 3.8 60.1 1.0
N B:CYS27 4.1 48.8 1.0
N B:ASP25 4.3 51.1 1.0
CA B:CYS27 4.3 51.8 1.0
OD2 B:ASP21 4.3 49.9 1.0
CG B:GLU32 4.3 51.9 1.0
CA B:ASP21 4.3 45.4 1.0
N B:ILE28 4.4 44.3 1.0
CB B:ASP21 4.4 45.6 1.0
N B:ASP23 4.5 49.2 1.0
CA B:ILE28 4.5 38.6 1.0
C B:ASP21 4.5 54.0 1.0
CB B:ASP25 4.5 56.5 1.0
CB B:ASP23 4.6 61.4 1.0
N B:GLY24 4.7 48.1 1.0
CG2 B:THR29 4.7 52.4 1.0
N B:LYS22 4.7 48.5 1.0
CB B:CYS27 4.8 50.7 1.0
N B:THR29 4.8 49.7 1.0
O B:HOH2025 4.8 51.3 1.0
CA B:ASP25 4.8 44.2 1.0
N B:GLY26 4.8 47.6 1.0
CA B:ASP23 4.9 55.5 1.0
O B:ASP21 4.9 50.3 1.0
C B:ASP23 4.9 49.6 1.0

Calcium binding site 6 out of 8 in 4aqr

Go back to Calcium Binding Sites List in 4aqr
Calcium binding site 6 out of 8 in the Crystal Structure of A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase


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 A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca151

b:51.3
occ:0.81
 OD1 B:ASP57 2.2 53.0 1.0
OD1 B:ASN61 2.4 57.1 1.0
OE2 B:GLU68 2.4 60.3 1.0
O B:THR63 2.4 61.3 1.0
O B:HOH2050 2.5 61.7 1.0
OE1 B:GLU68 2.5 50.7 1.0
OD1 B:ASP59 2.5 59.0 1.0
O B:HOH2051 2.8 51.8 1.0
CD B:GLU68 2.8 52.9 1.0
CG B:ASP59 3.4 71.2 1.0
CG B:ASP57 3.4 54.5 1.0
CG B:ASN61 3.4 68.2 1.0
C B:THR63 3.6 62.4 1.0
OD2 B:ASP59 3.8 75.0 1.0
ND2 B:ASN61 3.9 63.0 1.0
CA B:ASP57 4.1 50.1 1.0
CB B:ASP57 4.2 51.8 1.0
OD2 B:ASP57 4.2 62.9 1.0
CG B:GLU68 4.3 51.8 1.0
N B:ASP59 4.3 65.2 1.0
N B:ASN61 4.4 74.2 1.0
CA B:ILE64 4.4 43.4 1.0
N B:THR63 4.4 59.1 1.0
N B:ASP65 4.4 47.6 1.0
C B:ASP57 4.4 69.6 1.0
N B:ILE64 4.5 50.4 1.0
CB B:ASP59 4.5 74.0 1.0
N B:ALA58 4.6 54.4 1.0
CA B:THR63 4.6 59.0 1.0
CB B:ASN61 4.6 69.7 1.0
OG1 B:THR63 4.6 55.9 1.0
OD2 B:ASP65 4.7 66.3 1.0
N B:GLY60 4.8 72.2 1.0
CA B:ASP59 4.8 63.8 1.0
CG B:ASP65 4.8 57.1 1.0
C B:ILE64 4.8 45.2 1.0
CA B:ASN61 4.9 62.3 1.0
O B:HOH2049 4.9 55.4 1.0
N B:GLY62 4.9 70.5 1.0
C B:ASP59 4.9 64.7 1.0
O B:ASP57 4.9 72.9 1.0

Calcium binding site 7 out of 8 in 4aqr

Go back to Calcium Binding Sites List in 4aqr
Calcium binding site 7 out of 8 in the Crystal Structure of A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase


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 A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca152

b:67.8
occ:0.71
 OD1 B:ASP130 2.3 0.1 1.0
OE2 B:GLU141 2.4 98.8 1.0
OD1 B:ASP134 2.4 0.6 1.0
O B:GLN136 2.4 0.8 1.0
OD1 B:ASP132 2.4 0.5 1.0
OE1 B:GLU141 2.5 94.0 1.0
O B:HOH2076 2.5 70.0 1.0
CD B:GLU141 2.7 95.1 1.0
CG B:ASP134 3.2 0.3 1.0
CG B:ASP132 3.3 0.4 1.0
OD2 B:ASP132 3.4 0.9 1.0
CG B:ASP130 3.5 0.8 1.0
C B:GLN136 3.5 0.6 1.0
OD2 B:ASP134 3.5 0.7 1.0
O B:HOH2074 4.1 69.3 1.0
OD2 B:ASP130 4.2 0.6 1.0
CG B:GLU141 4.2 92.4 1.0
N B:ASP134 4.3 0.6 1.0
N B:GLN136 4.3 0.0 1.0
N B:ILE137 4.3 0.3 1.0
N B:ASN138 4.3 93.2 1.0
CA B:ILE137 4.3 97.5 1.0
CB B:ASP134 4.3 0.2 1.0
CA B:GLN136 4.4 0.8 1.0
CB B:ASP130 4.5 0.6 1.0
CA B:ASP130 4.6 0.7 1.0
N B:ASP132 4.6 0.6 1.0
CG B:ASN138 4.6 93.7 1.0
N B:GLY133 4.6 0.4 1.0
ND2 B:ASN138 4.7 97.4 1.0
CB B:ASP132 4.7 0.1 1.0
OD1 B:ASN138 4.7 91.8 1.0
CA B:ASP134 4.7 0.8 1.0
N B:VAL131 4.7 0.0 1.0
C B:ILE137 4.8 95.6 1.0
CB B:GLN136 4.9 0.6 1.0
C B:ASP130 4.9 0.6 1.0

Calcium binding site 8 out of 8 in 4aqr

Go back to Calcium Binding Sites List in 4aqr
Calcium binding site 8 out of 8 in the Crystal Structure of A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase


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 A Calmodulin in Complex with the Regulatory Domain of A Plasma-Membrane CA2+-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca153

b:52.0
occ:0.55
 O B:PHE100 2.3 77.1 1.0
OE2 B:GLU105 2.3 74.3 1.0
OD1 B:ASN98 2.4 78.8 1.0
OD1 B:ASP94 2.4 67.1 1.0
CB B:ASP96 2.5 0.7 1.0
OE1 B:GLU105 2.5 71.8 1.0
OD2 B:ASP96 2.6 0.5 1.0
CD B:GLU105 2.7 72.4 1.0
O B:HOH2063 2.9 75.6 1.0
CG B:ASP96 2.9 0.7 1.0
CG B:ASN98 3.3 81.0 1.0
C B:PHE100 3.5 73.5 1.0
CG B:ASP94 3.5 66.5 1.0
CA B:ASP96 3.6 78.0 1.0
N B:ASP96 3.7 75.6 1.0
ND2 B:ASN98 4.0 81.8 1.0
OD1 B:ASP96 4.1 0.5 1.0
CG B:GLU105 4.2 71.0 1.0
N B:PHE100 4.2 80.0 1.0
OD2 B:ASP94 4.3 67.9 1.0
CA B:PHE100 4.3 75.8 1.0
CB B:ASN98 4.3 84.3 1.0
CA B:ASP94 4.4 70.2 1.0
CB B:ASP94 4.4 64.0 1.0
N B:ILE101 4.4 71.9 1.0
N B:ASN98 4.4 84.1 1.0
C B:ASP96 4.4 79.5 1.0
N B:SER102 4.5 63.9 1.0
CA B:ILE101 4.5 70.3 1.0
N B:GLN97 4.5 78.5 1.0
C B:ASP94 4.6 71.9 1.0
N B:LYS95 4.7 83.1 1.0
CB B:PHE100 4.8 70.6 1.0
NE2 B:GLN136 4.8 0.9 1.0
CA B:ASN98 4.8 86.9 1.0
C B:LYS95 4.9 0.5 1.0
C B:ILE101 5.0 70.1 1.0

Reference:

H.Tidow, L.R.Poulsen, A.Andreeva, M.Knudsen, K.L.Hein, C.Wiuf, M.G.Palmgren, P.Nissen. A Bimodular Mechanism of Calcium Control in Eukaryotes Nature V. 491 468 2012.
ISSN: ISSN 0028-0836
PubMed: 23086147
DOI: 10.1038/NATURE11539
Page generated: Sat Jul 13 22:17:13 2024

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