Calcium in PDB 6iej: The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine

Enzymatic activity of The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine

All present enzymatic activity of The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine:
3.1.1.4;

Protein crystallography data

The structure of The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine, PDB code: 6iej was solved by Y.Hirano, Y.G.Gao, D.J.Stephenson, N.T.Vu, L.Malinina, C.E.Chalfant, D.J.Patel, R.E.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.88 / 2.21
Space group C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 108.294, 187.388, 68.754, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 24.9

Other elements in 6iej:

The structure of The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine (pdb code 6iej). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine, PDB code: 6iej:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 6iej

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Calcium binding site 1 out of 9 in the The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:46.5
occ:1.00
 OD1 A:ASN95 2.3 46.9 1.0
OD2 A:ASP43 2.4 39.2 1.0
OD2 A:ASP40 2.4 46.3 1.0
O A:ALA94 2.4 52.5 1.0
OD1 A:ASP93 2.7 46.7 1.0
OD2 A:ASP93 2.7 49.6 1.0
CG A:ASP93 3.0 51.2 1.0
CG A:ASP40 3.3 54.0 1.0
CG A:ASN95 3.4 41.0 1.0
OD1 A:ASP40 3.4 46.5 1.0
CG A:ASP43 3.5 43.3 1.0
C A:ALA94 3.6 50.6 1.0
CB A:ASP43 4.0 36.0 1.0
ND2 A:ASN95 4.0 50.9 1.0
CA A:CA202 4.2 48.0 1.0
CAD A:HXG205 4.2 58.5 1.0
N A:ASP43 4.3 39.8 1.0
NZ A:LYS32 4.3 59.9 1.0
N A:ALA94 4.3 41.8 1.0
CA A:ASN95 4.4 48.2 1.0
N A:ASN95 4.4 44.6 1.0
CB A:ASN95 4.5 40.7 1.0
CB A:ASP93 4.5 42.8 1.0
O A:THR41 4.5 42.7 1.0
OAH A:HXG205 4.5 54.3 1.0
OD1 A:ASP43 4.5 43.9 1.0
C A:ASP93 4.6 49.9 1.0
CA A:ALA94 4.6 38.9 1.0
CB A:ASP40 4.7 49.6 1.0
CA A:ASP43 4.8 36.1 1.0
O A:ASP93 4.9 50.0 1.0

Calcium binding site 2 out of 9 in 6iej

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Calcium binding site 2 out of 9 in the The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:48.0
occ:1.00
 OAH A:HXG205 2.0 54.3 1.0
O A:THR41 2.3 42.7 1.0
OD1 A:ASP40 2.4 46.5 1.0
OD1 A:ASN65 2.4 37.5 1.0
OD2 A:ASP43 2.6 39.2 1.0
OD1 A:ASP43 2.6 43.9 1.0
CG A:ASP43 2.9 43.3 1.0
CA A:CA203 3.4 80.1 1.0
PBD A:HXG205 3.4 58.3 1.0
C A:THR41 3.4 43.2 1.0
CG A:ASP40 3.5 54.0 1.0
CG A:ASN65 3.5 42.4 1.0
N A:THR41 3.7 43.4 1.0
OAI A:HXG205 3.8 48.2 1.0
CA A:THR41 4.0 47.3 1.0
OD2 A:ASP40 4.1 46.3 1.0
CA A:CA201 4.2 46.5 1.0
OAW A:HXG205 4.2 63.7 1.0
ND2 A:ASN65 4.2 42.6 1.0
CB A:THR41 4.2 45.0 1.0
C A:ASP40 4.2 50.1 1.0
N A:ASN65 4.4 41.1 1.0
CB A:ASP43 4.4 36.0 1.0
CA A:ASN65 4.5 39.1 1.0
N A:PRO42 4.5 43.7 1.0
OAX A:HXG205 4.5 71.9 1.0
C A:PRO42 4.6 37.8 1.0
CA A:ASP40 4.6 48.1 1.0
CB A:ASN65 4.6 33.6 1.0
CB A:ASP40 4.6 49.6 1.0
N A:ASP43 4.7 39.8 1.0
CAD A:HXG205 4.7 58.5 1.0
O A:PRO42 4.7 38.7 1.0
CA A:PRO42 4.9 36.7 1.0
CAU A:HXG205 5.0 83.7 1.0
O A:ASP40 5.0 42.1 1.0

Calcium binding site 3 out of 9 in 6iej

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Calcium binding site 3 out of 9 in the The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:80.1
occ:1.00
 OAF A:HXG205 2.9 0.5 1.0
OD1 A:ASN65 3.2 37.5 1.0
CA A:CA202 3.4 48.0 1.0
OAH A:HXG205 3.5 54.3 1.0
OAI A:HXG205 3.6 48.2 1.0
N A:THR41 3.9 43.4 1.0
CG A:ASN65 3.9 42.4 1.0
CAZ A:HXG205 4.0 99.6 1.0
OD1 A:ASP40 4.0 46.5 1.0
PBD A:HXG205 4.0 58.3 1.0
CAU A:HXG205 4.1 83.7 1.0
ND2 A:ASN65 4.2 42.6 1.0
CB A:THR41 4.4 45.0 1.0
OG1 A:THR41 4.4 37.8 1.0
OAV A:HXG205 4.5 94.2 1.0
OAX A:HXG205 4.5 71.9 1.0
CA A:ASP40 4.5 48.1 1.0
CA A:THR41 4.7 47.3 1.0
C A:ASP40 4.7 50.1 1.0
O A:THR41 4.7 42.7 1.0
OG1 B:THR41 4.7 42.3 1.0
O A:LEU39 5.0 49.6 1.0

Calcium binding site 4 out of 9 in 6iej

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Calcium binding site 4 out of 9 in the The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:46.7
occ:1.00
 OD1 B:ASN95 2.4 43.1 1.0
OD2 B:ASP43 2.4 41.5 1.0
O B:ALA94 2.4 52.3 1.0
OD2 B:ASP40 2.5 51.7 1.0
OD1 B:ASP93 2.6 53.1 1.0
OD2 B:ASP93 2.7 56.5 1.0
CG B:ASP93 3.0 54.0 1.0
CG B:ASP40 3.3 57.9 1.0
CG B:ASN95 3.4 41.9 1.0
OD1 B:ASP40 3.5 50.3 1.0
CG B:ASP43 3.5 43.6 1.0
C B:ALA94 3.6 48.5 1.0
CB B:ASP43 4.0 33.8 1.0
ND2 B:ASN95 4.2 48.3 1.0
CA B:CA202 4.2 47.8 1.0
NZ B:LYS32 4.2 58.1 1.0
N B:ASP43 4.3 44.0 1.0
CA B:ASN95 4.3 49.9 1.0
N B:ASN95 4.3 47.7 1.0
N B:ALA94 4.4 40.8 1.0
O B:THR41 4.4 43.8 1.0
OAH B:HXG204 4.5 50.9 1.0
CB B:ASN95 4.5 42.2 1.0
CB B:ASP93 4.5 44.3 1.0
C B:ASP93 4.5 49.3 1.0
CA B:ALA94 4.6 42.4 1.0
OD1 B:ASP43 4.6 42.6 1.0
CB B:ASP40 4.8 54.5 1.0
CA B:ASP43 4.8 36.0 1.0
O B:ASP93 4.8 49.6 1.0

Calcium binding site 5 out of 9 in 6iej

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Calcium binding site 5 out of 9 in the The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:47.8
occ:1.00
 OAH B:HXG204 2.0 50.9 1.0
O B:THR41 2.3 43.8 1.0
OD1 B:ASP40 2.4 50.3 1.0
OD1 B:ASN65 2.5 37.3 1.0
OD2 B:ASP43 2.5 41.5 1.0
OD1 B:ASP43 2.7 42.6 1.0
CG B:ASP43 2.9 43.6 1.0
CA B:CA203 3.3 79.9 1.0
PBD B:HXG204 3.4 56.6 1.0
C B:THR41 3.4 39.3 1.0
CG B:ASP40 3.5 57.9 1.0
CG B:ASN65 3.6 42.8 1.0
N B:THR41 3.6 45.6 1.0
OAI B:HXG204 3.7 49.6 1.0
CA B:THR41 3.9 47.8 1.0
OD2 B:ASP40 4.1 51.7 1.0
CB B:THR41 4.1 47.1 1.0
CA B:CA201 4.2 46.7 1.0
ND2 B:ASN65 4.2 43.3 1.0
C B:ASP40 4.3 51.3 1.0
OAW B:HXG204 4.4 61.3 1.0
OAX B:HXG204 4.4 65.5 1.0
CB B:ASP43 4.4 33.8 1.0
N B:ASN65 4.5 42.9 1.0
CA B:ASP40 4.6 49.4 1.0
N B:PRO42 4.6 42.0 1.0
C B:PRO42 4.6 42.3 1.0
CA B:ASN65 4.6 38.2 1.0
CB B:ASP40 4.6 54.5 1.0
N B:ASP43 4.7 44.0 1.0
CB B:ASN65 4.7 33.1 1.0
O B:PRO42 4.7 42.5 1.0
CAS B:HXG204 4.9 65.2 1.0
CA B:PRO42 5.0 37.6 1.0

Calcium binding site 6 out of 9 in 6iej

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Calcium binding site 6 out of 9 in the The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:79.9
occ:1.00
 OD1 B:ASN65 3.2 37.3 1.0
CA B:CA202 3.3 47.8 1.0
OAF B:HXG204 3.3 0.2 1.0
OAI B:HXG204 3.6 49.6 1.0
N B:THR41 3.7 45.6 1.0
OAH B:HXG204 3.7 50.9 1.0
OD1 B:ASP40 3.9 50.3 1.0
CG B:ASN65 4.0 42.8 1.0
CAU B:HXG204 4.1 80.2 1.0
CB B:THR41 4.1 47.1 1.0
OG1 B:THR41 4.1 42.3 1.0
PBD B:HXG204 4.1 56.6 1.0
CAZ B:HXG204 4.2 0.0 1.0
ND2 B:ASN65 4.3 43.3 1.0
CA B:ASP40 4.4 49.4 1.0
CA B:THR41 4.5 47.8 1.0
OAV B:HXG204 4.5 95.6 1.0
OAX B:HXG204 4.5 65.5 1.0
C B:ASP40 4.5 51.3 1.0
OG1 A:THR41 4.6 37.8 1.0
O B:THR41 4.7 43.8 1.0
CG B:ASP40 4.9 57.9 1.0
O B:LEU39 5.0 51.5 1.0

Calcium binding site 7 out of 9 in 6iej

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Calcium binding site 7 out of 9 in the The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:48.1
occ:1.00
 OD2 C:ASP43 2.3 45.5 1.0
OD2 C:ASP40 2.4 51.3 1.0
O C:ALA94 2.6 51.0 1.0
OD2 C:ASP93 2.6 50.7 1.0
OD1 C:ASP93 2.7 47.6 1.0
OD1 C:ASN95 2.9 46.4 1.0
CG C:ASP93 3.0 50.2 1.0
CG C:ASP40 3.3 55.9 1.0
OD1 C:ASP40 3.4 51.1 1.0
CG C:ASP43 3.5 47.0 1.0
CG C:ASN95 3.6 47.0 1.0
C C:ALA94 3.6 49.5 1.0
CB C:ASP43 4.0 33.5 1.0
ND2 C:ASN95 4.0 51.9 1.0
NZ C:LYS32 4.2 59.8 1.0
N C:ASP43 4.3 41.6 1.0
CA C:CA202 4.3 52.2 1.0
N C:ALA94 4.4 43.9 1.0
CA C:ASN95 4.4 53.9 1.0
N C:ASN95 4.4 48.3 1.0
O C:THR41 4.4 44.8 1.0
CB C:ASP93 4.4 43.1 1.0
OD1 C:ASP43 4.5 44.8 1.0
C C:ASP93 4.5 48.3 1.0
OAH C:HXG205 4.6 54.8 1.0
CB C:ASN95 4.6 47.4 1.0
CA C:ALA94 4.6 40.7 1.0
CB C:ASP40 4.7 53.8 1.0
CA C:ASP43 4.8 37.9 1.0
O C:ASP93 4.9 51.8 1.0
CA C:ASP93 5.0 45.5 1.0

Calcium binding site 8 out of 9 in 6iej

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Calcium binding site 8 out of 9 in the The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:52.2
occ:1.00
 OAH C:HXG205 1.7 54.8 1.0
OD1 C:ASP40 2.4 51.1 1.0
OD1 C:ASP43 2.8 44.8 1.0
O C:THR41 2.8 44.8 1.0
OD2 C:ASP43 2.8 45.5 1.0
OD1 C:ASN65 2.9 41.8 1.0
PBD C:HXG205 3.1 54.6 1.0
CG C:ASP43 3.2 47.0 1.0
CA C:CA203 3.2 76.7 1.0
OAI C:HXG205 3.4 48.0 1.0
CG C:ASP40 3.6 55.9 1.0
CG C:ASN65 3.6 47.2 1.0
N C:THR41 3.8 41.8 1.0
C C:THR41 3.8 41.8 1.0
ND2 C:ASN65 3.9 46.2 1.0
OAW C:HXG205 4.0 62.9 1.0
CA C:THR41 4.2 45.5 1.0
OAX C:HXG205 4.2 72.5 1.0
OD2 C:ASP40 4.2 51.3 1.0
CA C:CA201 4.3 48.1 1.0
CB C:THR41 4.4 44.6 1.0
C C:ASP40 4.5 51.5 1.0
N C:ASN65 4.6 43.7 1.0
CAU C:HXG205 4.6 85.5 1.0
CB C:ASP43 4.7 33.5 1.0
CA C:ASP40 4.7 48.1 1.0
CB C:ASP40 4.7 53.8 1.0
CAS C:HXG205 4.8 69.1 1.0
CB C:ASN65 4.8 35.9 1.0
CA C:ASN65 4.8 42.4 1.0
CAP C:HXG205 4.9 68.9 1.0
OAF C:HXG205 4.9 0.1 1.0
C C:PRO42 4.9 42.1 1.0
N C:PRO42 5.0 44.1 1.0

Calcium binding site 9 out of 9 in 6iej

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Calcium binding site 9 out of 9 in the The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The C2 Domain of Cytosolic Phospholipase A2 Alpha Bound to Phosphatidylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:76.7
occ:1.00
 OD1 C:ASN65 3.1 41.8 1.0
OAF C:HXG205 3.2 0.1 1.0
CA C:CA202 3.2 52.2 1.0
OAI C:HXG205 3.6 48.0 1.0
N C:THR41 3.7 41.8 1.0
OAH C:HXG205 3.8 54.8 1.0
OD1 C:ASP40 4.0 51.1 1.0
CG C:ASN65 4.0 47.2 1.0
CAZ C:HXG205 4.1 0.9 1.0
CB C:THR41 4.2 44.6 1.0
OG1 C:THR41 4.2 41.3 1.0
PBD C:HXG205 4.2 54.6 1.0
CAU C:HXG205 4.3 85.5 1.0
OAV C:HXG205 4.3 0.3 1.0
ND2 C:ASN65 4.3 46.2 1.0
CA C:ASP40 4.5 48.1 1.0
CA C:THR41 4.5 45.5 1.0
C C:ASP40 4.6 51.5 1.0
OAX C:HXG205 4.8 72.5 1.0
O C:THR41 4.8 44.8 1.0

Reference:

Y.Hirano, Y.G.Gao, D.J.Stephenson, N.T.Vu, L.Malinina, D.K.Simanshu, C.E.Chalfant, D.J.Patel, R.E.Brown. Structural Basis of Phosphatidylcholine Recognition By the C2-Domain of Cytosolic Phospholipase A2ALPHA. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31050338
DOI: 10.7554/ELIFE.44760
Page generated: Sat Dec 12 06:11:13 2020

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