Calcium in PDB 1cjy: Human Cytosolic Phospholipase A2

All present enzymatic activity of Human Cytosolic Phospholipase A2:
3.1.1.4;

The structure of Human Cytosolic Phospholipase A2, PDB code: 1cjy was solved by A.Dessen, J.Tang, H.Schmidt, M.Stahl, J.D.Clark, J.Seehra, W.S.Somers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	153.590, 95.490, 139.130, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 29.8

The binding sites of Calcium atom in the Human Cytosolic Phospholipase A2 (pdb code 1cjy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Human Cytosolic Phospholipase A2, PDB code: 1cjy:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Human Cytosolic Phospholipase A2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Cytosolic Phospholipase A2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca950 b:52.0 occ:1.00 O2S A:MES3000 2.0 58.5 1.0 OD1 A:ASP40 2.2 55.5 1.0 O A:THR41 2.2 45.7 1.0 OD1 A:ASN65 2.4 57.5 1.0 OD1 A:ASP43 2.6 52.7 1.0 OD2 A:ASP43 2.7 52.3 1.0 O A:HOH3026 2.9 61.4 1.0 CG A:ASP43 3.0 53.4 1.0 CG A:ASP40 3.2 56.8 1.0 C A:THR41 3.3 49.6 1.0 N A:THR41 3.5 51.3 1.0 CG A:ASN65 3.6 57.0 1.0 S A:MES3000 3.6 64.0 1.0 OD2 A:ASP40 3.8 59.2 1.0 CA A:THR41 3.9 51.1 1.0 CA A:CA951 3.9 44.6 1.0 C A:ASP40 3.9 51.9 1.0 O3S A:MES3000 4.1 67.3 1.0 CB A:THR41 4.1 51.6 1.0 C8 A:MES3000 4.1 66.1 1.0 CA A:ASP40 4.3 53.1 1.0 CB A:ASP40 4.3 54.0 1.0 ND2 A:ASN65 4.3 56.4 1.0 N A:PRO42 4.4 49.9 1.0 N A:ASN65 4.4 62.0 1.0 CA A:ASN65 4.5 62.8 1.0 C A:PRO42 4.5 54.9 1.0 CB A:ASP43 4.5 53.0 1.0 CB A:ASN65 4.6 57.5 1.0 O A:ASP40 4.6 50.6 1.0 N A:ASP43 4.6 52.0 1.0 O A:PRO42 4.7 56.3 1.0 CA A:PRO42 4.8 53.0 1.0 O1S A:MES3000 4.9 65.0 1.0

Calcium binding site 2 out of 4 in the Human Cytosolic Phospholipase A2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Cytosolic Phospholipase A2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca951 b:44.6 occ:1.00 OD2 A:ASP43 2.3 52.3 1.0 OD2 A:ASP40 2.3 59.2 1.0 OD1 A:ASN95 2.4 39.3 1.0 OD1 A:ASP93 2.5 46.5 1.0 O A:ALA94 2.5 40.2 1.0 CG A:ASP40 3.1 56.8 1.0 CG A:ASP93 3.2 45.0 1.0 OD2 A:ASP93 3.2 48.1 1.0 OD1 A:ASP40 3.2 55.5 1.0 CG A:ASP43 3.4 53.4 1.0 C A:ALA94 3.5 38.0 1.0 CG A:ASN95 3.6 34.9 1.0 CA A:CA950 3.9 52.0 1.0 CA A:ASN95 4.0 41.8 1.0 CB A:ASP43 4.1 53.0 1.0 N A:ASN95 4.2 41.9 1.0 CB A:ASN95 4.3 39.2 1.0 C A:ASP93 4.4 41.1 1.0 O A:ASP93 4.4 39.9 1.0 OD1 A:ASP43 4.4 52.7 1.0 N A:ASP43 4.5 52.0 1.0 N A:ALA94 4.5 37.4 1.0 O3S A:MES3000 4.6 67.3 1.0 O A:THR41 4.6 45.7 1.0 CB A:ASP40 4.6 54.0 1.0 CB A:ASP93 4.6 45.0 1.0 ND2 A:ASN95 4.6 35.2 1.0 CA A:ALA94 4.6 37.0 1.0 NZ A:LYS32 4.8 39.7 1.0 O2S A:MES3000 4.9 58.5 1.0 CA A:ASP43 4.9 52.8 1.0 CA A:ASP93 5.0 42.4 1.0

Calcium binding site 3 out of 4 in the Human Cytosolic Phospholipase A2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Cytosolic Phospholipase A2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1950 b:37.8 occ:1.00 OD1 B:ASN1065 2.1 35.9 1.0 O3S B:MES4000 2.2 47.5 1.0 O B:THR1041 2.3 30.7 1.0 OD1 B:ASP1043 2.4 37.1 1.0 OD1 B:ASP1040 2.4 33.9 1.0 OD2 B:ASP1043 2.6 40.2 1.0 O B:HOH53 2.8 41.1 1.0 CG B:ASP1043 2.8 40.9 1.0 O2S B:MES4000 3.2 51.3 1.0 S B:MES4000 3.2 45.6 1.0 CG B:ASN1065 3.3 37.0 1.0 C B:THR1041 3.4 34.7 1.0 CG B:ASP1040 3.7 38.2 1.0 N B:THR1041 3.8 32.4 1.0 C8 B:MES4000 3.9 49.4 1.0 ND2 B:ASN1065 4.1 33.8 1.0 CA B:THR1041 4.1 33.1 1.0 N B:ASN1065 4.2 40.8 1.0 C B:ASP1040 4.2 33.9 1.0 CA B:CA1951 4.3 33.0 1.0 CB B:ASP1043 4.3 38.8 1.0 CB B:ASN1065 4.3 39.0 1.0 CB B:THR1041 4.3 38.5 1.0 CA B:ASN1065 4.4 43.2 1.0 OD2 B:ASP1040 4.4 32.3 1.0 O B:HOH54 4.5 32.1 1.0 C B:PRO1042 4.5 36.8 1.0 N B:PRO1042 4.5 36.1 1.0 N B:ASP1043 4.6 33.0 1.0 CA B:ASP1040 4.6 35.1 1.0 O B:PRO1042 4.7 33.0 1.0 CB B:ASP1040 4.7 34.8 1.0 O1S B:MES4000 4.7 46.0 1.0 O B:ASP1040 4.8 30.8 1.0 CA B:PRO1042 4.9 35.9 1.0 CA B:ASP1043 4.9 37.5 1.0 C7 B:MES4000 5.0 47.6 1.0

Calcium binding site 4 out of 4 in the Human Cytosolic Phospholipase A2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Cytosolic Phospholipase A2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1951 b:33.0 occ:1.00 OD2 B:ASP1043 2.3 40.2 1.0 OD2 B:ASP1040 2.4 32.3 1.0 OD1 B:ASN1095 2.4 29.9 1.0 O B:HOH54 2.4 32.1 1.0 OD1 B:ASP1093 2.5 37.2 1.0 O B:ALA1094 2.6 30.3 1.0 OD2 B:ASP1093 2.9 37.4 1.0 CG B:ASP1093 3.0 34.5 1.0 CG B:ASP1040 3.2 38.2 1.0 OD1 B:ASP1040 3.3 33.9 1.0 CG B:ASP1043 3.4 40.9 1.0 C B:ALA1094 3.5 29.7 1.0 CG B:ASN1095 3.6 30.1 1.0 CB B:ASP1043 3.9 38.8 1.0 CA B:ASN1095 4.1 32.8 1.0 N B:ASN1095 4.2 31.4 1.0 CA B:CA1950 4.3 37.8 1.0 N B:ASP1043 4.3 33.0 1.0 NZ B:LYS1032 4.3 40.0 1.0 C B:ASP1093 4.3 31.7 1.0 O3S B:MES4000 4.3 47.5 1.0 N B:ALA1094 4.4 29.4 1.0 CB B:ASP1093 4.4 32.1 1.0 CB B:ASN1095 4.4 27.3 1.0 OD1 B:ASP1043 4.5 37.1 1.0 O B:ASP1093 4.5 27.9 1.0 O B:HOH52 4.5 42.6 1.0 O B:THR1041 4.5 30.7 1.0 ND2 B:ASN1095 4.5 30.7 1.0 CA B:ALA1094 4.6 29.5 1.0 CB B:ASP1040 4.7 34.8 1.0 CA B:ASP1043 4.8 37.5 1.0 CA B:ASP1093 4.8 29.4 1.0

A.Dessen, J.Tang, H.Schmidt, M.Stahl, J.D.Clark, J.Seehra, W.S.Somers. Crystal Structure of Human Cytosolic Phospholipase A2 Reveals A Novel Topology and Catalytic Mechanism. Cell(Cambridge,Mass.) V. 97 349 1999.
ISSN: ISSN 0092-8674
PubMed: 10319815
DOI: 10.1016/S0092-8674(00)80744-8