Calcium in PDB 5p2p: X-Ray Structure of Phospholipase A2 Complexed with A Substrate-Derived Inhibitor

All present enzymatic activity of X-Ray Structure of Phospholipase A2 Complexed with A Substrate-Derived Inhibitor:
3.1.1.4;

The structure of X-Ray Structure of Phospholipase A2 Complexed with A Substrate-Derived Inhibitor, PDB code: 5p2p was solved by B.W.Dijkstra, M.M.G.M.Thunnissen, K.H.Kalk, J.Drenth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.570, 62.440, 85.580, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Calcium atom in the X-Ray Structure of Phospholipase A2 Complexed with A Substrate-Derived Inhibitor (pdb code 5p2p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the X-Ray Structure of Phospholipase A2 Complexed with A Substrate-Derived Inhibitor, PDB code: 5p2p:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the X-Ray Structure of Phospholipase A2 Complexed with A Substrate-Derived Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Phospholipase A2 Complexed with A Substrate-Derived Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca125 b:9.1 occ:1.00 O A:GLY32 2.3 12.3 1.0 O A:GLY30 2.3 13.2 1.0 O2P A:DHG126 2.4 9.9 1.0 OD2 A:ASP49 2.4 3.9 1.0 OD1 A:ASP49 2.4 4.9 1.0 O1 A:DHG126 2.6 11.0 1.0 O A:TYR28 2.6 10.2 1.0 CG A:ASP49 2.7 4.2 1.0 C1 A:DHG126 3.3 13.1 1.0 C A:GLY32 3.4 11.7 1.0 N A:GLY32 3.6 11.2 1.0 C A:GLY30 3.6 13.4 1.0 P A:DHG126 3.6 12.0 1.0 C A:TYR28 3.8 11.1 1.0 N A:DHG126 4.0 14.2 1.0 CH2 A:DHG126 4.0 13.9 1.0 CA A:GLY32 4.0 10.9 1.0 OG1 A:DHG126 4.1 10.8 1.0 N A:GLY30 4.1 10.6 1.0 CB A:ASP49 4.2 5.0 1.0 CH1 A:DHG126 4.2 12.8 1.0 C A:TRP31 4.2 11.8 1.0 O3P A:DHG126 4.3 11.8 1.0 C2 A:DHG126 4.4 14.8 1.0 N A:GLY33 4.4 12.1 1.0 N A:TRP31 4.4 12.6 1.0 CA A:TYR28 4.5 11.2 1.0 CA A:TRP31 4.5 12.5 1.0 CA A:GLY30 4.5 11.4 1.0 O A:HOH133 4.6 26.1 1.0 CA A:GLY33 4.7 13.2 1.0 C A:CYS29 4.7 10.7 1.0 N A:CYS29 4.8 11.0 1.0 CA A:CYS29 4.9 10.9 1.0 O1P A:DHG126 4.9 10.7 1.0 CB A:TYR28 4.9 10.0 1.0

Calcium binding site 2 out of 3 in the X-Ray Structure of Phospholipase A2 Complexed with A Substrate-Derived Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Phospholipase A2 Complexed with A Substrate-Derived Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca125 b:7.5 occ:1.00 O B:GLY32 2.4 11.4 1.0 O B:GLY30 2.4 10.2 1.0 OD2 B:ASP49 2.4 7.8 1.0 O2P B:DHG127 2.4 16.7 1.0 OD1 B:ASP49 2.4 7.7 1.0 O B:TYR28 2.5 10.4 1.0 O1 B:DHG127 2.5 13.4 1.0 CG B:ASP49 2.7 7.7 1.0 C1 B:DHG127 3.5 13.6 1.0 C B:GLY32 3.5 10.5 1.0 C B:GLY30 3.6 10.1 1.0 C B:TYR28 3.7 11.0 1.0 P B:DHG127 3.8 16.3 1.0 N B:GLY32 3.9 9.7 1.0 N B:GLY30 4.0 7.9 1.0 CH2 B:DHG127 4.0 13.3 1.0 CH1 B:DHG127 4.2 13.9 1.0 CB B:ASP49 4.2 8.0 1.0 N B:DHG127 4.2 12.9 1.0 CA B:GLY32 4.3 9.9 1.0 OG1 B:DHG127 4.3 17.3 1.0 O3P B:DHG127 4.3 15.7 1.0 CA B:TYR28 4.4 12.2 1.0 CA B:GLY30 4.4 8.0 1.0 C B:TRP31 4.4 10.6 1.0 C2 B:DHG127 4.5 13.3 1.0 N B:TRP31 4.5 9.3 1.0 N B:GLY33 4.6 10.2 1.0 CA B:TRP31 4.6 10.1 1.0 N B:CYS29 4.6 10.1 1.0 CB B:TYR28 4.7 12.9 1.0 O B:HOH147 4.7 13.4 1.0 CA B:GLY33 4.8 11.4 1.0 CA B:CYS29 4.8 8.8 1.0 C B:CYS29 4.8 8.0 1.0 O1P B:DHG127 4.8 17.2 1.0 O B:CYS45 4.8 11.2 1.0

Calcium binding site 3 out of 3 in the X-Ray Structure of Phospholipase A2 Complexed with A Substrate-Derived Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Phospholipase A2 Complexed with A Substrate-Derived Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca126 b:14.1 occ:1.00 O B:SER72 2.4 9.7 1.0 OE1 A:GLU71 2.4 17.4 1.0 OE1 A:GLU92 2.4 12.4 1.0 O A:SER72 2.5 10.8 1.0 OE1 B:GLU92 2.5 7.1 1.0 OE1 B:GLU71 2.8 21.5 1.0 CD A:GLU92 3.3 12.8 1.0 CD B:GLU92 3.3 8.3 1.0 C B:SER72 3.5 9.7 1.0 C A:SER72 3.5 11.6 1.0 CD A:GLU71 3.5 17.7 1.0 CG B:GLU92 3.7 9.0 1.0 CD B:GLU71 3.7 21.7 1.0 N B:SER72 3.7 12.3 1.0 CG A:GLU92 3.7 13.4 1.0 N A:SER72 3.7 14.1 1.0 CA A:SER72 4.0 13.0 1.0 CA B:SER72 4.0 10.3 1.0 CG B:GLU71 4.1 19.8 1.0 CB A:SER72 4.2 13.7 1.0 CB B:SER72 4.4 8.6 1.0 CG A:GLU71 4.4 17.0 1.0 C B:GLU71 4.5 12.5 1.0 OE2 A:GLU71 4.5 18.5 1.0 OE2 B:GLU92 4.5 8.7 1.0 OE2 A:GLU92 4.5 13.0 1.0 N B:TYR73 4.6 9.1 1.0 C A:GLU71 4.6 15.2 1.0 N A:TYR73 4.6 12.0 1.0 OE2 B:GLU71 4.8 23.5 1.0 CA B:GLU71 4.8 14.6 1.0 CA B:TYR73 4.9 8.3 1.0 CA A:TYR73 5.0 12.2 1.0 CB A:GLU92 5.0 13.3 1.0 CA A:GLU71 5.0 15.4 1.0

M.M.Thunnissen, E.Ab, K.H.Kalk, J.Drenth, B.W.Dijkstra, O.P.Kuipers, R.Dijkman, G.H.De Haas, H.M.Verheij. X-Ray Structure of Phospholipase A2 Complexed with A Substrate-Derived Inhibitor. Nature V. 347 689 1990.
ISSN: ISSN 0028-0836
PubMed: 2215698
DOI: 10.1038/347689A0