Calcium in PDB 5fyr: Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Myoinositol Complex

The structure of Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Myoinositol Complex, PDB code: 5fyr was solved by O.V.Moroz, E.Blagova, A.A.Lebedev, A.Norgaard, D.R.Segura, T.H.Blicher, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.93 / 1.45
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	135.443, 135.443, 113.732, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 19.2

The binding sites of Calcium atom in the Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Myoinositol Complex (pdb code 5fyr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Myoinositol Complex, PDB code: 5fyr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Myoinositol Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Myoinositol Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:16.0 occ:1.00 OD1 A:ASP50 2.3 17.6 1.0 OE2 A:GLU48 2.3 13.5 1.0 O2 A:INS301 2.4 14.7 1.0 OD1 A:ASN27 2.4 13.6 1.0 OD2 A:ASP119 2.4 14.4 1.0 O A:HOH2034 2.5 18.8 1.0 OD2 A:ASP50 2.7 18.1 1.0 CG A:ASP50 2.9 14.4 1.0 CD A:GLU48 3.3 14.1 1.0 CG A:ASP119 3.5 12.9 1.0 CG A:ASN27 3.5 14.8 1.0 C2 A:INS301 3.7 12.8 1.0 CB A:ASP119 3.8 11.1 1.0 ND2 A:ASN27 3.9 24.8 1.0 O3 A:INS301 4.0 12.8 1.0 OE1 A:GLU48 4.0 13.7 1.0 O A:HOH2033 4.1 20.8 1.0 CG A:GLU48 4.1 13.1 1.0 C3 A:INS301 4.1 12.1 1.0 NZ A:LYS121 4.1 16.6 1.0 C4 A:INS301 4.2 11.8 1.0 O1 A:INS301 4.3 19.0 1.0 CE A:LYS121 4.3 16.8 1.0 CB A:ASP50 4.4 13.3 1.0 C1 A:INS301 4.4 14.5 1.0 C6 A:INS301 4.5 13.9 1.0 OD1 A:ASP119 4.6 15.3 1.0 CD2 A:HIS26 4.7 15.3 1.0 NE2 A:HIS26 4.7 17.3 1.0 CB A:ASN27 4.8 12.9 1.0 C5 A:INS301 4.8 11.6 1.0 CE2 A:TYR29 4.9 14.7 1.0

Calcium binding site 2 out of 4 in the Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Myoinositol Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Myoinositol Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:16.7 occ:1.00 OD1 B:ASP50 2.3 18.7 1.0 OE2 B:GLU48 2.3 13.5 1.0 OD1 B:ASN27 2.4 14.2 1.0 O2 B:INS301 2.4 14.3 1.0 OD2 B:ASP119 2.4 14.9 1.0 O B:HOH2038 2.5 20.1 1.0 OD2 B:ASP50 2.7 19.8 1.0 CG B:ASP50 2.9 15.2 1.0 CD B:GLU48 3.3 14.4 1.0 CG B:ASN27 3.4 15.8 1.0 CG B:ASP119 3.5 12.7 1.0 C2 B:INS301 3.8 12.7 1.0 CB B:ASP119 3.8 11.1 1.0 ND2 B:ASN27 3.8 23.5 1.0 O3 B:INS301 4.0 13.4 1.0 OE1 B:GLU48 4.0 13.4 1.0 C3 B:INS301 4.0 13.0 1.0 CG B:GLU48 4.0 13.1 1.0 O B:HOH2037 4.1 23.4 1.0 NZ B:LYS121 4.2 17.6 1.0 C4 B:INS301 4.2 12.7 1.0 CB B:ASP50 4.4 12.8 1.0 O1 B:INS301 4.4 20.1 1.0 CE B:LYS121 4.4 17.1 1.0 C1 B:INS301 4.4 14.0 1.0 C6 B:INS301 4.5 14.4 1.0 OD1 B:ASP119 4.6 14.3 1.0 NE2 B:HIS26 4.6 19.8 1.0 CD2 B:HIS26 4.7 15.8 1.0 CB B:ASN27 4.8 14.0 1.0 C5 B:INS301 4.8 12.4 1.0 CE2 B:TYR29 4.9 14.0 1.0

Calcium binding site 3 out of 4 in the Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Myoinositol Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Myoinositol Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:15.4 occ:1.00 OD1 C:ASP50 2.3 19.4 1.0 OE2 C:GLU48 2.4 13.0 1.0 OD2 C:ASP119 2.4 13.6 1.0 OD1 C:ASN27 2.4 14.1 1.0 O2 C:INS301 2.4 13.9 1.0 O C:HOH2037 2.5 18.1 1.0 OD2 C:ASP50 2.7 16.4 1.0 CG C:ASP50 2.9 15.1 1.0 CD C:GLU48 3.3 13.2 1.0 CG C:ASN27 3.4 15.6 1.0 CG C:ASP119 3.4 11.1 1.0 C2 C:INS301 3.8 11.0 1.0 CB C:ASP119 3.8 10.1 1.0 ND2 C:ASN27 3.8 23.5 1.0 CG C:GLU48 4.0 12.3 1.0 O3 C:INS301 4.0 12.6 1.0 OE1 C:GLU48 4.0 13.5 1.0 O C:HOH2036 4.1 21.8 1.0 NZ C:LYS121 4.1 14.9 1.0 C3 C:INS301 4.1 11.4 1.0 C4 C:INS301 4.3 11.7 1.0 CB C:ASP50 4.3 13.1 1.0 CE C:LYS121 4.4 14.5 1.0 O1 C:INS301 4.4 20.4 1.0 C1 C:INS301 4.5 13.6 1.0 C6 C:INS301 4.5 13.8 1.0 OD1 C:ASP119 4.5 13.2 1.0 CD2 C:HIS26 4.7 17.1 1.0 NE2 C:HIS26 4.7 18.0 1.0 CB C:ASN27 4.8 13.5 1.0 C5 C:INS301 4.8 10.6 1.0 CE2 C:TYR29 4.9 13.0 1.0

Calcium binding site 4 out of 4 in the Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Myoinositol Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Myoinositol Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:16.3 occ:1.00 OD1 D:ASP50 2.3 17.5 1.0 OE2 D:GLU48 2.4 14.2 1.0 OD2 D:ASP119 2.4 14.2 1.0 OD1 D:ASN27 2.4 15.2 1.0 O2 D:INS301 2.4 16.1 1.0 O D:HOH2033 2.5 18.9 1.0 OD2 D:ASP50 2.7 18.1 1.0 CG D:ASP50 2.9 14.7 1.0 CD D:GLU48 3.3 13.0 1.0 CG D:ASN27 3.4 14.6 1.0 CG D:ASP119 3.4 11.9 1.0 C2 D:INS301 3.8 13.5 1.0 CB D:ASP119 3.8 11.8 1.0 ND2 D:ASN27 3.8 26.6 1.0 O3 D:INS301 4.0 14.2 1.0 OE1 D:GLU48 4.0 13.9 1.0 CG D:GLU48 4.1 13.4 1.0 C3 D:INS301 4.1 13.8 1.0 O D:HOH2032 4.1 21.6 1.0 NZ D:LYS121 4.2 18.5 1.0 C4 D:INS301 4.3 12.6 1.0 CE D:LYS121 4.3 18.6 1.0 CB D:ASP50 4.3 14.8 1.0 O1 D:INS301 4.3 18.9 1.0 C1 D:INS301 4.4 13.2 1.0 OD1 D:ASP119 4.5 14.2 1.0 C6 D:INS301 4.5 12.8 1.0 CD2 D:HIS26 4.7 15.7 1.0 NE2 D:HIS26 4.7 18.4 1.0 CB D:ASN27 4.8 14.1 1.0 C5 D:INS301 4.8 12.0 1.0 CE2 D:TYR29 5.0 14.7 1.0

O.V.Moroz, E.Blagova, A.A.Lebedev, A.Nrgaard, D.R.Segura, T.H.Blicher, J.Brask, K.S.Wilson. The Structure of A Calcium-Dependent Phosphoinositide-Specific Phospholipase C From Pseudomonas Sp. 62186, the First From A Gram-Negative Bacterium. Acta Crystallogr D Struct V. 73 32 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28045383
DOI: 10.1107/S2059798316019616