Calcium in PDB 5fyo: Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Crystal Form 1

The structure of Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Crystal Form 1, PDB code: 5fyo 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)	48.81 / 1.50
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	96.080, 96.080, 113.340, 90.00, 90.00, 90.00
R / Rfree (%)	12.5 / 16.7

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

Calcium binding site 1 out of 2 in the Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Crystal Form 1


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, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:25.1 occ:1.00 OD1 A:ASP50 2.3 19.6 1.0 OE2 A:GLU48 2.3 21.4 1.0 O A:HOH2036 2.4 23.7 1.0 OD1 A:ASN27 2.4 19.7 1.0 OD2 A:ASP119 2.4 20.6 1.0 O A:HOH2035 2.6 41.5 1.0 CG A:ASP50 3.1 18.2 1.0 CD A:GLU48 3.2 18.9 1.0 OD2 A:ASP50 3.3 20.5 1.0 CG A:ASP119 3.4 18.2 1.0 CG A:ASN27 3.5 20.0 1.0 CB A:ASP119 3.7 15.0 1.0 ND2 A:ASN27 3.8 26.8 1.0 O A:HOH2034 3.8 38.1 1.0 OE1 A:GLU48 3.9 21.6 1.0 CG A:GLU48 4.0 19.4 1.0 NZ A:LYS121 4.1 22.6 1.0 CE A:LYS121 4.5 21.4 1.0 NE2 A:HIS26 4.6 26.1 1.0 CB A:ASP50 4.6 15.7 1.0 OD1 A:ASP119 4.6 20.6 1.0 CD2 A:HIS26 4.6 22.3 1.0 CB A:ASN27 4.8 20.4 1.0

Calcium binding site 2 out of 2 in the Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Crystal Form 1


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, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:21.2 occ:0.80 OD1 B:ASP50 2.3 19.3 1.0 OE2 B:GLU48 2.4 18.6 1.0 O B:HOH2032 2.4 24.7 1.0 OD2 B:ASP119 2.4 20.4 1.0 OD1 B:ASN27 2.4 19.6 1.0 O B:HOH2031 2.6 37.0 1.0 CG B:ASP50 3.2 17.6 1.0 CD B:GLU48 3.2 17.5 1.0 OD2 B:ASP50 3.3 20.9 1.0 CG B:ASP119 3.4 18.6 1.0 CG B:ASN27 3.4 19.4 1.0 CB B:ASP119 3.7 15.8 1.0 ND2 B:ASN27 3.8 25.6 1.0 O B:HOH2030 3.9 33.1 1.0 OE1 B:GLU48 4.0 19.8 1.0 CG B:GLU48 4.0 16.8 1.0 NZ B:LYS121 4.1 24.1 1.0 CE B:LYS121 4.5 21.7 1.0 OD1 B:ASP119 4.6 20.7 1.0 NE2 B:HIS26 4.6 25.9 1.0 CB B:ASP50 4.6 16.2 1.0 CD2 B:HIS26 4.6 21.8 1.0 CB B:ASN27 4.8 19.0 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