Calcium in PDB 5fyp: Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Crystal Form 2

The structure of Calcium-Dependent Phosphoinositol-Specific Phospholipase C From A Gram-Negative Bacterium, Pseudomonas Sp, Apo Form, Crystal Form 2, PDB code: 5fyp 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)	67.61 / 1.17
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	135.210, 135.210, 112.470, 90.00, 90.00, 90.00
R / Rfree (%)	12.5 / 14.8

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 2 (pdb code 5fyp). 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, Crystal Form 2, PDB code: 5fyp:
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, Crystal Form 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1303 b:12.0 occ:0.80 OD1 A:ASP50 2.3 12.1 1.0 OE2 A:GLU48 2.4 10.3 1.0 O A:HOH2070 2.4 23.5 1.0 OD1 A:ASN27 2.4 9.7 1.0 O A:HOH2071 2.4 14.4 1.0 OD2 A:ASP119 2.4 12.0 1.0 CG A:ASP50 3.1 9.3 1.0 OD2 A:ASP50 3.2 10.8 1.0 CD A:GLU48 3.2 8.1 1.0 CG A:ASP119 3.4 10.5 1.0 CG A:ASN27 3.4 11.1 1.0 CB A:ASP119 3.7 8.2 1.0 ND2 A:ASN27 3.8 16.6 1.0 O A:HOH2233 3.8 45.0 1.0 OE1 A:GLU48 3.9 9.2 1.0 O A:HOH2069 3.9 24.5 1.0 O A:HOH2119 4.0 20.0 1.0 CG A:GLU48 4.0 7.8 1.0 NZ A:LYS121 4.1 15.9 1.0 CE A:LYS121 4.4 14.6 1.0 CB A:ASP50 4.6 8.9 1.0 OD1 A:ASP119 4.6 12.7 1.0 CD2 A:HIS26 4.6 11.8 1.0 NE2 A:HIS26 4.6 13.5 1.0 CB A:ASN27 4.8 9.5 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, Crystal Form 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1302 b:12.3 occ:0.80 OD1 B:ASP50 2.3 11.4 1.0 OE2 B:GLU48 2.4 10.3 1.0 O B:HOH2064 2.4 23.0 1.0 OD1 B:ASN27 2.4 10.6 1.0 OD2 B:ASP119 2.4 11.8 1.0 O B:HOH2068 2.5 13.7 1.0 CG B:ASP50 3.1 9.4 1.0 CD B:GLU48 3.2 8.7 1.0 OD2 B:ASP50 3.2 10.3 1.0 CG B:ASP119 3.4 10.4 1.0 CG B:ASN27 3.5 11.2 1.0 CB B:ASP119 3.7 8.4 1.0 O B:HOH2239 3.7 36.3 1.0 ND2 B:ASN27 3.8 16.7 1.0 OE1 B:GLU48 3.9 8.8 1.0 O B:HOH2065 3.9 20.3 1.0 O B:HOH2114 3.9 21.4 1.0 CG B:GLU48 4.0 8.1 1.0 NZ B:LYS121 4.1 15.3 1.0 CE B:LYS121 4.5 13.2 1.0 O B:HOH2066 4.5 52.1 1.0 CB B:ASP50 4.6 8.6 1.0 OD1 B:ASP119 4.6 11.5 1.0 CD2 B:HIS26 4.7 13.2 1.0 NE2 B:HIS26 4.7 16.5 1.0 CB B:ASN27 4.8 9.4 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, Crystal Form 2


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, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1302 b:13.8 occ:0.80 OD1 C:ASP50 2.3 12.4 1.0 O C:HOH2062 2.4 27.4 1.0 OD1 C:ASN27 2.4 11.7 1.0 O C:HOH2064 2.4 14.8 1.0 OE2 C:GLU48 2.4 11.8 1.0 OD2 C:ASP119 2.5 13.3 1.0 OD2 C:ASP50 2.9 11.7 1.0 CG C:ASP50 3.0 9.5 1.0 CD C:GLU48 3.2 9.2 1.0 CG C:ASN27 3.4 11.8 1.0 CG C:ASP119 3.5 11.2 1.0 CB C:ASP119 3.7 9.3 1.0 ND2 C:ASN27 3.7 18.2 1.0 O C:HOH2252 3.9 38.6 1.0 OE1 C:GLU48 3.9 9.7 1.0 O C:HOH2129 4.0 19.7 1.0 O C:HOH2061 4.0 25.6 1.0 CG C:GLU48 4.0 9.5 1.0 NZ C:LYS121 4.1 19.3 1.0 O C:HOH2060 4.1 27.3 1.0 CE C:LYS121 4.3 16.0 1.0 CB C:ASP50 4.5 8.4 1.0 OD1 C:ASP119 4.6 12.7 1.0 CD2 C:HIS26 4.7 12.2 1.0 NE2 C:HIS26 4.7 13.8 1.0 CB C:ASN27 4.8 10.4 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, Crystal Form 2


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, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1299 b:9.6 occ:0.70 OD1 D:ASP50 2.3 10.1 1.0 OE2 D:GLU48 2.4 8.8 1.0 OD1 D:ASN27 2.4 9.0 1.0 OD2 D:ASP119 2.4 9.8 1.0 O D:HOH2048 2.4 11.6 1.0 O D:HOH2046 2.4 24.1 1.0 CG D:ASP50 3.1 8.2 1.0 CD D:GLU48 3.2 7.8 1.0 OD2 D:ASP50 3.2 9.6 1.0 CG D:ASP119 3.4 8.1 1.0 CG D:ASN27 3.4 9.7 1.0 CB D:ASP119 3.6 6.9 1.0 O D:HOH2219 3.7 65.4 1.0 ND2 D:ASN27 3.7 14.9 1.0 O D:HOH2103 3.9 15.8 1.0 OE1 D:GLU48 3.9 8.8 1.0 CG D:GLU48 3.9 8.3 1.0 O D:HOH2045 4.0 21.2 1.0 NZ D:LYS121 4.1 13.1 1.0 CE D:LYS121 4.4 10.9 1.0 OD1 D:ASP119 4.5 9.8 1.0 CB D:ASP50 4.6 7.6 1.0 CD2 D:HIS26 4.8 11.0 1.0 CB D:ASN27 4.8 8.5 1.0 NE2 D:HIS26 4.8 12.6 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