Calcium in PDB 4u65: Structure of the Periplasmic Output Domain of the Legionella Pneumophila Lapd Ortholog CDGS9 in Complex with Pseudomonas Fluorescens Lapg

The structure of Structure of the Periplasmic Output Domain of the Legionella Pneumophila Lapd Ortholog CDGS9 in Complex with Pseudomonas Fluorescens Lapg, PDB code: 4u65 was solved by D.Chatterjee, R.B.Cooley, C.D.Boyd, R.A.Mehl, G.A.O'toole, H.S.Sondermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.06 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.854, 73.674, 88.223, 90.00, 92.88, 90.00
R / Rfree (%)	17 / 21.1

The binding sites of Calcium atom in the Structure of the Periplasmic Output Domain of the Legionella Pneumophila Lapd Ortholog CDGS9 in Complex with Pseudomonas Fluorescens Lapg (pdb code 4u65). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the Periplasmic Output Domain of the Legionella Pneumophila Lapd Ortholog CDGS9 in Complex with Pseudomonas Fluorescens Lapg, PDB code: 4u65:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the Periplasmic Output Domain of the Legionella Pneumophila Lapd Ortholog CDGS9 in Complex with Pseudomonas Fluorescens Lapg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Periplasmic Output Domain of the Legionella Pneumophila Lapd Ortholog CDGS9 in Complex with Pseudomonas Fluorescens Lapg within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca301 b:32.5 occ:1.00 O E:TYR120 2.3 23.6 1.0 OD1 E:ASP134 2.4 19.5 1.0 OE1 E:GLU136 2.4 21.8 1.0 OD2 E:ASP137 2.4 20.3 1.0 OD1 E:ASP111 2.5 28.8 1.0 OD1 E:ASP137 2.5 18.3 1.0 OD2 E:ASP111 2.7 24.5 1.0 CG E:ASP137 2.8 17.8 1.0 CG E:ASP111 2.9 26.4 1.0 CG E:ASP134 3.3 23.5 1.0 CD E:GLU136 3.3 28.1 1.0 C E:TYR120 3.4 25.0 1.0 CA E:CA302 3.6 36.9 1.0 OD2 E:ASP134 3.7 28.8 1.0 OE2 E:GLU136 4.1 28.6 1.0 CG E:GLU136 4.1 20.1 1.0 CB E:ASP137 4.2 15.0 1.0 CA E:TRP121 4.2 27.2 1.0 O E:HOH539 4.2 32.8 1.0 N E:TRP121 4.3 25.4 1.0 N E:ASP134 4.3 19.5 1.0 N E:TYR120 4.3 23.8 1.0 CA E:TYR120 4.4 28.7 1.0 N E:GLU122 4.4 19.3 1.0 CB E:ASP134 4.4 18.7 1.0 CB E:ASP111 4.4 25.1 1.0 N E:ASP137 4.5 19.2 1.0 CG E:GLU122 4.6 17.2 1.0 CA E:ASP134 4.8 17.7 1.0 C E:TRP121 4.8 21.4 1.0 CA E:ASP137 4.8 17.7 1.0 CB E:TYR120 4.8 28.9 1.0 CD1 E:TRP121 4.9 38.4 1.0 OD1 E:ASP119 4.9 44.4 1.0 CD E:GLU122 5.0 21.0 1.0 C E:ASP134 5.0 16.8 1.0

Calcium binding site 2 out of 4 in the Structure of the Periplasmic Output Domain of the Legionella Pneumophila Lapd Ortholog CDGS9 in Complex with Pseudomonas Fluorescens Lapg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Periplasmic Output Domain of the Legionella Pneumophila Lapd Ortholog CDGS9 in Complex with Pseudomonas Fluorescens Lapg within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca302 b:36.9 occ:1.00 OD1 E:ASP119 2.3 44.4 1.0 OD2 E:ASP134 2.4 28.8 1.0 OD2 E:ASP111 2.5 24.5 1.0 OE1 E:GLU136 2.5 21.8 1.0 O E:HOH543 2.5 46.3 1.0 OE2 E:GLU136 2.5 28.6 1.0 O E:HOH561 2.7 53.1 1.0 CD E:GLU136 2.8 28.1 1.0 CG E:ASP134 3.2 23.5 1.0 OD1 E:ASP134 3.3 19.5 1.0 CG E:ASP111 3.5 26.4 1.0 CG E:ASP119 3.6 51.8 1.0 CA E:CA301 3.6 32.5 1.0 O E:HOH491 4.0 32.5 1.0 OD1 E:ASP111 4.2 28.8 1.0 CA E:ASP119 4.3 28.2 1.0 CG E:GLU136 4.3 20.1 1.0 N E:TYR120 4.3 23.8 1.0 O E:HOH518 4.4 40.9 1.0 OD2 E:ASP119 4.4 58.7 1.0 CB E:ASP111 4.5 25.1 1.0 CB E:ASP119 4.5 39.1 1.0 O E:VAL118 4.6 27.9 1.0 CB E:ASP134 4.7 18.7 1.0 O E:TYR120 4.7 23.6 1.0 CD1 E:TRP121 4.8 38.4 1.0 NE1 E:TRP121 4.8 38.7 1.0 SG E:CYS135 4.8 38.4 1.0 C E:ASP119 4.9 26.4 1.0

Calcium binding site 3 out of 4 in the Structure of the Periplasmic Output Domain of the Legionella Pneumophila Lapd Ortholog CDGS9 in Complex with Pseudomonas Fluorescens Lapg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Periplasmic Output Domain of the Legionella Pneumophila Lapd Ortholog CDGS9 in Complex with Pseudomonas Fluorescens Lapg within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca301 b:36.2 occ:1.00 O F:TYR120 2.3 25.5 1.0 OD1 F:ASP134 2.3 18.1 1.0 OE1 F:GLU136 2.3 30.9 1.0 OD1 F:ASP111 2.5 34.8 1.0 OD2 F:ASP137 2.5 19.3 1.0 OD2 F:ASP111 2.6 29.0 1.0 OD1 F:ASP137 2.7 21.3 1.0 CG F:ASP111 2.9 26.3 1.0 CG F:ASP137 2.9 20.7 1.0 CG F:ASP134 3.2 21.5 1.0 CD F:GLU136 3.2 42.2 1.0 C F:TYR120 3.4 24.9 1.0 CA F:CA302 3.5 35.7 1.0 OD2 F:ASP134 3.6 23.7 1.0 OE2 F:GLU136 4.0 43.1 1.0 CG F:GLU136 4.0 35.9 1.0 N F:TYR120 4.2 23.8 1.0 N F:TRP121 4.3 18.1 1.0 CA F:TRP121 4.3 18.1 1.0 CB F:ASP137 4.3 13.4 1.0 N F:ASP134 4.3 20.1 1.0 O F:HOH516 4.4 23.1 1.0 CA F:TYR120 4.4 25.0 1.0 CB F:ASP111 4.4 23.6 1.0 CB F:ASP134 4.4 24.4 1.0 N F:GLU122 4.5 19.1 1.0 N F:ASP137 4.5 13.6 1.0 CG F:GLU122 4.8 18.0 1.0 CA F:ASP134 4.8 16.6 1.0 CB F:TYR120 4.8 23.3 1.0 OD1 F:ASP119 4.9 41.4 1.0 CD1 F:TRP121 4.9 36.4 1.0 C F:TRP121 4.9 23.5 1.0 CA F:ASP137 4.9 19.0 1.0

Calcium binding site 4 out of 4 in the Structure of the Periplasmic Output Domain of the Legionella Pneumophila Lapd Ortholog CDGS9 in Complex with Pseudomonas Fluorescens Lapg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Periplasmic Output Domain of the Legionella Pneumophila Lapd Ortholog CDGS9 in Complex with Pseudomonas Fluorescens Lapg within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca302 b:35.7 occ:1.00 OD2 F:ASP134 2.3 23.7 1.0 OD1 F:ASP119 2.4 41.4 1.0 OD2 F:ASP111 2.4 29.0 1.0 OE1 F:GLU136 2.4 30.9 1.0 OE2 F:GLU136 2.5 43.1 1.0 O F:HOH517 2.5 45.3 1.0 O F:HOH533 2.7 55.7 1.0 CD F:GLU136 2.8 42.2 1.0 CG F:ASP134 3.2 21.5 1.0 OD1 F:ASP134 3.3 18.1 1.0 CG F:ASP111 3.5 26.3 1.0 CA F:CA301 3.5 36.2 1.0 CG F:ASP119 3.6 51.6 1.0 O F:HOH515 4.0 25.3 1.0 OD1 F:ASP111 4.2 34.8 1.0 O F:HOH534 4.2 49.8 1.0 CA F:ASP119 4.3 22.1 1.0 CG F:GLU136 4.3 35.9 1.0 N F:TYR120 4.3 23.8 1.0 CB F:ASP111 4.4 23.6 1.0 OD2 F:ASP119 4.4 62.4 1.0 CB F:ASP119 4.5 35.4 1.0 CB F:ASP134 4.6 24.4 1.0 O F:VAL118 4.7 26.9 1.0 O F:TYR120 4.7 25.5 1.0 C F:ASP119 4.9 21.8 1.0 CD1 F:TRP121 4.9 36.4 1.0 NE1 F:TRP121 4.9 35.9 1.0 SG F:CYS135 4.9 38.2 1.0

D.Chatterjee, R.B.Cooley, C.D.Boyd, R.A.Mehl, G.A.O'toole, H.Sondermann. Mechanistic Insight Into the Conserved Allosteric Regulation of Periplasmic Proteolysis By the Signaling Molecule Cyclic-Di-Gmp. Elife V. 3 03650 2014.
ISSN: ESSN 2050-084X
PubMed: 25182848
DOI: 10.7554/ELIFE.03650