Calcium in PDB 5m3c: Structure of the Hybrid Domain (Ggdef-Eal) of PA0575 From Pseudomonas Aeruginosa PAO1 at 2.8 Ang. with Gtp and CA2+ Bound to the Active Site of the Ggdef Domain

The structure of Structure of the Hybrid Domain (Ggdef-Eal) of PA0575 From Pseudomonas Aeruginosa PAO1 at 2.8 Ang. with Gtp and CA2+ Bound to the Active Site of the Ggdef Domain, PDB code: 5m3c was solved by G.Giardina, P.Brunotti, F.Cutruzzola, S.Rinaldo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.10 / 2.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	122.307, 133.931, 69.141, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 27.7

The binding sites of Calcium atom in the Structure of the Hybrid Domain (Ggdef-Eal) of PA0575 From Pseudomonas Aeruginosa PAO1 at 2.8 Ang. with Gtp and CA2+ Bound to the Active Site of the Ggdef Domain (pdb code 5m3c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structure of the Hybrid Domain (Ggdef-Eal) of PA0575 From Pseudomonas Aeruginosa PAO1 at 2.8 Ang. with Gtp and CA2+ Bound to the Active Site of the Ggdef Domain, PDB code: 5m3c:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Structure of the Hybrid Domain (Ggdef-Eal) of PA0575 From Pseudomonas Aeruginosa PAO1 at 2.8 Ang. with Gtp and CA2+ Bound to the Active Site of the Ggdef Domain


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 Hybrid Domain (Ggdef-Eal) of PA0575 From Pseudomonas Aeruginosa PAO1 at 2.8 Ang. with Gtp and CA2+ Bound to the Active Site of the Ggdef Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1301 b:49.5 occ:1.00 OE1 A:GLU1106 2.0 47.0 1.0 OE2 A:GLU1015 2.4 45.5 1.0 OD1 A:ASN1074 2.5 54.0 1.0 OD2 A:ASP1136 2.7 50.4 1.0 CD A:GLU1106 3.2 47.4 1.0 CD A:GLU1015 3.2 45.2 1.0 CG A:ASN1074 3.4 53.9 1.0 OE1 A:GLU1015 3.5 44.3 1.0 CG A:ASP1136 3.5 50.3 1.0 ND2 A:ASN1074 3.6 53.9 1.0 OD1 A:ASP1136 3.7 51.4 1.0 OE2 A:GLU1106 3.8 47.2 1.0 NZ A:LYS1157 4.2 45.9 1.0 CG A:GLU1106 4.4 47.6 1.0 CB A:GLU1106 4.4 47.8 1.0 OE1 A:GLU1193 4.5 55.4 1.0 CG A:GLU1015 4.6 45.2 1.0 CB A:ASP1136 4.8 50.4 1.0 CB A:ASN1074 4.9 52.8 1.0 CD A:LYS1157 4.9 46.2 1.0

Calcium binding site 2 out of 5 in the Structure of the Hybrid Domain (Ggdef-Eal) of PA0575 From Pseudomonas Aeruginosa PAO1 at 2.8 Ang. with Gtp and CA2+ Bound to the Active Site of the Ggdef Domain


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 Hybrid Domain (Ggdef-Eal) of PA0575 From Pseudomonas Aeruginosa PAO1 at 2.8 Ang. with Gtp and CA2+ Bound to the Active Site of the Ggdef Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1302 b:51.1 occ:1.00 OD1 A:ASP846 2.1 44.0 1.0 OD2 A:ASP889 2.3 56.3 1.0 O2B A:GTP1304 2.4 53.8 1.0 O A:LEU847 2.5 49.5 1.0 O2G A:GTP1304 2.5 52.3 1.0 O2A A:GTP1304 2.6 56.1 1.0 CG A:ASP846 2.9 44.9 1.0 OD2 A:ASP846 3.1 45.8 1.0 CG A:ASP889 3.2 55.1 1.0 OD1 A:ASP889 3.4 55.1 1.0 PB A:GTP1304 3.6 53.8 1.0 C A:LEU847 3.6 51.7 1.0 PA A:GTP1304 3.7 56.4 1.0 N A:LEU847 3.7 48.7 1.0 O3A A:GTP1304 3.8 56.1 1.0 PG A:GTP1304 3.8 52.0 1.0 CA A:CA1303 3.9 60.6 1.0 O3B A:GTP1304 4.0 52.9 1.0 CA A:LEU847 4.1 50.5 1.0 O5' A:GTP1304 4.1 59.6 1.0 C A:ASP846 4.3 47.2 1.0 CB A:ASP846 4.3 45.1 1.0 NZ A:LYS959 4.4 61.0 1.0 CB A:LEU847 4.5 51.0 1.0 C5' A:GTP1304 4.5 63.7 1.0 CB A:ASP889 4.6 55.1 1.0 N A:ASP848 4.7 54.8 1.0 CA A:ASP846 4.7 45.4 1.0 O1G A:GTP1304 4.7 51.9 1.0 CE A:LYS959 4.7 60.2 1.0 O A:ASP889 4.7 51.8 1.0 CB A:PHE850 4.8 63.6 1.0 O3G A:GTP1304 4.8 51.6 1.0 O1B A:GTP1304 4.9 55.4 1.0 N A:ARG849 4.9 61.1 1.0 O A:ASP846 4.9 48.2 1.0 N A:PHE850 5.0 64.0 1.0

Calcium binding site 3 out of 5 in the Structure of the Hybrid Domain (Ggdef-Eal) of PA0575 From Pseudomonas Aeruginosa PAO1 at 2.8 Ang. with Gtp and CA2+ Bound to the Active Site of the Ggdef Domain


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 Hybrid Domain (Ggdef-Eal) of PA0575 From Pseudomonas Aeruginosa PAO1 at 2.8 Ang. with Gtp and CA2+ Bound to the Active Site of the Ggdef Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1303 b:60.6 occ:1.00 OE2 A:GLU890 2.5 53.0 1.0 OD1 A:ASP889 2.6 55.1 1.0 O2A A:GTP1304 2.7 56.1 1.0 OD2 A:ASP846 2.7 45.8 1.0 CD A:GLU890 3.3 52.8 1.0 CG A:GLU890 3.5 52.0 1.0 CG A:ASP889 3.7 55.1 1.0 CG A:ASP846 3.8 44.9 1.0 CA A:CA1302 3.9 51.1 1.0 PA A:GTP1304 3.9 56.4 1.0 OD2 A:ASP889 4.1 56.3 1.0 C5' A:GTP1304 4.1 63.7 1.0 O1A A:GTP1304 4.3 57.1 1.0 OE1 A:GLU890 4.3 53.0 1.0 OD1 A:ASP846 4.4 44.0 1.0 O5' A:GTP1304 4.5 59.6 1.0 N A:ASP889 4.6 56.5 1.0 CB A:ASP889 4.9 55.1 1.0 C A:ASP889 4.9 53.2 1.0 O A:ASP889 4.9 51.8 1.0 CB A:GLU890 5.0 51.1 1.0

Calcium binding site 4 out of 5 in the Structure of the Hybrid Domain (Ggdef-Eal) of PA0575 From Pseudomonas Aeruginosa PAO1 at 2.8 Ang. with Gtp and CA2+ Bound to the Active Site of the Ggdef Domain


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 Hybrid Domain (Ggdef-Eal) of PA0575 From Pseudomonas Aeruginosa PAO1 at 2.8 Ang. with Gtp and CA2+ Bound to the Active Site of the Ggdef Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1301 b:45.1 occ:1.00 OD1 B:ASP846 2.2 48.8 1.0 OD2 B:ASP889 2.3 41.4 1.0 O3G B:GTP1303 2.3 48.0 1.0 O2B B:GTP1303 2.3 50.4 1.0 O B:LEU847 2.3 49.7 1.0 O2A B:GTP1303 2.5 52.4 1.0 CG B:ASP889 3.3 42.0 1.0 CG B:ASP846 3.3 47.4 1.0 PB B:GTP1303 3.4 50.8 1.0 C B:LEU847 3.5 48.8 1.0 PG B:GTP1303 3.5 48.0 1.0 PA B:GTP1303 3.5 51.9 1.0 O3A B:GTP1303 3.5 51.6 1.0 OD1 B:ASP889 3.6 42.9 1.0 O B:HOH1404 3.6 39.3 1.0 OD2 B:ASP846 3.8 47.5 1.0 O3B B:GTP1303 3.8 49.5 1.0 NZ B:LYS959 3.9 56.4 1.0 O2G B:GTP1303 4.0 48.8 1.0 O5' B:GTP1303 4.0 51.9 1.0 N B:LEU847 4.1 46.2 1.0 C5' B:GTP1303 4.2 53.1 1.0 CA B:LEU847 4.2 47.7 1.0 C B:ASP846 4.3 45.7 1.0 CE B:LYS959 4.3 56.1 1.0 N B:ASP848 4.5 50.0 1.0 CB B:ASP846 4.5 46.5 1.0 CB B:LEU847 4.6 47.9 1.0 CB B:ASP889 4.6 41.9 1.0 O B:ASP846 4.6 45.7 1.0 N B:ARG849 4.6 52.9 1.0 CA B:ASP848 4.7 51.2 1.0 O1B B:GTP1303 4.8 51.0 1.0 O1G B:GTP1303 4.8 45.8 1.0 N B:PHE850 4.9 55.9 1.0 CA B:ASP846 4.9 45.7 1.0 C B:ASP848 4.9 52.0 1.0 O1A B:GTP1303 4.9 52.5 1.0 CB B:PHE850 5.0 56.6 1.0

Calcium binding site 5 out of 5 in the Structure of the Hybrid Domain (Ggdef-Eal) of PA0575 From Pseudomonas Aeruginosa PAO1 at 2.8 Ang. with Gtp and CA2+ Bound to the Active Site of the Ggdef Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Hybrid Domain (Ggdef-Eal) of PA0575 From Pseudomonas Aeruginosa PAO1 at 2.8 Ang. with Gtp and CA2+ Bound to the Active Site of the Ggdef Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1302 b:57.7 occ:1.00 OE1 B:GLU1106 2.1 53.6 1.0 OE2 B:GLU1015 2.3 52.1 1.0 OD2 B:ASP1136 2.4 62.1 1.0 OD1 B:ASN1074 2.6 64.2 1.0 ND2 B:ASN1074 3.2 63.6 1.0 CG B:ASN1074 3.3 62.6 1.0 CG B:ASP1136 3.3 61.3 1.0 CD B:GLU1106 3.3 54.0 1.0 CD B:GLU1015 3.3 53.3 1.0 OD1 B:ASP1136 3.6 62.4 1.0 OE1 B:GLU1015 3.7 52.9 1.0 OE2 B:GLU1106 4.0 53.5 1.0 NZ B:LYS1157 4.3 65.4 1.0 CB B:GLU1106 4.4 55.0 1.0 CG B:GLU1106 4.5 54.6 1.0 CB B:ASP1136 4.6 60.5 1.0 CG B:GLU1015 4.6 54.3 1.0 CB B:ASN1074 4.8 60.8 1.0 CD B:LYS1157 4.9 64.7 1.0

F.Mantoni, A.Paiardini, P.Brunotti, C.D'angelo, L.Cervoni, A.Paone, L.Cappellacci, R.Petrelli, M.Ricciutelli, L.Leoni, G.Rampioni, A.Arcovito, S.Rinaldo, F.Cutruzzola, G.Giardina. Insights Into the Gtp-Dependent Allosteric Control of C-Di-Gmp Hydrolysis From the Crystal Structure of PA0575 Protein From Pseudomonas Aeruginosa. Febs J. V. 285 3815 2018.
ISSN: ISSN 1742-4658
PubMed: 30106221
DOI: 10.1111/FEBS.14634