Calcium in PDB 5d0e: Crystal Structure of An Adenylyl Cyclase MA1120-Cat in Complex with Gtp and Calcium From Mycobacterium Avium

The structure of Crystal Structure of An Adenylyl Cyclase MA1120-Cat in Complex with Gtp and Calcium From Mycobacterium Avium, PDB code: 5d0e was solved by N.G.Bharambe, D.V.Barathy, K.Suguna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.10 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.590, 55.710, 55.270, 90.00, 109.74, 90.00
R / Rfree (%)	18.9 / 22.5

The structure of Crystal Structure of An Adenylyl Cyclase MA1120-Cat in Complex with Gtp and Calcium From Mycobacterium Avium also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of An Adenylyl Cyclase MA1120-Cat in Complex with Gtp and Calcium From Mycobacterium Avium (pdb code 5d0e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of An Adenylyl Cyclase MA1120-Cat in Complex with Gtp and Calcium From Mycobacterium Avium, PDB code: 5d0e:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of An Adenylyl Cyclase MA1120-Cat in Complex with Gtp and Calcium From Mycobacterium Avium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of An Adenylyl Cyclase MA1120-Cat in Complex with Gtp and Calcium From Mycobacterium Avium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:20.1 occ:1.00 OD2 A:ASP157 2.2 34.2 1.0 OD1 A:ASP113 2.3 28.6 1.0 O2A A:GTP303 2.4 24.4 1.0 O2B A:GTP303 2.4 21.5 1.0 O2G A:GTP303 2.4 26.0 1.0 O A:ILE114 2.4 21.7 1.0 OD1 A:ASP157 2.9 50.4 1.0 CG A:ASP157 2.9 32.8 1.0 HG A:SER117 3.4 23.8 1.0 CG A:ASP113 3.5 33.6 1.0 PB A:GTP303 3.5 20.2 1.0 C A:ILE114 3.5 19.8 1.0 PA A:GTP303 3.6 22.9 0.9 PG A:GTP303 3.7 24.0 0.9 HH12 A:ARG195 3.7 36.0 1.0 H A:SER117 3.7 20.8 1.0 H A:ILE114 3.8 21.7 1.0 O3A A:GTP303 3.8 25.8 1.0 N A:ILE114 3.9 21.7 1.0 HB3 A:SER117 4.0 20.0 1.0 OG A:SER117 4.0 23.8 1.0 OD2 A:ASP113 4.0 61.8 1.0 O3B A:GTP303 4.0 23.4 1.0 HB A:ILE114 4.1 20.1 1.0 CA A:ILE114 4.2 19.1 1.0 H A:GLU116 4.2 21.6 1.0 HH11 A:ARG195 4.3 36.0 1.0 HA A:GLU115 4.3 23.0 1.0 NH1 A:ARG195 4.3 36.0 1.0 CB A:ASP157 4.4 27.7 1.0 O3G A:GTP303 4.4 22.6 1.0 O5' A:GTP303 4.4 35.2 1.0 C A:ASP113 4.4 19.1 1.0 H A:ASP157 4.5 54.5 1.0 CB A:SER117 4.5 20.0 1.0 N A:GLU115 4.6 19.0 1.0 N A:SER117 4.6 20.8 1.0 HA A:ASP113 4.6 20.7 1.0 CB A:ASP113 4.6 21.4 1.0 HB3 A:ASP157 4.6 27.7 1.0 N A:GLU116 4.6 21.6 1.0 H4' A:GTP303 4.6 49.8 1.0 CB A:ILE114 4.7 20.1 1.0 O1A A:GTP303 4.7 25.0 1.0 HB2 A:ASP157 4.8 27.7 1.0 O1G A:GTP303 4.8 23.3 0.9 HB3 A:ASP113 4.8 21.4 1.0 O1B A:GTP303 4.8 21.2 1.0 CA A:ASP113 4.8 20.7 1.0 O A:HOH521 4.8 46.8 1.0 CA A:GLU115 4.8 23.0 1.0 HG22 A:ILE114 4.9 22.7 1.0 C A:GLU115 5.0 25.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of An Adenylyl Cyclase MA1120-Cat in Complex with Gtp and Calcium From Mycobacterium Avium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of An Adenylyl Cyclase MA1120-Cat in Complex with Gtp and Calcium From Mycobacterium Avium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:22.3 occ:1.00 OD1 B:ASP113 2.3 60.4 1.0 OD2 B:ASP157 2.4 51.4 1.0 OD1 B:ASP157 2.4 72.6 1.0 O1B A:GTP302 2.4 78.5 1.0 O3G A:GTP302 2.4 26.5 1.0 O B:ILE114 2.4 23.8 1.0 O1A A:GTP302 2.4 24.7 0.8 OD2 B:ASP113 2.6 62.2 1.0 CG B:ASP157 2.7 40.7 1.0 CG B:ASP113 2.8 46.7 1.0 HH12 B:ARG195 3.2 21.4 0.6 PB A:GTP302 3.5 26.1 1.0 C B:ILE114 3.5 21.2 1.0 HG B:SER117 3.5 21.6 1.0 PA A:GTP302 3.6 25.6 0.8 PG A:GTP302 3.7 21.8 0.8 O3A A:GTP302 3.8 19.6 0.8 HH11 B:ARG195 3.8 21.4 0.6 H B:ILE114 3.8 19.2 1.0 NH1 B:ARG195 3.8 29.7 0.6 H B:SER117 3.9 20.3 1.0 N B:ILE114 3.9 19.2 1.0 HB3 B:SER117 4.0 22.9 1.0 O3B A:GTP302 4.1 20.7 0.9 OG B:SER117 4.1 21.6 1.0 CB B:ASP157 4.2 37.2 1.0 CB B:ASP113 4.2 31.4 1.0 HA B:GLU115 4.2 18.1 1.0 CA B:ILE114 4.3 17.0 1.0 HB B:ILE114 4.3 19.2 1.0 C B:ASP113 4.3 19.5 1.0 H B:GLU116 4.3 21.9 1.0 O5' A:GTP302 4.4 54.9 1.0 O1G A:GTP302 4.4 20.5 0.9 HB2 B:ASP157 4.4 37.2 1.0 HE B:ARG195 4.5 28.9 0.4 HA B:ASP113 4.5 21.7 1.0 CB B:SER117 4.5 22.9 1.0 N B:GLU115 4.6 17.6 1.0 H B:ASP157 4.6 55.3 1.0 HB3 B:ASP157 4.6 37.2 1.0 CA B:ASP113 4.6 21.7 1.0 HB2 B:ASP113 4.7 31.4 1.0 N B:SER117 4.7 20.3 1.0 HB3 B:ASP113 4.7 31.4 1.0 N B:GLU116 4.7 21.9 1.0 O2A A:GTP302 4.8 36.4 0.9 CA B:GLU115 4.8 18.1 1.0 O2B A:GTP302 4.8 21.5 0.8 O2G A:GTP302 4.8 33.0 1.0 CB B:ILE114 4.8 19.2 1.0 O B:ASP113 4.9 20.8 1.0

N.G.Bharambe, D.V.Barathy, W.Syed, S.S.Visweswariah, M.Cola Sigmaf O, S.Misquith, K.Suguna. Substrate Specificity Determinants of Class III Nucleotidyl Cyclases Febs J. V. 283 3723 2016.
ISSN: ISSN 1742-464X
PubMed: 27542992
DOI: 10.1111/FEBS.13837