Calcium in PDB 5d15: Crystal Structure of An Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with Atp and Calcium Ion

The structure of Crystal Structure of An Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with Atp and Calcium Ion, PDB code: 5d15 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)	37.92 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.530, 55.640, 55.070, 90.00, 109.79, 90.00
R / Rfree (%)	19.5 / 21.2

The binding sites of Calcium atom in the Crystal Structure of An Adenylyl Cyclase MA1120 From Mycobacterium Avium in Complex with Atp and Calcium Ion (pdb code 5d15). 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 From Mycobacterium Avium in Complex with Atp and Calcium Ion, PDB code: 5d15:
Jump to Calcium binding site number: 1; 2;

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


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 From Mycobacterium Avium in Complex with Atp and Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:19.5 occ:1.00 OD1 A:ASP113 2.3 32.8 1.0 O A:ILE114 2.3 22.1 1.0 O2A A:ATP301 2.3 21.8 1.0 O2B A:ATP301 2.3 18.1 1.0 OD2 A:ASP157 2.3 30.4 1.0 O2G A:ATP301 2.4 22.4 1.0 OD2 A:ASP113 2.6 26.2 1.0 CG A:ASP113 2.8 26.4 1.0 O A:HOH402 3.1 29.8 1.0 CG A:ASP157 3.4 31.0 1.0 PB A:ATP301 3.4 20.0 1.0 C A:ILE114 3.5 20.1 1.0 PA A:ATP301 3.5 26.0 1.0 HH12 A:ARG195 3.6 36.5 1.0 H A:ILE114 3.6 22.2 1.0 PG A:ATP301 3.6 21.3 1.0 O3A A:ATP301 3.7 24.1 1.0 OD1 A:ASP157 3.8 33.9 1.0 H A:SER117 3.8 22.1 1.0 N A:ILE114 3.8 18.2 1.0 O3B A:ATP301 3.9 20.4 1.0 H5'2 A:ATP301 4.0 48.9 1.0 HH11 A:ARG195 4.0 36.5 1.0 HG A:SER117 4.1 24.7 1.0 H A:GLU116 4.1 24.6 1.0 NH1 A:ARG195 4.1 25.0 1.0 HB3 A:SER117 4.2 24.0 1.0 O A:HOH499 4.2 27.3 1.0 OG A:SER117 4.2 19.7 1.0 HA A:GLU115 4.2 23.7 1.0 CA A:ILE114 4.2 18.7 1.0 CB A:ASP113 4.2 19.8 1.0 HB A:ILE114 4.3 26.1 1.0 O3G A:ATP301 4.3 21.5 1.0 O A:HOH515 4.3 37.6 1.0 C A:ASP113 4.4 19.2 1.0 O5' A:ATP301 4.5 29.6 1.0 N A:GLU115 4.5 19.5 1.0 N A:GLU116 4.6 21.9 1.0 O1A A:ATP301 4.6 27.7 1.0 HA A:ASP113 4.6 21.5 1.0 O1G A:ATP301 4.7 19.8 1.0 HB2 A:ASP113 4.7 22.6 1.0 N A:SER117 4.7 19.7 1.0 CB A:ASP157 4.7 28.9 1.0 CB A:SER117 4.7 19.7 1.0 CA A:GLU115 4.7 21.4 1.0 HB2 A:ASP157 4.7 34.8 1.0 CA A:ASP113 4.7 18.3 1.0 C5' A:ATP301 4.7 40.7 1.0 O1B A:ATP301 4.7 18.5 1.0 HB3 A:ASP113 4.8 22.6 1.0 CB A:ILE114 4.8 20.7 1.0 C A:GLU115 4.9 23.3 1.0 O A:HOH501 4.9 42.6 1.0 O A:HOH533 4.9 32.8 1.0 O A:HOH490 5.0 39.4 1.0

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


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 From Mycobacterium Avium in Complex with Atp and Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:18.5 occ:1.00 O1B B:ATP301 2.2 17.2 0.2 O1B B:ATP301 2.2 17.6 0.8 OD1 B:ASP113 2.3 46.5 1.0 O B:ILE114 2.3 28.1 1.0 OD2 B:ASP157 2.3 29.3 1.0 O1A B:ATP301 2.4 33.6 0.2 O3G B:ATP301 2.4 19.6 0.8 O1A B:ATP301 2.4 29.5 0.8 O3G B:ATP301 2.4 18.5 0.2 OD2 B:ASP113 2.4 40.4 1.0 CG B:ASP113 2.7 37.7 1.0 PB B:ATP301 3.4 17.9 0.2 PB B:ATP301 3.4 18.0 0.8 O B:HOH402 3.4 42.8 1.0 C B:ILE114 3.4 25.9 1.0 HH12 B:ARG195 3.5 32.3 0.6 PA B:ATP301 3.5 27.2 0.2 CG B:ASP157 3.5 35.9 1.0 HG B:SER117 3.6 19.5 1.0 PG B:ATP301 3.6 17.7 0.2 PA B:ATP301 3.6 30.4 0.8 PG B:ATP301 3.6 21.2 0.8 H B:ILE114 3.7 23.8 1.0 O3A B:ATP301 3.7 22.0 0.8 H B:SER117 3.8 20.2 1.0 O3B B:ATP301 3.8 18.2 0.2 O3A B:ATP301 3.8 21.1 0.2 N B:ILE114 3.9 20.7 1.0 HH11 B:ARG195 3.9 32.3 0.6 HH21 B:ARG195 3.9 36.1 0.4 O3B B:ATP301 3.9 17.4 0.8 NH1 B:ARG195 4.0 22.6 0.6 OD1 B:ASP157 4.1 38.3 1.0 HB3 B:SER117 4.1 18.8 1.0 O2A B:ATP301 4.1 24.7 0.2 O1G B:ATP301 4.1 18.7 0.2 CB B:ASP113 4.2 27.0 1.0 HA B:GLU115 4.2 23.7 1.0 OG B:SER117 4.2 15.3 1.0 HE B:ARG195 4.2 31.3 0.4 CA B:ILE114 4.2 22.6 1.0 O1G B:ATP301 4.3 19.1 0.8 O5' B:ATP301 4.3 35.4 0.8 HB B:ILE114 4.3 26.8 1.0 C B:ASP113 4.4 21.1 1.0 H5'2 B:ATP301 4.4 49.5 0.8 N B:GLU115 4.4 18.4 1.0 H5'1 B:ATP301 4.4 49.1 0.2 HB2 B:ASP157 4.5 58.2 1.0 N B:GLU116 4.6 23.8 1.0 HA B:ASP113 4.6 27.8 1.0 CB B:SER117 4.6 14.9 1.0 HB2 B:ASP113 4.6 36.4 1.0 N B:SER117 4.6 20.2 1.0 HB3 B:ASP113 4.7 36.4 1.0 CB B:ASP157 4.7 39.4 1.0 CA B:GLU115 4.7 21.2 1.0 CA B:ASP113 4.7 21.9 1.0 NH2 B:ARG195 4.7 25.1 0.4 O2B B:ATP301 4.7 16.4 0.2 O2B B:ATP301 4.8 16.7 0.8 O2G B:ATP301 4.8 17.3 0.8 O5' B:ATP301 4.8 35.4 0.2 CB B:ILE114 4.8 24.3 1.0 O2G B:ATP301 4.9 17.5 0.2 C5' B:ATP301 4.9 41.3 0.8 O2A B:ATP301 4.9 25.4 0.8 C B:GLU115 4.9 21.5 1.0 O B:ASP113 5.0 20.9 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