Calcium in PDB 5k21: Pyocyanin Demethylase

The structure of Pyocyanin Demethylase, PDB code: 5k21 was solved by K.C.Costa, N.R.Glasser, D.K.Newman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.98 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.330, 72.980, 79.700, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 19.5

The binding sites of Calcium atom in the Pyocyanin Demethylase (pdb code 5k21). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Pyocyanin Demethylase, PDB code: 5k21:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Pyocyanin Demethylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pyocyanin Demethylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:21.0 occ:1.00 OD1 A:ASP56 2.2 23.0 1.0 OD1 A:ASP63 2.3 23.3 1.0 O A:LYS59 2.3 25.2 1.0 O A:PHE57 2.4 21.4 1.0 O A:GLY61 2.4 19.8 1.0 OD2 A:ASP66 2.5 23.5 1.0 OD1 A:ASP66 2.6 18.9 1.0 CG A:ASP66 2.9 20.7 1.0 CG A:ASP63 3.3 26.4 1.0 CG A:ASP56 3.4 27.4 1.0 C A:LYS59 3.5 22.1 1.0 H A:ASP63 3.5 26.7 1.0 C A:PHE57 3.5 22.0 1.0 C A:GLY61 3.5 23.4 1.0 HA A:ASP56 3.6 26.4 1.0 H A:PHE57 3.7 26.7 1.0 N A:PHE57 3.8 22.2 1.0 N A:ASP63 3.9 22.2 1.0 HA A:PRO60 4.0 29.7 1.0 OD2 A:ASP63 4.0 27.9 1.0 HA A:MET62 4.0 30.5 1.0 C A:ASP56 4.1 23.6 1.0 N A:GLY61 4.1 25.4 1.0 N A:LYS59 4.1 24.4 1.0 OD2 A:ASP56 4.1 26.4 1.0 H A:GLY61 4.2 30.5 1.0 H A:LYS59 4.2 29.3 1.0 C A:PRO60 4.2 26.3 1.0 CA A:ASP56 4.2 22.0 1.0 CA A:PHE57 4.3 22.9 1.0 C A:GLY58 4.3 25.4 1.0 CB A:ASP63 4.4 25.0 1.0 CA A:PRO60 4.4 24.7 1.0 O A:HOH331 4.4 19.6 1.0 HB3 A:ASP63 4.4 30.0 1.0 N A:PRO60 4.4 22.7 1.0 CA A:LYS59 4.4 24.8 1.0 C A:MET62 4.4 23.4 1.0 CB A:ASP56 4.4 25.8 1.0 CB A:ASP66 4.4 19.9 1.0 O A:HOH326 4.4 26.5 1.0 CA A:GLY61 4.4 26.6 1.0 N A:MET62 4.5 24.0 1.0 CA A:MET62 4.5 25.4 1.0 O A:HOH321 4.5 31.8 1.0 HA3 A:GLY58 4.5 31.8 1.0 N A:GLY58 4.6 25.2 1.0 CA A:ASP63 4.6 23.0 1.0 O A:PRO60 4.7 24.1 1.0 O A:GLY58 4.7 25.8 1.0 CA A:GLY58 4.7 26.5 1.0 O A:ASP56 4.8 24.1 1.0 O A:ASP63 4.8 19.6 1.0 HB3 A:ASP66 4.8 23.8 1.0 HB2 A:ASP66 4.8 23.8 1.0 HB2 A:ASP56 4.9 31.0 1.0 HB2 A:PHE57 5.0 27.1 1.0 HA A:PHE57 5.0 27.5 1.0

Calcium binding site 2 out of 3 in the Pyocyanin Demethylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pyocyanin Demethylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:22.6 occ:1.00 OD1 B:ASP56 2.3 26.2 1.0 O B:GLY61 2.3 24.3 1.0 OD1 B:ASP63 2.3 28.1 1.0 O B:LYS59 2.4 26.4 1.0 O B:PHE57 2.4 21.3 1.0 OD1 B:ASP66 2.4 23.2 1.0 OD2 B:ASP66 2.6 25.7 1.0 CG B:ASP66 2.9 22.7 1.0 CG B:ASP63 3.4 32.4 1.0 H B:ASP63 3.5 34.6 1.0 CG B:ASP56 3.5 26.7 1.0 C B:GLY61 3.5 27.1 1.0 C B:LYS59 3.5 28.3 1.0 C B:PHE57 3.6 22.2 1.0 HA B:ASP56 3.6 25.3 1.0 HA B:PRO60 3.8 36.7 1.0 N B:PHE57 3.8 22.1 1.0 H B:PHE57 3.9 26.5 1.0 N B:ASP63 3.9 28.9 1.0 C B:ASP56 3.9 22.2 1.0 N B:GLY61 4.0 27.6 1.0 HA B:MET62 4.0 43.4 1.0 H B:GLY61 4.0 33.1 1.0 O B:HOH329 4.1 21.5 1.0 OD2 B:ASP63 4.1 33.2 1.0 CA B:ASP56 4.1 21.1 1.0 N B:LYS59 4.2 27.0 1.0 C B:PRO60 4.2 31.0 1.0 H B:LYS59 4.2 32.4 1.0 OD2 B:ASP56 4.2 29.6 1.0 CA B:PRO60 4.3 30.6 1.0 CA B:GLY61 4.3 27.8 1.0 N B:PRO60 4.3 29.8 1.0 CA B:PHE57 4.4 22.7 1.0 C B:GLY58 4.4 24.4 1.0 CB B:ASP63 4.4 28.5 1.0 CB B:ASP66 4.4 22.0 1.0 HA3 B:GLY58 4.4 28.1 1.0 HB3 B:ASP63 4.4 34.2 1.0 CB B:ASP56 4.4 22.8 1.0 N B:MET62 4.4 32.0 1.0 C B:MET62 4.4 33.0 1.0 O B:ASP56 4.5 24.4 1.0 CA B:MET62 4.5 36.1 1.0 CA B:LYS59 4.5 28.5 1.0 N B:GLY58 4.6 23.2 1.0 CA B:ASP63 4.6 27.1 1.0 O B:ASP63 4.6 27.8 1.0 CA B:GLY58 4.7 23.4 1.0 O B:GLY58 4.8 23.8 1.0 HB3 B:ASP66 4.8 26.4 1.0 O B:PRO60 4.8 30.9 1.0 HB2 B:ASP66 4.8 26.4 1.0 HA B:ASP66 4.9 23.3 1.0 HA3 B:GLY61 5.0 33.4 1.0 C B:ASP63 5.0 26.4 1.0 HA2 B:GLY61 5.0 33.4 1.0 HB2 B:ASP56 5.0 27.4 1.0

Calcium binding site 3 out of 3 in the Pyocyanin Demethylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pyocyanin Demethylase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:25.6 occ:1.00 OD1 C:ASP56 2.2 31.2 1.0 O C:PHE57 2.3 24.5 1.0 OD1 C:ASP63 2.3 28.8 1.0 O C:GLY61 2.3 31.6 1.0 O C:LYS59 2.4 29.5 1.0 OD1 C:ASP66 2.5 21.8 1.0 OD2 C:ASP66 2.5 28.9 1.0 CG C:ASP66 2.9 25.4 1.0 CG C:ASP63 3.4 32.0 1.0 CG C:ASP56 3.4 32.6 1.0 H C:PHE57 3.5 29.4 1.0 C C:PHE57 3.5 23.4 1.0 H C:ASP63 3.5 35.9 1.0 C C:GLY61 3.5 31.5 1.0 C C:LYS59 3.6 33.0 1.0 HA C:ASP56 3.6 31.5 1.0 N C:PHE57 3.7 24.5 1.0 N C:ASP63 3.9 29.9 1.0 HA C:MET62 4.0 43.3 1.0 OD2 C:ASP63 4.0 37.6 1.0 N C:LYS59 4.1 33.1 1.0 H C:LYS59 4.1 39.7 1.0 C C:ASP56 4.1 25.2 1.0 N C:GLY61 4.1 32.9 1.0 O C:HOH329 4.1 22.9 1.0 CA C:ASP56 4.2 26.2 1.0 OD2 C:ASP56 4.2 36.2 1.0 H C:GLY61 4.2 39.5 1.0 CA C:PHE57 4.2 23.3 1.0 HA C:PRO60 4.2 41.7 1.0 C C:PRO60 4.3 35.5 1.0 C C:GLY58 4.3 30.7 1.0 CB C:ASP63 4.4 30.7 1.0 HA3 C:GLY58 4.4 39.1 1.0 CA C:LYS59 4.4 35.4 1.0 HB3 C:ASP63 4.4 36.8 1.0 CB C:ASP56 4.4 27.6 1.0 CB C:ASP66 4.4 23.9 1.0 C C:MET62 4.5 32.5 1.0 CA C:GLY61 4.5 32.3 1.0 N C:MET62 4.5 34.2 1.0 N C:PRO60 4.5 33.9 1.0 CA C:MET62 4.5 36.1 1.0 N C:GLY58 4.5 29.2 1.0 CA C:PRO60 4.5 34.8 1.0 O C:HOH350 4.6 39.1 1.0 CA C:ASP63 4.6 29.1 1.0 CA C:GLY58 4.6 32.6 1.0 O C:PRO60 4.7 39.2 1.0 O C:ASP63 4.8 27.3 1.0 O C:GLY58 4.8 32.9 1.0 HB2 C:ASP66 4.8 28.6 1.0 HB3 C:ASP66 4.8 28.6 1.0 HA C:PHE57 4.9 27.9 1.0 HB2 C:PHE57 4.9 31.8 1.0 HB2 C:ASP56 4.9 33.1 1.0 O C:ASP56 5.0 25.7 1.0

K.C.Costa, N.R.Glasser, S.J.Conway, D.K.Newman. Pyocyanin Degradation By A Tautomerizing Demethylase Inhibits Pseudomonas Aeruginosa Biofilms. Science V. 355 170 2017.
ISSN: ESSN 1095-9203
PubMed: 27940577
DOI: 10.1126/SCIENCE.AAG3180