Calcium in PDB 6nvw: Crystal Structure of Penicillin G Acylase From Bacillus Megaterium

All present enzymatic activity of Crystal Structure of Penicillin G Acylase From Bacillus Megaterium:
3.5.1.11;

The structure of Crystal Structure of Penicillin G Acylase From Bacillus Megaterium, PDB code: 6nvw was solved by W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.03 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.238, 77.961, 84.086, 90.00, 101.67, 90.00
R / Rfree (%)	21.5 / 27.5

The binding sites of Calcium atom in the Crystal Structure of Penicillin G Acylase From Bacillus Megaterium (pdb code 6nvw). 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 Penicillin G Acylase From Bacillus Megaterium, PDB code: 6nvw:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Penicillin G Acylase From Bacillus Megaterium


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 Penicillin G Acylase From Bacillus Megaterium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:39.0 occ:1.00 OE2 B:GLU256 2.0 54.9 1.0 OD1 B:ASN73 2.3 42.7 1.0 O B:THR75 2.3 23.4 1.0 O B:HOH727 2.4 62.0 1.0 OD1 B:ASP76 2.4 30.9 1.0 OE2 A:GLU154 2.5 35.1 1.0 HA B:ASP76 2.6 27.1 1.0 CD B:GLU256 2.8 53.0 1.0 HD21 B:ASN73 3.0 55.7 1.0 OE1 B:GLU256 3.1 53.2 1.0 C B:THR75 3.1 25.0 1.0 CG B:ASP76 3.2 27.5 1.0 HH21 B:ARG203 3.2 40.4 1.0 CG B:ASN73 3.2 44.9 1.0 CA B:ASP76 3.3 21.6 1.0 ND2 B:ASN73 3.5 45.5 1.0 CD A:GLU154 3.5 35.9 1.0 N B:ASP76 3.5 20.1 1.0 HG3 A:GLU154 3.7 44.9 1.0 CB B:ASP76 3.8 23.9 1.0 NH2 B:ARG203 3.8 32.8 1.0 H B:THR75 3.8 35.8 1.0 OD2 B:ASP76 4.0 31.1 1.0 HE B:ARG203 4.1 56.0 1.0 O B:HOH726 4.1 34.6 1.0 CG A:GLU154 4.1 36.5 1.0 HH22 B:ARG203 4.2 40.4 1.0 CG B:GLU256 4.2 47.0 1.0 HB3 B:ASP76 4.2 29.8 1.0 HG2 B:GLU256 4.3 57.4 1.0 HG2 A:GLU154 4.3 44.9 1.0 H B:ASP76 4.3 25.2 1.0 N B:THR75 4.3 28.9 1.0 HD22 B:ASN73 4.3 55.7 1.0 CA B:THR75 4.3 29.2 1.0 H B:ILE77 4.4 32.1 1.0 OE1 A:GLU154 4.5 36.6 1.0 H B:GLU256 4.5 39.1 1.0 HB3 B:GLU256 4.5 46.5 1.0 HA B:ASN73 4.5 46.7 1.0 O B:GLU209 4.6 32.7 1.0 HB2 B:ASP76 4.6 29.8 1.0 CZ B:ARG203 4.6 39.2 1.0 CB B:ASN73 4.6 41.9 1.0 NE B:ARG203 4.6 45.7 1.0 C B:ASP76 4.6 26.7 1.0 HB B:THR75 4.8 35.1 1.0 HG3 B:GLU256 4.8 57.4 1.0 N B:ILE77 4.9 25.9 1.0 CA B:ASN73 5.0 38.0 1.0 CB B:GLU256 5.0 37.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Penicillin G Acylase From Bacillus Megaterium


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 Penicillin G Acylase From Bacillus Megaterium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:41.1 occ:1.00 OD1 B:ASP344 2.1 54.5 1.0 O B:TYR342 2.1 54.8 1.0 O B:HOH755 2.2 38.1 1.0 OD1 B:ASN338 2.2 45.2 1.0 HD21 B:ASN338 2.3 52.7 1.0 OD1 B:ASP340 2.3 35.7 1.0 OD1 B:ASP336 2.7 36.4 1.0 ND2 B:ASN338 2.8 43.0 1.0 CG B:ASN338 2.8 46.6 1.0 HA B:ASP336 3.1 49.9 1.0 CG B:ASP340 3.2 38.7 1.0 C B:TYR342 3.2 49.9 1.0 CG B:ASP344 3.3 51.7 1.0 HA B:ASP344 3.4 59.2 1.0 OD2 B:ASP340 3.5 35.8 1.0 CG B:ASP336 3.6 36.6 1.0 C B:TYR343 3.6 47.2 1.0 HD22 B:ASN338 3.6 52.7 1.0 H B:TYR342 3.6 65.5 1.0 HA B:TYR343 3.7 56.6 1.0 N B:ASP344 3.7 46.6 1.0 H B:ASP340 3.8 67.5 1.0 O B:TYR343 3.8 46.7 1.0 H B:ASN338 3.9 70.7 1.0 CA B:ASP344 3.9 48.5 1.0 CA B:ASP336 3.9 40.6 1.0 CA B:TYR343 4.0 46.2 1.0 N B:TYR343 4.0 48.4 1.0 H B:ASP344 4.1 57.0 1.0 OD2 B:ASP344 4.1 53.5 1.0 CB B:ASP336 4.2 40.6 1.0 CB B:ASP344 4.2 51.3 1.0 HB2 B:TYR342 4.2 57.3 1.0 CA B:TYR342 4.2 51.0 1.0 N B:TYR342 4.2 53.6 1.0 HB2 B:ASP336 4.3 49.8 1.0 CB B:ASN338 4.3 51.7 1.0 OD2 B:ASP336 4.3 36.0 1.0 C B:ASP336 4.5 43.3 1.0 N B:ASP340 4.5 55.3 1.0 CB B:ASP340 4.5 44.3 1.0 H B:LYS339 4.5 71.7 1.0 O B:GLU335 4.5 40.8 1.0 N B:ASN338 4.6 58.0 1.0 HB3 B:ASP344 4.6 62.7 1.0 HB3 B:ASN338 4.7 63.1 1.0 CB B:TYR342 4.7 46.8 1.0 HB3 B:ASP340 4.7 54.2 1.0 N B:LYS339 4.8 58.8 1.0 HB2 B:ASN338 4.8 63.1 1.0 H B:GLU337 4.8 60.2 1.0 CA B:ASN338 4.8 55.7 1.0 H B:TYR343 4.9 59.1 1.0 N B:GLU337 4.9 49.3 1.0 CA B:ASP340 4.9 51.3 1.0 C B:ASP340 4.9 55.7 1.0 HB2 B:ASP344 4.9 62.7 1.0 C B:ASN338 5.0 57.5 1.0 O B:ASP340 5.0 60.9 1.0

J.Mayer, J.Pippel, G.Gunther, C.Muller, A.Lauermann, T.Knuuti, W.Blankenfeldt, D.Jahn, R.Biedendieck. Crystal Structures and Protein Engineering of Three Different Penicillin G Acylases From Gram-Positive Bacteria with Different Thermostability. Appl.Microbiol.Biotechnol. V. 103 7537 2019.
ISSN: ESSN 1432-0614
PubMed: 31227867
DOI: 10.1007/S00253-019-09977-8