Calcium in PDB 6nvx: Crystal Structure of Penicillin G Acylase From Bacillus Sp. Fjat-27231

The structure of Crystal Structure of Penicillin G Acylase From Bacillus Sp. Fjat-27231, PDB code: 6nvx was solved by W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.15 / 1.36
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.366, 77.686, 210.365, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 16.7

The binding sites of Calcium atom in the Crystal Structure of Penicillin G Acylase From Bacillus Sp. Fjat-27231 (pdb code 6nvx). 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 Sp. Fjat-27231, PDB code: 6nvx:
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 Sp. Fjat-27231


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 Sp. Fjat-27231 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca605 b:19.6 occ:1.00 O B:TYR342 2.3 18.8 1.0 OD1 B:ASP340 2.3 22.4 1.0 OD1 B:ASP344 2.3 17.9 1.0 OD1 B:ASP336 2.3 19.8 1.0 OD1 B:ASN338 2.4 25.6 1.0 O B:HOH1163 2.4 23.2 1.0 HA B:ASP336 3.1 19.7 1.0 CG B:ASP340 3.2 26.2 1.0 H B:TYR342 3.3 24.5 1.0 CG B:ASP336 3.4 20.8 1.0 H B:ASP340 3.4 29.4 1.0 C B:TYR342 3.4 16.3 1.0 CG B:ASN338 3.5 27.8 1.0 HA B:ASP344 3.5 20.7 1.0 CG B:ASP344 3.6 16.9 1.0 OD2 B:ASP340 3.7 29.0 1.0 H B:ASN338 3.7 25.6 1.0 HD21 B:ASN338 3.7 35.3 1.0 HB2 B:TYR342 3.8 23.6 1.0 CA B:ASP336 3.9 16.4 1.0 N B:TYR342 4.0 20.4 1.0 ND2 B:ASN338 4.0 29.4 1.0 CB B:ASP336 4.1 19.0 1.0 N B:ASP344 4.2 15.8 1.0 CA B:TYR342 4.2 18.7 1.0 CA B:ASP344 4.2 17.3 1.0 HB2 B:ASP336 4.2 22.8 1.0 N B:ASP340 4.2 24.5 1.0 C B:TYR343 4.2 16.5 1.0 OD2 B:ASP336 4.3 21.8 1.0 H B:LYS337 4.4 21.8 1.0 C B:ASP336 4.4 20.0 1.0 CB B:ASP340 4.4 24.6 1.0 HA B:TYR343 4.4 19.1 1.0 OD2 B:ASP344 4.4 18.3 1.0 CB B:TYR342 4.4 19.7 1.0 CB B:ASP344 4.5 15.8 1.0 H B:ASP344 4.5 19.0 1.0 N B:ASN338 4.5 21.4 1.0 N B:TYR343 4.5 15.9 1.0 H B:HIS339 4.5 30.9 1.0 H B:GLY341 4.5 26.2 1.0 N B:LYS337 4.6 18.1 1.0 O B:TYR343 4.6 18.2 1.0 O B:HOH813 4.6 44.0 1.0 O B:HOH1222 4.6 43.1 1.0 O B:GLU335 4.6 15.5 1.0 HB3 B:ASP340 4.6 29.6 1.0 CA B:TYR343 4.6 15.9 1.0 CA B:ASP340 4.7 25.9 1.0 HB3 B:TYR342 4.7 23.6 1.0 O B:HOH1122 4.7 36.7 1.0 CB B:ASN338 4.8 23.4 1.0 N B:HIS339 4.8 25.7 1.0 N B:GLY341 4.8 21.9 1.0 HD3 B:ARG433 4.9 28.1 1.0 HB3 B:ASP344 4.9 19.0 1.0 C B:ASP340 4.9 23.1 1.0 HD22 B:ASN338 4.9 35.3 1.0 CA B:ASN338 4.9 22.6 1.0 C B:ASN338 4.9 30.2 1.0 HB3 B:ASP336 5.0 22.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Penicillin G Acylase From Bacillus Sp. Fjat-27231


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 Sp. Fjat-27231 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca606 b:13.1 occ:1.00 OE2 A:GLU154 2.3 14.9 1.0 O B:THR75 2.3 13.3 1.0 OD1 B:ASN73 2.4 13.4 1.0 OD1 B:ASP76 2.4 13.0 1.0 O B:HOH900 2.4 14.2 1.0 OE2 B:GLU256 2.5 15.6 1.0 OE1 B:GLU256 2.5 13.2 1.0 CD B:GLU256 2.8 14.1 1.0 HA B:ASP76 2.9 16.9 1.0 HD21 B:ASN73 3.1 16.0 1.0 CG B:ASN73 3.3 11.3 1.0 C B:THR75 3.4 13.4 1.0 CD A:GLU154 3.5 14.9 1.0 CG B:ASP76 3.5 13.4 1.0 ND2 B:ASN73 3.6 13.3 1.0 HH21 B:ARG203 3.7 18.2 1.0 CA B:ASP76 3.7 14.1 1.0 HG3 A:GLU154 3.8 17.4 1.0 N B:ASP76 4.0 13.4 1.0 CB B:ASP76 4.1 15.0 1.0 CG A:GLU154 4.1 14.5 1.0 H B:THR75 4.2 15.0 1.0 NH2 B:ARG203 4.2 15.1 1.0 CG B:GLU256 4.3 14.4 1.0 H B:GLU256 4.3 16.4 1.0 HE B:ARG203 4.3 17.9 1.0 HG2 A:GLU154 4.4 17.4 1.0 O B:HOH921 4.4 19.9 1.0 HD22 B:ASN73 4.4 16.0 1.0 OE1 A:GLU154 4.4 15.2 1.0 OD2 B:ASP76 4.5 15.3 1.0 O B:ASP209 4.5 13.4 1.0 HB3 B:ASP76 4.5 18.0 1.0 O B:HOH1086 4.5 15.9 1.0 HH22 B:ARG203 4.5 18.2 1.0 HG3 B:GLU256 4.5 17.3 1.0 O B:HOH1221 4.5 16.2 1.0 H B:ILE77 4.6 16.3 1.0 N B:THR75 4.6 12.5 1.0 CA B:THR75 4.7 12.2 1.0 HA B:ASN73 4.7 14.5 1.0 HB3 B:GLU256 4.7 17.3 1.0 CB B:ASN73 4.7 14.0 1.0 HA3 B:GLY255 4.7 15.3 1.0 HB B:THR75 4.7 16.9 1.0 HG2 B:GLU256 4.8 17.3 1.0 NE B:ARG203 4.8 14.9 1.0 H B:ASP76 4.8 16.1 1.0 CZ B:ARG203 4.8 14.4 1.0 O B:HOH800 4.9 15.3 1.0 C B:ASP76 4.9 14.1 1.0 HB2 B:ASP76 5.0 18.0 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