Calcium in PDB 8brr: Crystal Structure of A Variant of Penicillin G Acylase From Bacillaceae I. S. Sp. Fjat-27231 with Reduced Surface Entropy and Additionally Engineered Crystal Contact

The structure of Crystal Structure of A Variant of Penicillin G Acylase From Bacillaceae I. S. Sp. Fjat-27231 with Reduced Surface Entropy and Additionally Engineered Crystal Contact, PDB code: 8brr was solved by J.Wichmann, J.Mayer, H.Mattes, P.Lukat, W.Blankenfeldt, R.Biedendieck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.30 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.276, 139.227, 100.638, 90, 91.51, 90
R / Rfree (%)	19.1 / 23.2

The binding sites of Calcium atom in the Crystal Structure of A Variant of Penicillin G Acylase From Bacillaceae I. S. Sp. Fjat-27231 with Reduced Surface Entropy and Additionally Engineered Crystal Contact (pdb code 8brr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of A Variant of Penicillin G Acylase From Bacillaceae I. S. Sp. Fjat-27231 with Reduced Surface Entropy and Additionally Engineered Crystal Contact, PDB code: 8brr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of A Variant of Penicillin G Acylase From Bacillaceae I. S. Sp. Fjat-27231 with Reduced Surface Entropy and Additionally Engineered Crystal Contact


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 A Variant of Penicillin G Acylase From Bacillaceae I. S. Sp. Fjat-27231 with Reduced Surface Entropy and Additionally Engineered Crystal Contact within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:21.8 occ:1.00 O B:THR75 2.2 27.6 1.0 OE2 A:GLU154 2.3 26.5 1.0 OE2 B:GLU256 2.3 23.6 1.0 OD1 B:ASP76 2.3 24.8 1.0 OD1 B:ASN73 2.3 24.1 1.0 OE1 B:GLU256 2.5 20.9 1.0 O B:HOH795 2.5 20.9 1.0 CD B:GLU256 2.7 27.9 1.0 HA B:ASP76 2.9 31.2 1.0 HD21 B:ASN73 3.0 30.0 1.0 CG B:ASN73 3.2 25.1 1.0 C B:THR75 3.3 26.8 1.0 CD A:GLU154 3.5 26.6 1.0 ND2 B:ASN73 3.5 24.9 1.0 CG B:ASP76 3.5 26.5 1.0 HH21 B:ARG203 3.5 32.7 1.0 CA B:ASP76 3.7 25.9 1.0 HG3 A:GLU154 3.8 28.3 1.0 N B:ASP76 3.9 25.5 1.0 H B:THR75 4.0 26.8 1.0 NH2 B:ARG203 4.1 27.2 1.0 CG A:GLU154 4.2 23.5 1.0 O B:HOH793 4.2 31.4 1.0 CB B:ASP76 4.2 26.3 1.0 H B:GLU256 4.2 30.5 1.0 CG B:GLU256 4.2 21.5 1.0 HE B:ARG203 4.3 32.0 1.0 HD22 B:ASN73 4.3 30.0 1.0 HG2 A:GLU154 4.4 28.3 1.0 OD2 B:ASP76 4.4 26.6 1.0 OE1 A:GLU154 4.4 27.2 1.0 HH22 B:ARG203 4.5 32.7 1.0 HG3 B:GLU256 4.5 25.9 1.0 O B:ASP209 4.5 23.9 1.0 CA B:THR75 4.5 23.7 1.0 N B:THR75 4.5 22.2 1.0 O B:HOH1021 4.5 27.8 1.0 O A:HOH416 4.6 25.4 1.0 HB3 B:GLU256 4.6 29.7 1.0 H B:ILE77 4.6 31.6 1.0 HA B:ASN73 4.6 32.4 1.0 CB B:ASN73 4.7 26.8 1.0 HB B:THR75 4.7 33.9 1.0 HB3 B:ASP76 4.7 31.6 1.0 H B:ASP76 4.7 30.7 1.0 HG2 B:GLU256 4.7 25.9 1.0 NE B:ARG203 4.8 26.6 1.0 CZ B:ARG203 4.8 27.0 1.0 O A:HOH329 4.9 24.7 1.0 HA3 B:GLY255 4.9 31.0 1.0 HB2 B:ASP76 4.9 31.6 1.0 C B:ASP76 4.9 23.0 1.0 CB B:GLU256 5.0 24.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of A Variant of Penicillin G Acylase From Bacillaceae I. S. Sp. Fjat-27231 with Reduced Surface Entropy and Additionally Engineered Crystal Contact


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 A Variant of Penicillin G Acylase From Bacillaceae I. S. Sp. Fjat-27231 with Reduced Surface Entropy and Additionally Engineered Crystal Contact within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca604 b:34.2 occ:1.00 O B:TYR342 2.2 30.9 1.0 OD1 B:ASP340 2.3 35.1 1.0 OD1 B:ASP344 2.3 36.5 1.0 OD1 B:ASN338 2.3 39.8 1.0 OD1 B:ASP336 2.4 32.2 1.0 CG B:ASP340 2.9 36.8 1.0 OD2 B:ASP340 3.0 39.4 1.0 HA B:ASP336 3.1 37.3 1.0 H B:TYR342 3.3 38.6 1.0 C B:TYR342 3.4 30.7 1.0 H B:ASP340 3.4 48.4 1.0 CG B:ASN338 3.4 39.2 1.0 CG B:ASP336 3.4 33.5 1.0 HD21 B:ASN338 3.5 47.1 1.0 CG B:ASP344 3.6 35.5 1.0 HA B:ASP344 3.7 41.5 1.0 H B:ASN338 3.8 46.4 1.0 ND2 B:ASN338 3.8 39.1 1.0 CA B:ASP336 3.9 31.0 1.0 HB2 B:TYR342 3.9 37.9 1.0 N B:TYR342 4.0 32.1 1.0 N B:ASP344 4.1 31.8 1.0 CB B:ASP336 4.1 34.4 1.0 CA B:TYR342 4.1 33.4 1.0 N B:ASP340 4.2 40.3 1.0 H B:HIS339 4.2 47.7 1.0 C B:TYR343 4.2 31.6 1.0 CA B:ASP344 4.2 34.5 1.0 CB B:ASP340 4.2 40.3 1.0 HA B:TYR343 4.3 39.0 1.0 HB2 B:ASP336 4.3 41.3 1.0 H B:LYS337 4.3 43.7 1.0 OD2 B:ASP336 4.3 33.7 1.0 H B:ASP344 4.3 38.2 1.0 OD2 B:ASP344 4.4 34.0 1.0 N B:TYR343 4.4 29.6 1.0 C B:ASP336 4.4 37.7 1.0 H B:GLY341 4.4 46.0 1.0 CB B:TYR342 4.5 31.5 1.0 CB B:ASP344 4.5 35.6 1.0 N B:ASN338 4.5 38.5 1.0 HB3 B:ASP340 4.5 48.4 1.0 CA B:TYR343 4.5 32.4 1.0 N B:LYS337 4.5 36.3 1.0 O B:TYR343 4.6 28.2 1.0 N B:HIS339 4.6 39.7 1.0 O B:GLU335 4.6 33.8 1.0 CA B:ASP340 4.7 37.1 1.0 HD22 B:ASN338 4.7 47.1 1.0 HD3 B:ARG433 4.7 43.2 1.0 CB B:ASN338 4.7 40.9 1.0 N B:GLY341 4.7 38.2 1.0 HB3 B:TYR342 4.8 37.9 1.0 HB3 B:ASP344 4.9 42.9 1.0 C B:ASP340 4.9 36.5 1.0 HB2 B:ASP340 4.9 48.4 1.0 CA B:ASN338 5.0 40.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of A Variant of Penicillin G Acylase From Bacillaceae I. S. Sp. Fjat-27231 with Reduced Surface Entropy and Additionally Engineered Crystal Contact


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Variant of Penicillin G Acylase From Bacillaceae I. S. Sp. Fjat-27231 with Reduced Surface Entropy and Additionally Engineered Crystal Contact within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca603 b:19.3 occ:1.00 OE2 C:GLU154 2.1 25.6 1.0 O D:THR75 2.2 24.7 1.0 OD1 D:ASP76 2.4 28.3 1.0 OE1 D:GLU256 2.4 24.2 1.0 OD1 D:ASN73 2.4 24.6 1.0 O D:HOH758 2.4 24.7 1.0 OE2 D:GLU256 2.4 25.8 1.0 CD D:GLU256 2.7 25.9 1.0 HA D:ASP76 2.9 29.5 1.0 HD21 D:ASN73 3.1 34.5 1.0 CG D:ASN73 3.3 25.3 1.0 C D:THR75 3.3 25.5 1.0 CD C:GLU154 3.4 24.6 1.0 CG D:ASP76 3.5 26.9 1.0 ND2 D:ASN73 3.5 28.6 1.0 HH21 D:ARG203 3.6 32.0 1.0 CA D:ASP76 3.7 24.5 1.0 HG3 C:GLU154 3.8 31.9 1.0 N D:ASP76 3.9 27.0 1.0 CG C:GLU154 4.1 26.5 1.0 H D:GLU256 4.1 30.0 1.0 H D:THR75 4.1 32.4 1.0 NH2 D:ARG203 4.2 26.6 1.0 CB D:ASP76 4.2 23.8 1.0 CG D:GLU256 4.2 22.6 1.0 OE1 C:GLU154 4.3 26.8 1.0 HE D:ARG203 4.3 37.6 1.0 O D:HOH740 4.3 30.2 1.0 HD22 D:ASN73 4.4 34.5 1.0 HG2 C:GLU154 4.4 31.9 1.0 O D:ASP209 4.4 24.6 1.0 OD2 D:ASP76 4.5 27.3 1.0 HG3 D:GLU256 4.5 27.2 1.0 O D:HOH983 4.5 26.7 1.0 HH22 D:ARG203 4.5 32.0 1.0 CA D:THR75 4.5 25.2 1.0 HB3 D:GLU256 4.6 32.3 1.0 H D:ILE77 4.6 32.2 1.0 N D:THR75 4.6 26.9 1.0 O C:HOH384 4.6 22.7 1.0 HB D:THR75 4.7 31.4 1.0 HA D:ASN73 4.7 30.6 1.0 CB D:ASN73 4.7 25.1 1.0 HA3 D:GLY255 4.7 28.4 1.0 HB3 D:ASP76 4.7 28.6 1.0 O D:HOH753 4.7 28.9 1.0 HG2 D:GLU256 4.8 27.2 1.0 H D:ASP76 4.8 32.4 1.0 NE D:ARG203 4.8 31.2 1.0 CZ D:ARG203 4.8 25.9 1.0 HB2 D:ASP76 4.9 28.6 1.0 C D:ASP76 4.9 29.5 1.0 CB D:GLU256 5.0 26.8 1.0 N D:GLU256 5.0 24.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of A Variant of Penicillin G Acylase From Bacillaceae I. S. Sp. Fjat-27231 with Reduced Surface Entropy and Additionally Engineered Crystal Contact


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Variant of Penicillin G Acylase From Bacillaceae I. S. Sp. Fjat-27231 with Reduced Surface Entropy and Additionally Engineered Crystal Contact within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca604 b:38.4 occ:1.00 O D:TYR342 2.3 31.2 1.0 OD1 D:ASP336 2.3 34.8 1.0 OD1 D:ASN338 2.4 34.1 1.0 OD1 D:ASP340 2.4 35.9 1.0 OD1 D:ASP344 2.4 33.4 1.0 O D:HOH707 2.6 38.5 1.0 CG D:ASP340 3.1 34.5 1.0 HA D:ASP336 3.1 36.1 1.0 H D:ASP340 3.3 47.0 1.0 H D:TYR342 3.4 40.4 1.0 OD2 D:ASP340 3.4 42.0 1.0 CG D:ASP336 3.4 35.0 1.0 CG D:ASN338 3.5 30.9 1.0 C D:TYR342 3.5 32.7 1.0 HD21 D:ASN338 3.6 45.0 1.0 CG D:ASP344 3.7 34.4 1.0 HA D:ASP344 3.7 40.1 1.0 H D:ASN338 3.8 37.3 1.0 HB2 D:TYR342 3.9 40.8 1.0 CA D:ASP336 3.9 30.1 1.0 ND2 D:ASN338 3.9 37.4 1.0 HH21 D:ARG433 4.0 79.2 1.0 N D:TYR342 4.1 33.6 1.0 N D:ASP340 4.1 39.1 1.0 CB D:ASP336 4.1 30.9 1.0 N D:ASP344 4.2 31.5 1.0 H D:HIS339 4.2 48.4 1.0 CA D:TYR342 4.2 31.3 1.0 H D:LYS337 4.3 40.1 1.0 C D:TYR343 4.3 31.0 1.0 C D:ASP336 4.3 35.8 1.0 CB D:ASP340 4.3 36.4 1.0 CA D:ASP344 4.3 33.4 1.0 HB2 D:ASP336 4.3 37.2 1.0 OD2 D:ASP336 4.4 38.0 1.0 H D:ASP344 4.4 37.9 1.0 HE D:ARG433 4.4 66.5 1.0 HA D:TYR343 4.4 36.8 1.0 N D:LYS337 4.5 33.4 1.0 N D:ASN338 4.5 31.0 1.0 HB3 D:ASP340 4.5 43.7 1.0 OD2 D:ASP344 4.5 35.6 1.0 N D:TYR343 4.5 29.2 1.0 CB D:TYR342 4.5 33.9 1.0 N D:HIS339 4.5 40.2 1.0 CB D:ASP344 4.6 32.3 1.0 O D:TYR343 4.6 28.7 1.0 CA D:ASP340 4.7 37.2 1.0 CA D:TYR343 4.7 30.6 1.0 H D:GLY341 4.7 39.7 1.0 CB D:ASN338 4.7 36.9 1.0 NH2 D:ARG433 4.8 66.0 1.0 O D:GLU335 4.8 27.5 1.0 HD22 D:ASN338 4.8 45.0 1.0 N D:GLY341 4.9 33.0 1.0 C D:ASN338 4.9 38.8 1.0 C D:ASP340 4.9 33.7 1.0 HB3 D:TYR342 4.9 40.8 1.0 CA D:ASN338 4.9 37.5 1.0 O D:ASP336 5.0 33.3 1.0 HB3 D:ASP344 5.0 38.9 1.0

J.Wichmann, J.Mayer, M.Hintmann, P.Lukat, W.Blankenfeldt, R.Biedendieck. Multistep Engineering of A Penicillin G Acylase For Systematic Improvement of Crystallization Efficiency Cryst.Growth Des. 2023.
ISSN: ESSN 1528-7505
DOI: 10.1021/ACS.CGD.2C01408