Sodium in PDB 6jyv: Structure of An Isopenicillin N Synthase From Pseudomonas Aeruginosa PAO1

The structure of Structure of An Isopenicillin N Synthase From Pseudomonas Aeruginosa PAO1, PDB code: 6jyv was solved by Z.Hao, S.Che, R.Wang, R.Liu, Q.Zhang, M.Bartlam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.91 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.510, 115.690, 68.830, 90.00, 90.90, 90.00
R / Rfree (%)	16.3 / 20.8

The binding sites of Sodium atom in the Structure of An Isopenicillin N Synthase From Pseudomonas Aeruginosa PAO1 (pdb code 6jyv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of An Isopenicillin N Synthase From Pseudomonas Aeruginosa PAO1, PDB code: 6jyv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of An Isopenicillin N Synthase From Pseudomonas Aeruginosa PAO1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of An Isopenicillin N Synthase From Pseudomonas Aeruginosa PAO1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:28.3 occ:1.00 O A:HOH963 2.2 31.9 1.0 OD1 A:ASP203 2.5 16.5 1.0 NE2 A:HIS201 2.8 20.5 1.0 HZ A:PHE274 3.0 15.6 1.0 CG A:ASP203 3.5 16.2 1.0 O A:HOH545 3.5 31.9 1.0 HD2 A:HIS201 3.6 21.4 1.0 HE1 A:PHE274 3.6 14.1 1.0 CD2 A:HIS201 3.6 17.9 1.0 CZ A:PHE274 3.7 13.0 1.0 NE2 A:HIS257 3.7 21.2 1.0 OD2 A:ASP203 3.9 14.3 1.0 CE1 A:HIS201 3.9 15.9 1.0 CE1 A:PHE274 4.0 11.7 1.0 HE1 A:HIS201 4.1 19.1 1.0 HE1 A:HIS257 4.2 18.3 1.0 O A:HOH1016 4.3 34.1 1.0 O A:HOH949 4.3 31.1 1.0 O A:HOH925 4.3 31.9 1.0 CE1 A:HIS257 4.4 15.2 1.0 O A:HOH944 4.4 28.5 1.0 O A:HOH736 4.5 21.6 1.0 HA A:ASP203 4.6 13.7 1.0 O A:HOH830 4.7 17.6 1.0 CD2 A:HIS257 4.8 14.9 1.0 CG A:HIS201 4.8 12.5 1.0 CB A:ASP203 4.9 12.4 1.0 HG21 A:THR208 4.9 17.9 1.0 CE2 A:PHE274 4.9 12.5 1.0 ND1 A:HIS201 5.0 15.2 1.0 HG1 A:THR208 5.0 14.4 1.0

Sodium binding site 2 out of 2 in the Structure of An Isopenicillin N Synthase From Pseudomonas Aeruginosa PAO1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of An Isopenicillin N Synthase From Pseudomonas Aeruginosa PAO1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:29.4 occ:1.00 OD1 B:ASP203 2.6 17.7 1.0 NE2 B:HIS201 2.7 17.2 1.0 HZ B:PHE274 3.2 14.7 1.0 O B:HOH743 3.3 32.8 1.0 HE2 B:PHE274 3.5 14.6 1.0 NE2 B:HIS257 3.5 23.8 1.0 CG B:ASP203 3.5 21.9 1.0 CE1 B:HIS201 3.6 16.1 1.0 CD2 B:HIS201 3.6 20.4 1.0 HE1 B:HIS201 3.7 19.3 1.0 HD2 B:HIS201 3.7 24.5 1.0 OD2 B:ASP203 3.7 15.6 1.0 CZ B:PHE274 3.9 12.3 1.0 HE1 B:HIS257 3.9 19.0 1.0 CE2 B:PHE274 4.0 12.2 1.0 CE1 B:HIS257 4.1 15.8 1.0 O B:HOH985 4.3 37.5 1.0 O B:HOH968 4.5 33.3 1.0 CD2 B:HIS257 4.6 14.3 1.0 HG21 B:THR208 4.7 16.3 1.0 ND1 B:HIS201 4.8 15.1 1.0 CG B:HIS201 4.8 17.6 1.0 HA B:ASP203 4.8 14.3 1.0 HD2 B:HIS257 4.9 17.1 1.0 HG1 B:THR208 4.9 15.5 1.0 CB B:ASP203 4.9 13.3 1.0

H.Zhang, S.Che, R.Wang, R.Liu, Q.Zhang, M.Bartlam. Structural Characterization of An Isopenicillin N Synthase Family Oxygenase From Pseudomonas Aeruginosa PAO1. Biochem.Biophys.Res.Commun. V. 514 1031 2019.
ISSN: ESSN 1090-2104
PubMed: 31097228
DOI: 10.1016/J.BBRC.2019.05.062