Sodium in PDB 6c5b: Crystal Structure Analysis of Laphzm

The structure of Crystal Structure Analysis of Laphzm, PDB code: 6c5b was solved by D.G.Beltran, A.Schacht, L.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.42 / 1.42
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.275, 81.017, 72.164, 90.00, 98.23, 90.00
R / Rfree (%)	18.1 / 20.3

The binding sites of Sodium atom in the Crystal Structure Analysis of Laphzm (pdb code 6c5b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure Analysis of Laphzm, PDB code: 6c5b:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure Analysis of Laphzm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of Laphzm within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:32.4 occ:0.50 NH1 B:ARG67 0.7 15.1 0.5 CZ B:ARG67 2.0 17.6 0.5 OG1 B:THR68 2.6 13.3 1.0 OD2 A:ASP295 2.8 16.5 1.0 NH2 B:ARG67 2.8 17.3 0.5 O A:LYS292 2.9 12.4 1.0 NE B:ARG67 3.0 16.3 0.5 O B:HOH501 3.1 17.9 0.5 O B:ARG64 3.2 11.0 1.0 CD B:ARG67 3.4 17.0 0.5 CG A:ASP295 3.6 13.4 1.0 C B:ARG64 3.7 9.9 1.0 CB B:ARG64 3.7 11.5 1.0 CD2 A:LEU296 3.8 12.6 1.0 CB A:ASP295 3.8 13.4 1.0 C A:LYS292 3.8 11.6 1.0 CA B:ARG64 3.8 9.7 1.0 CB B:THR68 4.0 10.8 1.0 CA A:LYS292 4.0 11.2 1.0 CG A:LEU296 4.1 11.5 1.0 CG B:ARG64 4.2 12.6 1.0 CG B:ARG67 4.3 13.3 0.5 CB A:LYS292 4.4 11.7 1.0 O B:HOH502 4.6 18.0 0.5 N A:LEU296 4.6 10.8 1.0 N B:THR68 4.6 10.7 1.0 OD1 A:ASP295 4.7 15.5 1.0 CA B:THR68 4.8 11.5 1.0 CG2 B:THR68 4.8 12.8 1.0 N B:VAL65 4.8 10.1 1.0 CA A:ASP295 4.9 11.4 1.0 CG A:LYS292 4.9 12.9 1.0 NE B:ARG64 4.9 11.7 1.0 CD1 A:LEU296 4.9 10.9 1.0 C A:ASP295 5.0 9.3 1.0

Sodium binding site 2 out of 3 in the Crystal Structure Analysis of Laphzm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of Laphzm within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:34.5 occ:1.00 O A:HOH718 2.0 30.2 1.0 O B:ALA116 2.5 16.9 1.0 O A:GLY108 2.8 11.0 1.0 O A:HOH740 2.8 26.0 1.0 C B:ALA116 3.6 14.4 1.0 O B:HOH631 3.9 11.9 1.0 C A:GLY108 3.9 9.9 1.0 CA A:GLU109 4.1 9.6 1.0 NE2 A:GLN27 4.2 10.6 1.0 NE A:ARG113 4.2 19.3 0.5 CA B:ALA116 4.2 12.0 1.0 NH2 A:ARG113 4.2 22.7 0.5 CE2 A:TYR30 4.3 11.1 1.0 NH1 A:ARG113 4.4 26.9 0.5 CB B:ALA116 4.4 12.0 1.0 N A:GLU109 4.5 9.9 1.0 O B:HOH684 4.5 20.3 1.0 OE1 A:GLN27 4.5 10.6 1.0 CZ A:TYR30 4.6 11.9 1.0 OH A:TYR30 4.6 14.1 1.0 CZ A:ARG113 4.6 19.6 0.5 CG A:GLU109 4.7 11.4 1.0 N B:ASP117 4.7 14.3 1.0 CD A:GLN27 4.8 9.8 1.0 O A:GLU109 4.8 9.8 1.0 C A:GLU109 4.8 9.7 1.0 CD2 A:TYR30 4.9 10.4 1.0 CB A:GLU109 4.9 11.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure Analysis of Laphzm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure Analysis of Laphzm within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:19.0 occ:0.33 NH1 A:ARG67 1.0 20.1 0.7 CZ A:ARG67 2.1 22.6 0.7 OD2 B:ASP295 2.6 16.0 1.0 NH2 A:ARG67 2.7 23.5 0.7 OG1 A:THR68 2.7 16.1 1.0 O B:LYS292 3.1 13.2 1.0 NE A:ARG67 3.2 19.8 0.7 CG B:ASP295 3.4 14.4 1.0 O A:ARG64 3.4 11.9 1.0 CB B:ASP295 3.5 14.1 1.0 CD A:ARG67 3.8 19.4 0.7 CB A:ARG64 3.9 13.2 1.0 CD2 B:LEU296 3.9 16.1 1.0 C B:LYS292 3.9 14.2 1.0 C A:ARG64 4.0 11.3 1.0 CA A:ARG64 4.0 12.2 1.0 CA B:LYS292 4.0 13.2 1.0 CB A:THR68 4.2 13.3 1.0 CG A:ARG64 4.3 15.3 1.0 CG A:ARG67 4.3 16.3 0.7 CB B:LYS292 4.3 13.4 1.0 CG B:LEU296 4.4 12.8 1.0 OD1 B:ASP295 4.5 17.1 1.0 O A:HOH601 4.6 20.5 0.5 CA B:ASP295 4.7 12.8 1.0 N B:LEU296 4.8 10.8 1.0 N A:THR68 4.8 12.1 1.0 NE A:ARG64 4.8 15.0 1.0 CA A:THR68 4.9 11.8 1.0 CG B:LYS292 4.9 16.3 1.0 CG2 A:THR68 4.9 13.0 1.0 C B:ASP295 4.9 11.6 1.0

J.Jiang, D.Guiza Beltran, A.Schacht, S.Wright, L.Zhang, L.Du. Functional and Structural Analysis of Phenazine O-Methyltransferase Laphzm From Lysobacter Antibioticus OH13 and One-Pot Enzymatic Synthesis of the Antibiotic Myxin. Acs Chem. Biol. V. 13 1003 2018.
ISSN: ESSN 1554-8937
PubMed: 29510028
DOI: 10.1021/ACSCHEMBIO.8B00062