Zinc in PDB 6jx3: Lasso Peptide Synthetase B1 Complexed with the Leader Peptide

The structure of Lasso Peptide Synthetase B1 Complexed with the Leader Peptide, PDB code: 6jx3 was solved by T.Sumida, S.Tagami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.15 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	48.960, 90.300, 58.380, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 20.7

The binding sites of Zinc atom in the Lasso Peptide Synthetase B1 Complexed with the Leader Peptide (pdb code 6jx3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Lasso Peptide Synthetase B1 Complexed with the Leader Peptide, PDB code: 6jx3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Lasso Peptide Synthetase B1 Complexed with the Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Lasso Peptide Synthetase B1 Complexed with the Leader Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:17.1 occ:1.00 OE2 B:GLU13 1.9 17.9 1.0 OD2 B:ASP27 2.0 18.4 1.0 O B:HOH264 2.1 15.7 1.0 CG B:ASP27 2.8 16.3 1.0 OD1 B:ASP27 2.9 15.0 1.0 CD B:GLU13 3.0 19.0 1.0 CG B:GLU13 3.3 16.3 1.0 O B:GLY86 4.0 18.2 1.0 NE B:ARG11 4.0 22.8 1.0 OE1 B:GLU13 4.1 19.4 1.0 CB B:ASP27 4.2 15.1 1.0 CD B:ARG29 4.4 22.4 0.7 CB B:ARG29 4.6 16.9 1.0 CD B:ARG11 4.6 17.2 1.0 O B:HOH229 4.7 24.6 1.0 O B:HOH202 4.8 26.0 1.0 CB B:GLU13 4.8 15.1 1.0 CD1 B:ILE14 4.8 17.7 1.0 OG B:SER30 4.8 20.7 1.0 CZ B:ARG11 4.9 24.2 1.0 CG B:ARG29 5.0 21.1 1.0 N B:SER30 5.0 18.9 1.0

Zinc binding site 2 out of 7 in the Lasso Peptide Synthetase B1 Complexed with the Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Lasso Peptide Synthetase B1 Complexed with the Leader Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:27.3 occ:0.82 OD2 B:ASP49 1.8 27.5 1.0 O B:HOH275 2.2 28.4 1.0 CG B:ASP49 2.7 24.0 1.0 OD1 B:ASP49 2.9 26.8 1.0 O B:HOH216 3.3 30.3 1.0 O B:HOH262 4.0 35.0 1.0 CB B:ASP49 4.0 18.5 1.0 O B:GLN45 4.2 17.9 1.0 C B:GLN45 4.7 14.3 1.0 CB B:GLN45 5.0 21.8 1.0

Zinc binding site 3 out of 7 in the Lasso Peptide Synthetase B1 Complexed with the Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Lasso Peptide Synthetase B1 Complexed with the Leader Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:22.3 occ:0.84 OD2 B:ASP55 1.9 22.2 1.0 O B:HOH270 2.2 30.7 1.0 CG B:ASP55 2.8 21.8 1.0 OD1 B:ASP55 3.0 20.8 1.0 O B:HOH272 3.6 42.8 1.0 ND1 B:HIS51 4.0 33.8 1.0 CB B:ASP55 4.2 15.0 1.0 O B:HOH291 4.2 46.6 1.0 N B:SER52 4.4 14.2 1.0 OG B:SER52 4.5 15.2 1.0 CA B:HIS51 4.5 15.4 1.0 CB B:HIS51 4.9 15.6 1.0 CE1 B:HIS51 4.9 34.6 1.0 CG B:HIS51 4.9 21.6 1.0

Zinc binding site 4 out of 7 in the Lasso Peptide Synthetase B1 Complexed with the Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Lasso Peptide Synthetase B1 Complexed with the Leader Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn104 b:23.7 occ:0.42 ZN B:ZN105 1.6 31.7 0.4 ZN B:ZN107 1.8 24.5 0.3 O B:HOH268 2.1 36.1 1.0 OD2 B:ASP70 2.1 23.8 0.5 O B:HOH254 2.4 36.2 1.0 OD1 B:ASP70 2.5 27.0 0.5 OD2 B:ASP70 2.5 25.7 0.5 CG B:ASP70 2.7 27.4 0.5 OD1 B:ASP70 2.7 32.0 0.5 CG B:ASP70 2.8 27.3 0.5 NH1 B:ARG73 3.5 45.4 1.0 OG1 B:THR69 4.0 22.1 0.5 CB B:ASP70 4.2 18.1 0.5 CB B:ASP70 4.2 18.2 0.5 O B:HOH215 4.6 24.2 1.0 CZ B:ARG73 4.7 52.4 1.0 N B:ASP70 4.8 19.3 1.0 CA B:ASP70 4.8 22.0 0.5 CA B:ASP70 4.8 22.0 0.5 CB B:GLU67 4.9 23.9 1.0

Zinc binding site 5 out of 7 in the Lasso Peptide Synthetase B1 Complexed with the Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Lasso Peptide Synthetase B1 Complexed with the Leader Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn105 b:31.7 occ:0.38 ZN B:ZN104 1.6 23.7 0.4 O B:HOH254 1.9 36.2 1.0 OD2 B:ASP70 2.1 23.8 0.5 OG1 B:THR69 2.7 22.1 0.5 OD2 B:ASP70 3.2 25.7 0.5 OD1 B:ASP70 3.2 27.0 0.5 CG B:ASP70 3.3 27.4 0.5 CG B:ASP70 3.4 27.3 0.5 ZN B:ZN107 3.4 24.5 0.3 O B:HOH268 3.5 36.1 1.0 OD1 B:ASP70 3.8 32.0 0.5 CB B:THR69 4.0 24.3 0.5 CB B:GLU67 4.0 23.9 1.0 NH1 B:ARG73 4.1 45.4 1.0 CB B:THR69 4.2 24.3 0.5 CG B:GLU67 4.2 28.5 1.0 N B:ASP70 4.3 19.3 1.0 CB B:ASP70 4.4 18.1 0.5 CB B:ASP70 4.4 18.2 0.5 CG2 B:THR69 4.7 24.3 0.5 CG2 B:THR69 4.8 23.4 0.5 O B:HOH215 4.8 24.2 1.0 CA B:ASP70 4.8 22.0 0.5 CA B:ASP70 4.8 22.0 0.5 OG1 B:THR69 4.9 31.0 0.5 C B:THR69 4.9 21.4 1.0 CA B:THR69 5.0 19.3 0.5 CZ B:ARG73 5.0 52.4 1.0

Zinc binding site 6 out of 7 in the Lasso Peptide Synthetase B1 Complexed with the Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Lasso Peptide Synthetase B1 Complexed with the Leader Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn106 b:47.9 occ:0.42 O B:HOH278 2.6 43.8 1.0 OE1 B:GLU63 2.7 39.1 1.0 CD B:GLU63 3.7 42.4 1.0 CE A:LYS-19 3.9 36.2 0.9 NZ A:LYS-19 3.9 33.8 1.0 O B:HOH247 4.3 33.4 1.0 CG B:GLU63 4.4 39.8 1.0 OE2 B:GLU63 4.5 46.9 1.0 CB B:GLU63 4.8 29.2 1.0 CD A:LYS-19 4.9 30.4 1.0

Zinc binding site 7 out of 7 in the Lasso Peptide Synthetase B1 Complexed with the Leader Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Lasso Peptide Synthetase B1 Complexed with the Leader Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn107 b:24.5 occ:0.32 ZN B:ZN104 1.8 23.7 0.4 OD1 B:ASP70 2.0 32.0 0.5 O B:HOH268 2.0 36.1 1.0 OD2 B:ASP70 2.1 25.7 0.5 OD1 B:ASP70 2.6 27.0 0.5 CG B:ASP70 2.6 27.3 0.5 CG B:ASP70 2.7 27.4 0.5 OD2 B:ASP70 2.8 23.8 0.5 ZN B:ZN105 3.4 31.7 0.4 NH1 B:ARG73 4.1 45.4 1.0 O B:HOH254 4.1 36.2 1.0 CB B:ASP70 4.1 18.1 0.5 CB B:ASP70 4.1 18.2 0.5 O B:HOH215 4.2 24.2 1.0 O B:HOH274 4.3 36.4 1.0 O B:HOH246 4.6 44.9 1.0

T.Sumida, S.Dubiley, B.Wilcox, K.Severinov, S.Tagami. Structural Basis of Leader Peptide Recognition in Lasso Peptide Biosynthesis Pathway. Acs Chem.Biol. V. 14 1619 2019.
ISSN: ESSN 1554-8937
PubMed: 31188556
DOI: 10.1021/ACSCHEMBIO.9B00348