Zinc in PDB 4xb6: Structure of the E. Coli C-P Lyase Core Complex

All present enzymatic activity of Structure of the E. Coli C-P Lyase Core Complex:
2.7.8.37; 4.7.1.1;

The structure of Structure of the E. Coli C-P Lyase Core Complex, PDB code: 4xb6 was solved by D.E.Brodersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.36 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.510, 133.710, 176.740, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 17.6

The binding sites of Zinc atom in the Structure of the E. Coli C-P Lyase Core Complex (pdb code 4xb6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the E. Coli C-P Lyase Core Complex, PDB code: 4xb6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the E. Coli C-P Lyase Core Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the E. Coli C-P Lyase Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:20.6 occ:0.51 NE2 C:HIS328 2.0 21.0 1.0 NE2 C:HIS333 2.1 19.9 1.0 O C:HOH640 2.2 25.9 1.0 CE1 C:HIS328 2.9 18.1 1.0 CD2 C:HIS328 3.0 19.6 1.0 CE1 C:HIS333 3.0 20.1 1.0 HE1 C:HIS328 3.0 21.7 1.0 CD2 C:HIS333 3.1 20.1 1.0 HE1 C:HIS333 3.2 24.1 1.0 HD2 C:HIS328 3.3 23.6 1.0 HD2 C:HIS333 3.3 24.2 1.0 HH21 D:ARG107 3.3 19.7 1.0 HD23 C:LEU329 3.9 18.9 1.0 ND1 C:HIS328 4.0 17.5 1.0 O C:HOH809 4.0 37.0 1.0 HE1 D:HIS108 4.0 18.8 1.0 CG C:HIS328 4.1 15.2 1.0 NH2 D:ARG107 4.1 16.4 1.0 ND1 C:HIS333 4.2 19.1 1.0 O G:HOH542 4.2 20.2 1.0 CG C:HIS333 4.2 18.9 1.0 HH22 D:ARG107 4.3 19.7 1.0 HG3 D:PRO126 4.3 24.9 1.0 O D:HOH480 4.4 25.3 1.0 HE1 C:PHE325 4.5 20.6 1.0 HB3 D:PRO126 4.5 17.9 1.0 HA C:LEU329 4.6 17.9 1.0 HE2 D:HIS108 4.7 18.2 1.0 CD2 C:LEU329 4.7 15.7 1.0 HD1 C:HIS328 4.8 21.1 1.0 HD21 C:LEU329 4.8 18.9 1.0 CE1 D:HIS108 4.8 15.7 1.0 HE D:ARG107 4.8 24.0 1.0 O G:HOH556 4.8 20.5 1.0 HD1 C:HIS333 4.9 22.9 1.0 O C:HIS328 4.9 15.8 1.0 CE1 C:PHE325 5.0 17.1 1.0 HZ C:PHE325 5.0 19.1 1.0

Zinc binding site 2 out of 4 in the Structure of the E. Coli C-P Lyase Core Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the E. Coli C-P Lyase Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:28.5 occ:1.00 SG D:CYS272 2.3 27.7 1.0 SG D:CYS241 2.3 27.7 1.0 SG D:CYS244 2.3 28.3 1.0 SG D:CYS266 2.3 26.4 1.0 HB2 D:CYS266 2.9 34.6 1.0 HB3 D:CYS244 3.1 45.7 1.0 H D:CYS244 3.1 39.1 1.0 HB3 D:CYS241 3.1 43.7 1.0 HA D:CYS272 3.1 31.1 1.0 CB D:CYS241 3.1 36.4 1.0 H D:CYS266 3.1 32.1 1.0 HB2 D:CYS241 3.1 43.7 1.0 CB D:CYS266 3.2 28.9 1.0 HB2 D:CYS272 3.2 28.0 1.0 CB D:CYS272 3.2 23.3 1.0 CB D:CYS244 3.3 38.1 1.0 CA D:CYS272 3.7 25.9 1.0 N D:CYS244 3.8 32.6 1.0 HB D:ILE243 3.8 42.9 1.0 N D:CYS266 3.9 26.8 1.0 HB3 D:CYS266 3.9 34.6 1.0 HB3 D:SER246 4.0 40.8 1.0 HB2 D:CYS244 4.0 45.7 1.0 CA D:CYS244 4.1 36.7 1.0 HB3 D:CYS272 4.1 28.0 1.0 CA D:CYS266 4.1 25.7 1.0 H D:SER246 4.2 44.6 1.0 HG D:SER249 4.3 36.6 1.0 H D:ILE243 4.4 38.0 1.0 H D:GLY245 4.4 39.6 1.0 O D:HOH545 4.5 31.9 1.0 HD2 D:TYR271 4.6 34.9 1.0 CA D:CYS241 4.6 30.8 1.0 HA D:CYS266 4.6 30.9 1.0 C D:CYS272 4.6 26.8 1.0 O D:CYS272 4.6 29.2 1.0 CB D:ILE243 4.7 35.8 1.0 HA D:VAL265 4.7 33.0 1.0 HB2 D:GLN275 4.7 40.6 1.0 N D:CYS272 4.7 26.2 1.0 C D:CYS244 4.8 38.5 1.0 HG22 D:ILE243 4.8 56.1 1.0 HE2 D:TYR271 4.8 42.1 1.0 N D:GLY245 4.8 33.0 1.0 C D:ILE243 4.8 29.6 1.0 CB D:SER246 4.9 34.0 1.0 HA D:CYS241 4.9 37.0 1.0 HA D:CYS244 4.9 44.0 1.0 H D:CYS272 4.9 31.4 1.0 HB D:VAL265 5.0 42.5 1.0 HB2 D:SER246 5.0 40.8 1.0

Zinc binding site 3 out of 4 in the Structure of the E. Coli C-P Lyase Core Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the E. Coli C-P Lyase Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn402 b:21.9 occ:0.54 NE2 G:HIS328 2.0 21.3 1.0 O G:HOH631 2.1 27.4 1.0 NE2 G:HIS333 2.1 20.1 1.0 CE1 G:HIS328 2.8 19.3 1.0 HE1 G:HIS328 3.0 23.1 1.0 CD2 G:HIS328 3.0 22.9 1.0 CE1 G:HIS333 3.1 20.0 1.0 CD2 G:HIS333 3.1 23.5 1.0 HD2 G:HIS333 3.3 28.2 1.0 HE1 G:HIS333 3.3 24.0 1.0 HH21 H:ARG107 3.3 23.5 1.0 HD2 G:HIS328 3.3 27.4 1.0 O G:HOH578 3.5 26.6 1.0 HD23 G:LEU329 3.9 24.2 1.0 ND1 G:HIS328 4.0 19.1 1.0 O G:HOH715 4.0 35.3 1.0 NH2 H:ARG107 4.1 19.6 1.0 HE1 H:HIS108 4.1 25.5 1.0 CG G:HIS328 4.1 19.1 1.0 ND1 G:HIS333 4.2 20.2 1.0 O C:HOH535 4.2 19.9 1.0 CG G:HIS333 4.2 18.3 1.0 HH22 H:ARG107 4.3 23.5 1.0 HG3 H:PRO126 4.3 23.4 1.0 O H:HOH463 4.4 25.9 1.0 HE1 G:PHE325 4.5 22.4 1.0 HB3 H:PRO126 4.6 21.3 1.0 HA G:LEU329 4.6 19.0 1.0 HE2 H:HIS108 4.7 21.5 1.0 HD1 G:HIS328 4.7 22.9 1.0 CD2 G:LEU329 4.8 20.1 1.0 HE H:ARG107 4.8 23.7 1.0 HD21 G:LEU329 4.8 24.2 1.0 CE1 H:HIS108 4.8 21.2 1.0 O C:HOH565 4.9 21.6 1.0 HD1 G:HIS333 5.0 24.3 1.0 O G:HIS328 5.0 18.7 1.0 CE1 G:PHE325 5.0 18.7 1.0

Zinc binding site 4 out of 4 in the Structure of the E. Coli C-P Lyase Core Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the E. Coli C-P Lyase Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn302 b:32.8 occ:1.00 SG H:CYS272 2.2 33.4 1.0 SG H:CYS241 2.3 34.5 1.0 SG H:CYS244 2.3 36.8 1.0 SG H:CYS266 2.4 31.6 1.0 HB2 H:CYS266 2.8 44.9 1.0 HB3 H:CYS244 3.0 46.1 1.0 HA H:CYS272 3.0 43.3 1.0 H H:CYS266 3.1 36.0 1.0 HB3 H:CYS241 3.2 49.9 1.0 CB H:CYS241 3.2 41.6 1.0 CB H:CYS266 3.2 37.4 1.0 CB H:CYS272 3.2 32.0 1.0 HB2 H:CYS272 3.2 38.4 1.0 HB2 H:CYS241 3.2 49.9 1.0 H H:CYS244 3.2 46.8 1.0 CB H:CYS244 3.2 38.5 1.0 CA H:CYS272 3.6 36.1 1.0 HB H:ILE243 3.8 44.7 1.0 N H:CYS244 3.8 39.0 1.0 N H:CYS266 3.9 30.0 1.0 HB3 H:CYS266 3.9 44.9 1.0 HB2 H:CYS244 4.0 46.1 1.0 HB3 H:CYS272 4.1 38.4 1.0 HB3 H:SER246 4.1 52.2 1.0 CA H:CYS244 4.1 41.1 1.0 CA H:CYS266 4.1 32.2 1.0 H H:SER246 4.2 47.1 1.0 HG H:SER249 4.2 41.4 1.0 H H:ILE243 4.4 46.2 1.0 O H:CYS272 4.5 46.9 1.0 C H:CYS272 4.5 45.7 1.0 HB2 H:GLN275 4.5 48.0 1.0 H H:GLY245 4.6 49.9 1.0 O H:HOH503 4.6 32.5 1.0 HA H:CYS266 4.6 38.6 1.0 HB2 H:SER246 4.6 52.2 1.0 CA H:CYS241 4.7 43.6 1.0 HD2 H:TYR271 4.7 41.7 1.0 HA H:VAL265 4.7 37.2 1.0 CB H:ILE243 4.7 37.2 1.0 N H:CYS272 4.7 33.9 1.0 HG H:SER276 4.7 77.9 1.0 HG22 H:ILE243 4.8 45.0 1.0 C H:CYS244 4.8 46.4 1.0 CB H:SER246 4.8 43.5 1.0 C H:ILE243 4.9 41.8 1.0 HB H:VAL265 4.9 38.9 1.0 HA H:CYS244 4.9 49.3 1.0 N H:GLY245 4.9 41.6 1.0 H H:CYS272 4.9 40.7 1.0 HE2 H:TYR271 5.0 53.0 1.0 HA H:CYS241 5.0 52.3 1.0 HG3 H:GLN275 5.0 55.0 1.0

P.Seweryn, L.B.Van, M.Kjeldgaard, C.J.Russo, L.A.Passmore, B.Hove-Jensen, B.Jochimsen, D.E.Brodersen. Structural Insights Into the Bacterial Carbon-Phosphorus Lyase Machinery. Nature V. 525 68 2015.
ISSN: ESSN 1476-4687
PubMed: 26280334
DOI: 10.1038/NATURE14683