Zinc in PDB 5nj5: E. Coli Microcin-Processing Metalloprotease Tldd/E with Phosphate Bound

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E with Phosphate Bound, PDB code: 5nj5 was solved by D.Ghilarov, M.Serebryakova, C.E.M.Stevenson, S.J.Hearnshaw, D.Volkov, A.Maxwell, D.M.Lawson, K.Severinov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.29 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.770, 173.990, 83.520, 90.00, 90.00, 90.00
R / Rfree (%)	13.9 / 17.8

The binding sites of Zinc atom in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Phosphate Bound (pdb code 5nj5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Phosphate Bound, PDB code: 5nj5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Phosphate Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E. Coli Microcin-Processing Metalloprotease Tldd/E with Phosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:15.6 occ:1.00 O3 A:PO4502 1.9 17.9 1.0 NE2 A:HIS262 2.1 16.9 1.0 NE2 A:HIS267 2.1 16.2 1.0 SG A:CYS454 2.3 17.3 1.0 CE1 A:HIS267 3.0 16.5 1.0 CE1 A:HIS262 3.0 10.6 1.0 P A:PO4502 3.1 22.0 1.0 CD2 A:HIS262 3.1 18.2 1.0 CD2 A:HIS267 3.2 17.5 1.0 CB A:CYS454 3.2 13.7 1.0 O2 A:PO4502 3.3 23.1 1.0 CA A:CYS454 3.7 14.2 1.0 N A:GLY455 3.9 15.9 1.0 O A:GLY455 3.9 20.3 1.0 O4 A:PO4502 3.9 32.6 1.0 ND1 A:HIS267 4.1 15.3 1.0 ND1 A:HIS262 4.2 16.6 1.0 C A:CYS454 4.2 12.9 1.0 O1 A:PO4502 4.2 28.0 1.0 CG A:HIS262 4.2 17.6 1.0 CG A:HIS267 4.3 15.0 1.0 CE A:MET363 4.3 16.7 1.0 C1 A:EDO504 4.5 24.6 1.0 C A:GLY455 4.7 21.8 1.0 O A:HOH626 4.7 12.8 1.0 CA A:GLY455 4.9 19.9 1.0 O1 A:EDO504 5.0 48.4 1.0

Zinc binding site 2 out of 2 in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Phosphate Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E. Coli Microcin-Processing Metalloprotease Tldd/E with Phosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:16.8 occ:1.00 O3 C:PO4502 1.9 18.6 1.0 NE2 C:HIS262 2.0 12.4 1.0 NE2 C:HIS267 2.1 17.3 1.0 SG C:CYS454 2.3 17.8 1.0 CE1 C:HIS262 2.9 14.8 1.0 CE1 C:HIS267 3.0 14.9 1.0 CD2 C:HIS262 3.1 18.3 1.0 P C:PO4502 3.1 25.6 1.0 CD2 C:HIS267 3.2 14.7 1.0 CB C:CYS454 3.3 15.7 1.0 O2 C:PO4502 3.3 30.1 1.0 CA C:CYS454 3.7 15.5 1.0 O4 C:PO4502 3.8 26.0 1.0 N C:GLY455 3.9 13.4 1.0 O C:GLY455 4.0 22.5 1.0 ND1 C:HIS262 4.1 14.7 1.0 ND1 C:HIS267 4.1 15.9 1.0 CG C:HIS262 4.1 14.1 1.0 C C:CYS454 4.2 14.3 1.0 CG C:HIS267 4.2 13.1 1.0 O1 C:PO4502 4.3 23.8 1.0 CE C:MET363 4.3 18.5 1.0 C1 C:EDO504 4.5 31.2 1.0 O C:HOH712 4.7 17.7 1.0 C C:GLY455 4.8 18.1 1.0 O1 C:EDO504 4.9 44.0 1.0 CA C:GLY455 5.0 24.3 1.0

D.Ghilarov, M.Serebryakova, C.E.M.Stevenson, S.J.Hearnshaw, D.S.Volkov, A.Maxwell, D.M.Lawson, K.Severinov. The Origins of Specificity in the Microcin-Processing Protease Tldd/E. Structure V. 25 1549 2017.
ISSN: ISSN 1878-4186
PubMed: 28943336
DOI: 10.1016/J.STR.2017.08.006