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

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E with Actinonin Bound, PDB code: 5njb 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)	50.87 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.570, 172.880, 82.630, 90.00, 90.02, 90.00
R / Rfree (%)	13 / 16.9

The binding sites of Zinc atom in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Actinonin Bound (pdb code 5njb). 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 Actinonin Bound, PDB code: 5njb:
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 Actinonin 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 Actinonin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:10.0 occ:1.00 O4 A:BB2502 2.0 14.6 1.0 NE2 A:HIS262 2.1 10.7 1.0 NE2 A:HIS267 2.1 10.5 1.0 SG A:CYS454 2.4 10.3 1.0 O2 A:BB2502 2.5 16.1 1.0 C3 A:BB2502 2.8 14.8 1.0 CE1 A:HIS267 3.0 9.2 1.0 CE1 A:HIS262 3.0 12.3 1.0 N1 A:BB2502 3.1 14.9 1.0 CD2 A:HIS262 3.1 10.9 1.0 CD2 A:HIS267 3.1 9.3 1.0 CB A:CYS454 3.5 9.9 1.0 CA A:CYS454 3.9 8.9 1.0 O A:GLY455 4.0 13.9 1.0 N A:GLY455 4.0 9.9 1.0 ND1 A:HIS267 4.1 9.2 1.0 ND1 A:HIS262 4.1 12.5 1.0 CG A:HIS262 4.2 10.2 1.0 CG A:HIS267 4.2 9.0 1.0 C5 A:BB2502 4.2 14.2 1.0 C A:CYS454 4.4 9.3 1.0 CE A:MET363 4.4 9.9 1.0 C7 A:BB2502 4.5 15.6 1.0 C6 A:BB2502 4.6 13.8 1.0 OE1 A:GLU263 4.7 12.3 1.0 C A:GLY455 4.7 10.9 1.0 O A:HOH725 4.7 17.1 1.0 O A:HOH968 4.8 22.5 1.0 O A:HOH710 4.8 8.6 1.0 OE2 A:GLU263 5.0 14.0 1.0 C10 A:BB2502 5.0 19.0 1.0 CA A:GLY455 5.0 10.5 1.0

Zinc binding site 2 out of 2 in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Actinonin 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 Actinonin Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:11.2 occ:1.00 NE2 C:HIS267 2.0 11.0 1.0 O4 C:BB2502 2.1 16.8 1.0 NE2 C:HIS262 2.1 10.4 1.0 SG C:CYS454 2.4 10.4 1.0 O2 C:BB2502 2.5 14.7 1.0 C3 C:BB2502 2.8 14.6 1.0 CE1 C:HIS267 3.0 11.0 1.0 N1 C:BB2502 3.0 13.7 1.0 CE1 C:HIS262 3.0 11.1 1.0 CD2 C:HIS267 3.1 10.9 1.0 CD2 C:HIS262 3.1 11.2 1.0 CB C:CYS454 3.5 10.2 1.0 CA C:CYS454 3.9 9.3 1.0 O C:GLY455 4.0 14.9 1.0 N C:GLY455 4.0 9.9 1.0 ND1 C:HIS267 4.1 9.8 1.0 ND1 C:HIS262 4.2 10.9 1.0 CG C:HIS267 4.2 10.9 1.0 CG C:HIS262 4.2 9.2 1.0 C5 C:BB2502 4.2 14.8 1.0 C C:CYS454 4.4 8.9 1.0 CE C:MET363 4.4 10.5 1.0 C7 C:BB2502 4.6 16.2 1.0 C6 C:BB2502 4.6 14.3 1.0 OE1 C:GLU263 4.7 12.5 1.0 C C:GLY455 4.7 12.4 1.0 O C:HOH711 4.7 17.9 1.0 O C:HOH646 4.8 8.4 1.0 O C:HOH945 4.9 23.5 1.0 OE2 C:GLU263 5.0 13.2 1.0 CA C:GLY455 5.0 9.9 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