Zinc in PDB 4b52: Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa

All present enzymatic activity of Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa:
3.4.24.4;

The structure of Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa, PDB code: 4b52 was solved by A.Ruf, M.Stihle, J.Benz, M.Schmidt, H.Sobek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.60 / 1.76
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.121, 77.021, 64.443, 90.00, 103.58, 90.00
R / Rfree (%)	19.508 / 24.749

The structure of Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa also contains other interesting chemical elements:

Calcium	(Ca)	6 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa (pdb code 4b52). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa, PDB code: 4b52:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:10.9 occ:1.00 O1P A:RDF501 2.0 10.3 1.0 OE2 A:GLU159 2.0 17.4 1.0 NE2 A:HIS135 2.0 8.5 1.0 NE2 A:HIS139 2.1 11.6 1.0 CD A:GLU159 2.3 12.1 1.0 OE1 A:GLU159 2.3 18.9 1.0 P A:RDF501 2.8 12.1 1.0 O2P A:RDF501 3.0 11.6 1.0 CD2 A:HIS135 3.0 7.8 1.0 CE1 A:HIS139 3.0 10.8 1.0 CE1 A:HIS135 3.0 8.8 1.0 CD2 A:HIS139 3.1 11.1 1.0 CG A:GLU159 3.9 12.7 1.0 NE2 A:HIS219 3.9 12.1 1.0 O1 A:RDF501 4.0 13.8 1.0 N A:RDF501 4.2 11.4 1.0 ND1 A:HIS139 4.2 10.5 1.0 ND1 A:HIS135 4.2 8.4 1.0 CA A:RDF501 4.2 11.1 1.0 CG A:HIS135 4.2 8.1 1.0 CG A:HIS139 4.2 10.1 1.0 CD2 A:HIS219 4.4 11.8 1.0 C A:RDF501 4.5 11.6 1.0 O A:RDF501 4.5 10.4 1.0 O5 A:RDF501 4.6 18.0 1.0 CB A:GLU159 4.7 10.6 1.0 CA A:GLU159 4.7 9.3 1.0 C5 A:RDF501 4.7 19.1 1.0 CB A:SER162 4.8 8.4 1.0 O A:HOH2159 4.8 14.3 1.0 C6 A:RDF501 4.8 20.6 1.0 C1 A:RDF501 4.9 16.9 1.0 OG A:SER162 4.9 7.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:11.7 occ:1.00 O1P B:RDF501 1.9 10.1 1.0 OE1 B:GLU159 1.9 12.1 0.5 OE2 B:GLU159 2.0 15.6 0.5 NE2 B:HIS139 2.0 11.3 1.0 NE2 B:HIS135 2.1 10.2 1.0 OE1 B:GLU159 2.2 15.8 0.5 CD B:GLU159 2.3 13.5 0.5 CD B:GLU159 2.4 11.8 0.5 OE2 B:GLU159 2.6 11.9 0.5 P B:RDF501 2.8 12.0 1.0 CE1 B:HIS139 3.0 9.7 1.0 CD2 B:HIS139 3.0 10.1 1.0 CD2 B:HIS135 3.1 9.2 1.0 CE1 B:HIS135 3.1 10.5 1.0 O2P B:RDF501 3.1 11.4 1.0 CG B:GLU159 3.8 13.4 0.5 CG B:GLU159 3.9 11.4 0.5 N B:RDF501 4.0 11.9 1.0 O1 B:RDF501 4.0 14.6 1.0 NE2 B:HIS219 4.0 12.6 1.0 CA B:RDF501 4.1 11.6 1.0 ND1 B:HIS139 4.1 8.8 1.0 ND1 B:HIS135 4.2 9.2 1.0 CG B:HIS139 4.2 9.8 1.0 CG B:HIS135 4.2 9.3 1.0 C B:RDF501 4.5 12.5 1.0 O5 B:RDF501 4.5 17.6 1.0 CD2 B:HIS219 4.5 10.8 1.0 O B:RDF501 4.6 13.4 1.0 CB B:GLU159 4.7 10.3 0.5 CA B:GLU159 4.7 10.4 0.5 CA B:GLU159 4.7 10.8 0.5 CB B:GLU159 4.7 11.1 0.5 C1 B:RDF501 4.8 18.5 1.0 C5 B:RDF501 4.8 21.2 1.0 CB B:SER162 4.8 10.3 1.0 O A:HOH2183 4.8 12.4 1.0 OG B:SER162 5.0 10.4 1.0

A.Ruf, M.Stihle, J.Benz, M.Schmidt, H.Sobek. Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa Acta Crystallogr.,Sect.D V. 69 24 2013.
ISSN: ISSN 0907-4449
PubMed: 23275160
DOI: 10.1107/S0907444912041169