Zinc in PDB 4in9: Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp

The structure of Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp, PDB code: 4in9 was solved by T.Guevara, M.Ksiazek, P.D.Skottrup, N.Cerda-Costa, S.Trillo-Muyo, I.Dediego, E.Riise, J.Potempa, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.87 / 1.55
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	86.050, 86.050, 49.440, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 17.1

The structure of Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp also contains other interesting chemical elements:

Potassium	(K)	1 atom
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp (pdb code 4in9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp, PDB code: 4in9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.1 occ:1.00 NE2 A:HIS155 2.0 8.8 1.0 NE2 A:HIS165 2.1 11.1 1.0 NE2 A:HIS159 2.1 9.1 1.0 N B:SER1 2.2 10.4 1.0 O B:SER1 2.2 12.4 1.0 C B:SER1 3.0 13.4 1.0 CE1 A:HIS155 3.0 9.7 1.0 CA B:SER1 3.0 10.2 1.0 CD2 A:HIS165 3.1 10.5 1.0 CE1 A:HIS165 3.1 11.9 1.0 CD2 A:HIS155 3.1 9.0 1.0 CD2 A:HIS159 3.1 9.5 1.0 CE1 A:HIS159 3.1 10.1 1.0 OG B:SER1 3.5 14.9 1.0 CB B:SER1 3.8 12.9 1.0 OE2 A:GLU156 4.1 10.9 1.0 ND1 A:HIS155 4.2 9.9 1.0 CG A:HIS155 4.2 8.8 1.0 CG A:HIS165 4.2 11.1 1.0 ND1 A:HIS165 4.2 13.6 1.0 N B:TRP2 4.3 11.9 1.0 CG A:HIS159 4.3 9.8 1.0 ND1 A:HIS159 4.3 11.2 1.0 O A:HOH605 4.3 19.4 1.0 OE1 A:GLU156 4.6 10.4 1.0 CD A:GLU156 4.7 9.9 1.0 NE1 B:TRP2 4.8 11.4 1.0 O A:HOH594 4.8 43.5 1.0 CB A:PRO175 4.9 12.2 1.0 O3 A:GOL306 4.9 44.2 1.0 CD1 B:TRP2 4.9 13.0 1.0 CE2 B:TRP2 5.0 12.3 1.0 CE A:MET173 5.0 9.1 1.0 CA B:TRP2 5.0 12.8 1.0

Zinc binding site 2 out of 2 in the Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:11.4 occ:1.00 OD2 A:ASP104 2.0 10.3 1.0 NE2 A:HIS102 2.0 11.0 1.0 NE2 A:HIS117 2.0 10.8 1.0 ND1 A:HIS133 2.0 11.6 1.0 CG A:ASP104 2.8 12.9 1.0 CD2 A:HIS102 2.9 11.2 1.0 CE1 A:HIS133 2.9 12.2 1.0 CE1 A:HIS117 3.0 10.0 1.0 CD2 A:HIS117 3.0 10.9 1.0 CE1 A:HIS102 3.0 10.9 1.0 OD1 A:ASP104 3.1 12.0 1.0 CG A:HIS133 3.1 11.4 1.0 CB A:HIS133 3.5 9.6 1.0 CG A:HIS102 4.1 11.3 1.0 CG A:HIS117 4.1 9.3 1.0 ND1 A:HIS117 4.1 9.8 1.0 NE2 A:HIS133 4.1 12.4 1.0 ND1 A:HIS102 4.1 11.5 1.0 CD2 A:HIS133 4.2 12.8 1.0 CB A:ASP104 4.2 13.3 1.0 O A:TYR106 4.2 10.5 1.0 CE1 A:PHE119 4.4 13.1 1.0 CZ A:PHE119 4.7 13.5 1.0 CB A:TYR106 4.8 10.6 1.0 C A:TYR106 4.9 12.1 1.0 CE2 A:PHE108 4.9 12.8 1.0 O A:HOH429 5.0 13.4 1.0 CA A:HIS133 5.0 8.3 1.0

T.Guevara, M.Ksiazek, P.D.Skottrup, N.Cerda-Costa, S.Trillo-Muyo, I.De Diego, E.Riise, J.Potempa, F.X.Gomis-Ruth. Structure of the Catalytic Domain of the Tannerella Forsythia Matrix Metallopeptidase Karilysin in Complex with A Tetrapeptidic Inhibitor. Acta Crystallogr.,Sect.F V. 69 472 2013.
ISSN: ESSN 1744-3091
PubMed: 23695557
DOI: 10.1107/S1744309113007392