Zinc in PDB 5gwd: Structure of Myroilysin

The structure of Structure of Myroilysin, PDB code: 5gwd was solved by D.Xu, T.Ran, W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.90 / 1.89
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.223, 35.486, 93.757, 90.00, 101.41, 90.00
R / Rfree (%)	18.2 / 22.4

The binding sites of Zinc atom in the Structure of Myroilysin (pdb code 5gwd). 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 Myroilysin, PDB code: 5gwd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Myroilysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Myroilysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:22.6 occ:1.00 NE2 A:HIS152 2.0 14.3 1.0 NE2 A:HIS142 2.1 18.3 1.0 NE2 A:HIS146 2.1 17.9 1.0 SG A:CYS28 2.2 17.6 1.0 CD2 A:HIS152 2.9 14.1 1.0 CD2 A:HIS142 2.9 16.4 1.0 CD2 A:HIS146 3.0 15.9 1.0 CE1 A:HIS152 3.0 17.6 1.0 CE1 A:HIS142 3.1 17.4 1.0 CE1 A:HIS146 3.1 15.9 1.0 CB A:CYS28 3.3 19.0 1.0 CG A:HIS152 4.0 16.7 1.0 ND1 A:HIS152 4.0 18.0 1.0 CG A:HIS142 4.1 17.5 1.0 ND1 A:HIS142 4.1 16.4 1.0 CG A:HIS146 4.2 15.0 1.0 ND1 A:HIS146 4.2 19.3 1.0 OE2 A:GLU143 4.2 15.5 1.0 O A:HOH431 4.3 16.6 1.0 OE1 A:GLU143 4.4 15.9 1.0 O A:HOH497 4.5 24.7 1.0 CA A:CYS28 4.6 18.9 1.0 CD A:GLU143 4.7 18.1 1.0 CE A:MET208 4.8 15.3 1.0 C A:CYS28 4.9 17.4 1.0

Zinc binding site 2 out of 2 in the Structure of Myroilysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Myroilysin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:21.5 occ:1.00 NE2 B:HIS152 2.0 13.8 1.0 NE2 B:HIS142 2.0 14.8 1.0 NE2 B:HIS146 2.1 16.9 1.0 SG B:CYS28 2.2 15.9 1.0 CD2 B:HIS152 2.9 15.3 1.0 CD2 B:HIS142 2.9 16.1 1.0 CD2 B:HIS146 3.0 11.7 1.0 CE1 B:HIS152 3.0 18.8 1.0 CE1 B:HIS146 3.1 17.4 1.0 CE1 B:HIS142 3.1 15.6 1.0 CB B:CYS28 3.3 14.6 1.0 CG B:HIS152 4.0 18.4 1.0 ND1 B:HIS152 4.1 17.9 1.0 CG B:HIS142 4.1 13.9 1.0 CG B:HIS146 4.1 16.8 1.0 ND1 B:HIS142 4.1 14.7 1.0 ND1 B:HIS146 4.2 16.5 1.0 O B:HOH405 4.2 14.6 1.0 OE2 B:GLU143 4.3 15.4 1.0 O B:HOH488 4.4 22.8 1.0 OE1 B:GLU143 4.5 14.2 1.0 CA B:CYS28 4.6 16.4 1.0 O B:HOH428 4.7 28.5 1.0 CD B:GLU143 4.7 15.5 1.0 CE B:MET208 4.8 14.7 1.0 C B:CYS28 4.9 17.6 1.0 O B:CYS28 5.0 13.9 1.0

D.Xu, J.Zhou, X.Lou, J.He, T.Ran, W.Wang. Myroilysin Is A New Bacterial Member of the M12A Family of Metzincin Metallopeptidases and Is Activated By A Cysteine Switch Mechanism. J. Biol. Chem. V. 292 5195 2017.
ISSN: ESSN 1083-351X
PubMed: 28188295
DOI: 10.1074/JBC.M116.758110