Zinc in PDB 7v9p: Crystal Structure of the Lanthipeptide Zinc-Metallopeptidase Eryp From Saccharopolyspora Erythraea in Intermediate State

All present enzymatic activity of Crystal Structure of the Lanthipeptide Zinc-Metallopeptidase Eryp From Saccharopolyspora Erythraea in Intermediate State:
3.4.11.2;

The structure of Crystal Structure of the Lanthipeptide Zinc-Metallopeptidase Eryp From Saccharopolyspora Erythraea in Intermediate State, PDB code: 7v9p was solved by C.Zhao, N.L.Zhao, R.Bao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.06 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	91.42, 66.63, 153.74, 90, 93.41, 90
R / Rfree (%)	19 / 21

The binding sites of Zinc atom in the Crystal Structure of the Lanthipeptide Zinc-Metallopeptidase Eryp From Saccharopolyspora Erythraea in Intermediate State (pdb code 7v9p). 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 the Lanthipeptide Zinc-Metallopeptidase Eryp From Saccharopolyspora Erythraea in Intermediate State, PDB code: 7v9p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Lanthipeptide Zinc-Metallopeptidase Eryp From Saccharopolyspora Erythraea in Intermediate State


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 the Lanthipeptide Zinc-Metallopeptidase Eryp From Saccharopolyspora Erythraea in Intermediate State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:37.5 occ:0.34 NE2 A:HIS310 2.1 31.1 1.0 NE2 A:HIS306 2.2 27.4 1.0 O A:HOH1264 2.2 46.7 1.0 OE2 A:GLU329 2.5 54.3 1.0 OE1 A:GLU329 2.7 58.5 1.0 CD A:GLU329 2.8 48.7 1.0 CD2 A:HIS306 2.8 27.8 1.0 CD2 A:HIS310 3.1 30.8 1.0 CE1 A:HIS310 3.1 29.0 1.0 CE1 A:HIS306 3.3 34.1 1.0 CA A:GLU329 4.1 25.0 1.0 CG A:HIS306 4.1 30.2 1.0 CG A:GLU329 4.1 36.2 1.0 CB A:ALA332 4.2 22.9 1.0 ND1 A:HIS310 4.2 26.8 1.0 CG A:HIS310 4.2 27.1 1.0 ND1 A:HIS306 4.3 30.1 1.0 OE1 A:GLU275 4.3 36.9 1.0 CB A:GLU329 4.4 27.1 1.0 OE1 A:GLU307 4.4 41.4 1.0 OE2 A:GLU307 4.6 43.4 1.0 OE2 A:GLU275 4.7 34.3 1.0 CD A:GLU275 4.7 35.2 1.0 O A:HOH1037 4.7 44.2 1.0 O A:GLU329 4.8 27.3 1.0 CD A:GLU307 4.9 36.4 1.0 N A:GLU329 4.9 25.7 1.0 O A:ASN328 4.9 28.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Lanthipeptide Zinc-Metallopeptidase Eryp From Saccharopolyspora Erythraea in Intermediate State


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 the Lanthipeptide Zinc-Metallopeptidase Eryp From Saccharopolyspora Erythraea in Intermediate State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:37.4 occ:0.29 OE2 B:GLU329 1.5 44.3 1.0 NE2 B:HIS310 1.9 29.0 1.0 CD B:GLU329 2.3 42.5 1.0 O B:HOH1090 2.5 47.1 1.0 OE1 B:GLU329 2.5 54.1 1.0 NE2 B:HIS306 2.6 29.7 1.0 CD2 B:HIS310 2.9 29.3 1.0 CE1 B:HIS310 2.9 29.4 1.0 CD2 B:HIS306 3.2 26.4 1.0 CE1 B:HIS306 3.7 30.2 1.0 CG B:GLU329 3.8 32.6 1.0 OE1 B:GLU275 3.8 31.5 1.0 O B:HOH1084 3.9 48.5 1.0 ND1 B:HIS310 4.0 30.4 1.0 CG B:HIS310 4.0 28.9 1.0 CA B:GLU329 4.2 25.6 1.0 OE2 B:GLU275 4.2 38.8 1.0 CD B:GLU275 4.2 33.4 1.0 O B:HOH1013 4.4 40.4 1.0 CB B:GLU329 4.4 30.1 1.0 CB B:ALA332 4.4 24.2 1.0 OE1 B:GLU307 4.5 38.7 1.0 OE2 B:GLU307 4.5 37.3 1.0 CG B:HIS306 4.5 27.3 1.0 ND1 B:HIS306 4.7 27.2 1.0 O B:ASN328 4.8 28.5 1.0 ND2 B:ASN328 4.9 39.9 1.0 N B:GLU329 4.9 27.1 1.0 CD B:GLU307 4.9 33.4 1.0

C.Zhao, W.Sheng, Y.Wang, J.Zheng, X.Xie, Y.Liang, W.Wei, R.Bao, H.Wang. Conformational Remodeling Enhances Activity of Lanthipeptide Zinc-Metallopeptidases. Nat.Chem.Biol. V. 18 724 2022.
ISSN: ESSN 1552-4469
PubMed: 35513512
DOI: 10.1038/S41589-022-01018-2