Zinc in PDB 6ya1: Zinc Metalloprotease Proa

The structure of Zinc Metalloprotease Proa, PDB code: 6ya1 was solved by S.Schmelz, W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.39 / 1.48
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.262, 108.213, 47.39, 90, 90, 90
R / Rfree (%)	16.8 / 18.7

The structure of Zinc Metalloprotease Proa also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Zinc Metalloprotease Proa (pdb code 6ya1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Zinc Metalloprotease Proa, PDB code: 6ya1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Zinc Metalloprotease Proa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc Metalloprotease Proa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:22.7 occ:0.88 O A:HOH513 2.0 24.4 1.0 OD2 A:ASP254 2.2 17.5 1.0 ND1 A:HIS256 2.2 18.2 1.0 HB2 A:HIS256 2.8 14.7 1.0 CG A:ASP254 3.0 29.7 1.0 CE1 A:HIS256 3.1 16.3 1.0 CG A:HIS256 3.2 12.1 1.0 HE1 A:HIS256 3.2 19.5 1.0 OD1 A:ASP254 3.2 40.4 1.0 CB A:HIS256 3.5 12.3 1.0 H A:HIS256 3.6 14.7 1.0 HB3 A:HIS256 4.1 14.7 1.0 NE2 A:HIS256 4.2 15.1 1.0 CB A:ASP254 4.2 18.5 1.0 HB3 A:ASP254 4.3 22.2 1.0 CD2 A:HIS256 4.3 13.5 1.0 N A:HIS256 4.3 12.2 1.0 O A:HOH810 4.4 21.1 1.0 HG22 A:VAL255 4.5 17.6 1.0 CA A:HIS256 4.5 13.8 1.0 HB2 A:ASP254 4.6 22.2 1.0 HG23 A:VAL255 4.8 17.6 1.0 H A:VAL255 5.0 18.0 1.0 HE2 A:HIS256 5.0 18.1 1.0

Zinc binding site 2 out of 5 in the Zinc Metalloprotease Proa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc Metalloprotease Proa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:16.8 occ:0.92 OD2 A:ASP90 1.9 29.6 1.0 OD2 A:ASP154 1.9 20.4 1.0 NE2 A:HIS53 2.1 16.5 1.0 ND1 A:HIS135 2.1 19.1 1.0 O A:HOH504 2.7 31.5 1.0 CG A:ASP90 2.8 23.2 1.0 CG A:ASP154 2.9 18.8 1.0 CD2 A:HIS53 3.0 18.1 1.0 HB3 A:HIS135 3.0 18.5 1.0 CE1 A:HIS135 3.1 18.9 1.0 HD2 A:HIS53 3.1 21.8 1.0 CG A:HIS135 3.1 15.1 1.0 HA A:HIS135 3.1 16.8 1.0 CE1 A:HIS53 3.2 26.3 1.0 OD1 A:ASP154 3.2 17.3 1.0 HE1 A:HIS135 3.3 22.6 1.0 OD1 A:ASP90 3.3 22.5 1.0 HE1 A:HIS53 3.4 31.5 1.0 CB A:HIS135 3.4 15.4 1.0 CA A:HIS135 3.8 14.0 1.0 HB2 A:ASP90 3.9 25.0 1.0 CB A:ASP90 3.9 20.9 1.0 CB A:ASP154 4.1 14.6 1.0 CG A:HIS53 4.2 13.2 1.0 HB3 A:ASP90 4.2 25.0 1.0 NE2 A:HIS135 4.2 17.4 1.0 ND1 A:HIS53 4.2 21.3 1.0 CD2 A:HIS135 4.2 17.2 1.0 HB3 A:ASP154 4.3 17.5 1.0 HB2 A:ASP154 4.3 17.5 1.0 O A:HOH640 4.3 22.3 1.0 HB2 A:HIS135 4.4 18.5 1.0 O A:HOH715 4.6 19.4 1.0 C A:HIS135 4.7 15.5 1.0 O A:HIS135 4.8 14.3 1.0 H A:HIS135 4.9 15.9 1.0 N A:HIS135 4.9 13.3 1.0 HG2 A:PRO96 5.0 24.0 1.0 HE2 A:HIS135 5.0 20.9 1.0

Zinc binding site 3 out of 5 in the Zinc Metalloprotease Proa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc Metalloprotease Proa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:12.5 occ:1.00 OXT A:ACT406 1.9 14.1 1.0 OE1 A:GLU194 2.0 13.5 1.0 NE2 A:HIS170 2.1 10.2 1.0 NE2 A:HIS174 2.1 12.8 1.0 C A:ACT406 2.5 16.2 1.0 O A:ACT406 2.6 20.4 1.0 CD A:GLU194 2.8 10.6 1.0 OE2 A:GLU194 3.0 11.4 1.0 HH A:TYR185 3.0 28.1 1.0 CD2 A:HIS170 3.0 10.8 1.0 CE1 A:HIS170 3.0 12.1 1.0 CE1 A:HIS174 3.1 11.3 1.0 CD2 A:HIS174 3.2 11.9 1.0 HE1 A:HIS174 3.2 13.6 1.0 HD2 A:HIS170 3.2 12.9 1.0 HE1 A:HIS170 3.2 14.5 1.0 HD2 A:HIS174 3.4 14.3 1.0 HE2 A:HIS256 3.5 18.1 1.0 OH A:TYR185 3.6 23.4 1.0 HA A:GLU194 3.9 12.6 1.0 CH3 A:ACT406 3.9 23.4 1.0 ND1 A:HIS170 4.1 9.7 1.0 HE1 A:TYR185 4.2 22.6 1.0 H3 A:ACT406 4.2 28.1 1.0 CG A:HIS170 4.2 10.3 1.0 ND1 A:HIS174 4.2 9.9 1.0 NE2 A:HIS256 4.2 15.1 1.0 CG A:GLU194 4.2 13.6 1.0 HB2 A:SER197 4.2 15.1 1.0 CG A:HIS174 4.3 10.5 1.0 O A:HOH727 4.3 15.2 1.0 HG2 A:GLU194 4.4 16.4 1.0 H2 A:ACT406 4.4 28.1 1.0 HD2 A:HIS256 4.5 16.2 1.0 H1 A:ACT406 4.5 28.1 1.0 HB3 A:SER197 4.5 15.1 1.0 CZ A:TYR185 4.6 20.1 1.0 OE2 A:GLU171 4.6 15.7 1.0 OE1 A:GLU171 4.7 13.8 1.0 CE1 A:TYR185 4.7 18.8 1.0 CD2 A:HIS256 4.7 13.5 1.0 CB A:SER197 4.8 12.6 1.0 HG3 A:GLU194 4.8 16.4 1.0 CA A:GLU194 4.8 10.5 1.0 HD1 A:HIS170 4.9 11.6 1.0 HD1 A:HIS174 5.0 11.8 1.0 HH22 A:ARG231 5.0 15.1 1.0 CD A:GLU171 5.0 15.5 1.0

Zinc binding site 4 out of 5 in the Zinc Metalloprotease Proa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc Metalloprotease Proa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:18.0 occ:0.78 O A:ACT407 2.0 22.1 0.9 O A:HOH564 2.0 24.7 1.0 O A:HOH768 2.0 24.9 1.0 NE2 A:HIS264 2.1 17.4 1.0 C A:ACT407 2.4 26.9 0.9 OXT A:ACT407 2.4 25.9 0.9 CE1 A:HIS264 3.0 19.5 1.0 CD2 A:HIS264 3.1 16.3 1.0 HE1 A:HIS264 3.1 23.4 1.0 HD2 A:HIS264 3.3 19.5 1.0 HD11 A:ILE268 3.4 17.8 1.0 O A:ASP234 3.7 18.5 1.0 CH3 A:ACT407 3.9 31.6 0.9 HG12 A:ILE268 4.0 17.2 1.0 HG13 A:ILE268 4.1 17.2 1.0 O A:HOH509 4.1 39.3 1.0 ND1 A:HIS264 4.1 14.9 1.0 CG A:HIS264 4.2 13.7 1.0 CD1 A:ILE268 4.3 14.8 1.0 H2 A:ACT407 4.3 37.9 0.9 H1 A:ACT407 4.3 37.9 0.9 CG1 A:ILE268 4.3 14.3 1.0 H3 A:ACT407 4.4 37.9 0.9 HD2 A:TYR267 4.7 18.6 1.0 HD13 A:ILE268 4.7 17.8 1.0 HA A:LYS235 4.8 18.7 1.0 HD1 A:HIS264 4.9 17.9 1.0 HD12 A:ILE268 4.9 17.8 1.0 C A:ASP234 5.0 16.3 1.0

Zinc binding site 5 out of 5 in the Zinc Metalloprotease Proa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Zinc Metalloprotease Proa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:15.8 occ:0.50 OE1 A:GLU118 2.0 12.5 1.0 NE2 A:HIS112 2.1 11.7 1.0 CD A:GLU118 2.9 14.3 1.0 CD2 A:HIS112 3.0 12.7 1.0 OE2 A:GLU118 3.1 13.1 1.0 CE1 A:HIS112 3.1 15.7 1.0 HD2 A:HIS112 3.2 15.2 1.0 HE1 A:HIS112 3.3 18.8 1.0 O A:HOH709 3.8 30.5 1.0 CG A:HIS112 4.2 12.8 1.0 ND1 A:HIS112 4.2 15.7 1.0 CG A:GLU118 4.3 13.2 1.0 HG3 A:PRO127 4.4 22.9 1.0 HG2 A:GLU118 4.4 15.8 1.0 HG3 A:GLU118 4.6 15.8 1.0 HZ2 A:LYS108 4.8 19.5 1.0 HD1 A:HIS112 5.0 18.8 1.0

L.Scheithauer, S.Thiem, S.Schmelz, A.Dellmann, K.Bussow, R.M.H.J.Brouwer, C.M.Unal, W.Blankenfeldt, M.Steinert. Zinc Metalloprotease Proa of Legionella Pneumophila Increases Alveolar Septal Thickness in Human Lung Tissue Explants By Collagen IV Degradation. Cell.Microbiol. 13313 2021.
ISSN: ESSN 1462-5822
PubMed: 33491325
DOI: 10.1111/CMI.13313