Zinc in PDB 4yu6: Crystal Structure of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen

The structure of Crystal Structure of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen, PDB code: 4yu6 was solved by J.L.Arolas, T.Goulas, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.67 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	176.980, 108.870, 100.410, 90.00, 119.07, 90.00
R / Rfree (%)	17.1 / 21.1

The structure of Crystal Structure of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Calcium	(Ca)	9 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen (pdb code 4yu6). 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 Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen, PDB code: 4yu6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen


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 Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:56.7 occ:1.00 OD1 A:ASP389 2.0 55.3 1.0 NE2 A:HIS379 2.1 44.2 1.0 NE2 A:HIS383 2.1 40.2 1.0 N A:CCN1008 2.1 76.3 1.0 N A:ASN50 2.2 75.0 1.0 CD2 A:HIS379 2.9 44.1 1.0 CG A:ASP389 3.0 57.2 1.0 ND2 A:ASN93 3.1 0.0 1.0 CD2 A:HIS383 3.1 40.7 1.0 CE1 A:HIS383 3.1 39.4 1.0 C1 A:CCN1008 3.2 74.7 1.0 CE1 A:HIS379 3.3 43.6 1.0 OD2 A:ASP389 3.4 66.5 1.0 CA A:ASN50 3.4 75.5 1.0 CG A:HIS379 4.1 42.2 1.0 CG A:ASN93 4.1 0.9 1.0 CB A:ASN50 4.2 75.2 1.0 CG A:HIS383 4.2 39.1 1.0 ND1 A:HIS383 4.2 39.6 1.0 ND1 A:HIS379 4.3 43.5 1.0 OH A:TYR391 4.3 61.9 1.0 CE2 A:TYR391 4.3 45.4 1.0 CB A:ASP389 4.4 45.3 1.0 C2 A:CCN1008 4.6 73.1 1.0 OD1 A:ASN93 4.6 0.7 1.0 C A:ASN50 4.7 79.8 1.0 CZ A:TYR391 4.8 55.0 1.0 CA A:ASP389 4.9 43.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen


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 Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:54.8 occ:1.00 OD1 B:ASP389 2.0 47.7 1.0 NE2 B:HIS379 2.1 45.7 1.0 NE2 B:HIS383 2.1 44.9 1.0 O B:HOH1113 2.1 49.8 1.0 O B:HOH1108 2.2 61.6 1.0 N B:ASN50 2.2 70.7 1.0 CD2 B:HIS379 2.8 46.1 1.0 CD2 B:HIS383 3.1 45.3 1.0 CG B:ASP389 3.1 49.6 1.0 CE1 B:HIS383 3.1 45.1 1.0 CE1 B:HIS379 3.3 44.7 1.0 OD2 B:ASP389 3.4 60.6 1.0 CA B:ASN50 3.4 67.9 1.0 CG B:HIS379 4.0 43.0 1.0 CB B:ASN50 4.2 66.2 1.0 CG B:HIS383 4.2 44.3 1.0 ND1 B:HIS383 4.2 45.7 1.0 ND1 B:HIS379 4.3 44.5 1.0 OH B:TYR391 4.3 60.0 1.0 CE2 B:TYR391 4.4 39.1 1.0 CB B:ASP389 4.4 43.7 1.0 C B:ASN50 4.6 69.3 1.0 O B:HOH1177 4.7 63.6 1.0 CZ B:TYR391 4.8 49.5 1.0 CA B:ASP389 4.9 42.9 1.0 CE B:MET408 5.0 41.2 1.0

J.L.Arolas, T.Goulas, A.P.Pomerantsev, S.H.Leppla, F.X.Gomis-Ruth. Structural Basis For Latency and Function of Immune Inhibitor A Metallopeptidase, A Modulator of the Bacillus Anthracis Secretome. Structure V. 24 25 2016.
ISSN: ISSN 0969-2126
PubMed: 26745529
DOI: 10.1016/J.STR.2015.10.015