Zinc in PDB 6aem: Crystal Structure of the PKD1 Domain of Vibrio Anguillarum Epp

The structure of Crystal Structure of the PKD1 Domain of Vibrio Anguillarum Epp, PDB code: 6aem was solved by Q.Ma, P.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.25 / 1.27
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.096, 46.069, 41.616, 90.00, 97.39, 90.00
R / Rfree (%)	15.1 / 18.6

The structure of Crystal Structure of the PKD1 Domain of Vibrio Anguillarum Epp also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the PKD1 Domain of Vibrio Anguillarum Epp (pdb code 6aem). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the PKD1 Domain of Vibrio Anguillarum Epp, PDB code: 6aem:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of the PKD1 Domain of Vibrio Anguillarum Epp


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 PKD1 Domain of Vibrio Anguillarum Epp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:17.6 occ:1.00 OE2 A:GLU28 2.0 20.8 1.0 NE2 A:HIS26 2.1 14.6 1.0 CD A:GLU28 2.7 22.1 1.0 OE1 A:GLU28 2.7 23.5 1.0 CD2 A:HIS26 3.0 14.1 1.0 CE1 A:HIS26 3.0 14.5 1.0 CG A:GLU28 4.1 21.7 1.0 ND1 A:HIS26 4.1 14.0 1.0 CG A:HIS26 4.2 12.9 1.0 CG2 A:VAL7 4.6 14.6 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of the PKD1 Domain of Vibrio Anguillarum Epp


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 PKD1 Domain of Vibrio Anguillarum Epp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:36.9 occ:1.00 O A:HOH209 1.9 34.2 1.0 O A:HOH290 2.2 41.8 1.0 OE2 A:GLU31 2.2 19.0 1.0 OE1 A:GLU31 2.7 18.7 1.0 CD A:GLU31 2.8 17.4 1.0 CG A:GLU31 4.3 15.4 1.0 O A:HOH203 4.5 33.0 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of the PKD1 Domain of Vibrio Anguillarum Epp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the PKD1 Domain of Vibrio Anguillarum Epp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:72.0 occ:1.00 O B:HOH271 2.1 40.0 1.0 O A:HOH204 2.2 33.0 1.0 OE1 A:GLU83 2.2 35.4 1.0 OE2 A:GLU83 2.3 35.7 1.0 O A:HOH222 2.4 38.9 1.0 CD A:GLU83 2.6 33.7 1.0 O A:HOH280 2.6 39.6 1.0 CG A:GLU83 4.1 30.2 1.0 O B:HOH221 4.2 34.6 1.0 CB A:GLU83 4.9 25.9 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of the PKD1 Domain of Vibrio Anguillarum Epp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the PKD1 Domain of Vibrio Anguillarum Epp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:22.3 occ:1.00 OE2 B:GLU28 2.0 22.0 1.0 NE2 B:HIS26 2.0 14.7 1.0 O B:HOH274 2.5 28.3 1.0 CD B:GLU28 2.7 19.1 1.0 OE1 B:GLU28 2.7 20.1 1.0 CD2 B:HIS26 2.9 14.2 1.0 ZN B:ZN103 3.0 24.6 0.5 CE1 B:HIS26 3.0 15.4 1.0 CG B:HIS26 4.1 12.4 1.0 ND1 B:HIS26 4.1 12.9 1.0 CG B:GLU28 4.1 17.9 1.0 CG2 B:VAL7 4.8 14.8 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of the PKD1 Domain of Vibrio Anguillarum Epp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the PKD1 Domain of Vibrio Anguillarum Epp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:24.6 occ:0.50 O B:HOH274 1.9 28.3 1.0 ZN B:ZN102 3.0 22.3 1.0 OE2 B:GLU28 3.5 22.0 1.0 OE2 A:GLU11 3.7 20.7 1.0 CD A:GLU11 4.4 18.9 1.0 OE1 A:GLU11 4.4 20.3 1.0 CD B:GLU28 4.4 19.1 1.0 NE2 B:HIS26 4.7 14.7 1.0 OE1 B:GLU28 4.9 20.1 1.0

P.Li, K.Zang, Y.Li, C.Liu, Q.Ma. Structural Basis For Specific Calcium Binding By the Polycystic-Kidney-Disease Domain of Vibrio Anguillarum Protease Epp Biochem. Biophys. Res. V. 505 471 2018COMMUN..
ISSN: ESSN 1090-2104
PubMed: 30268503
DOI: 10.1016/J.BBRC.2018.09.108