Zinc in PDB 5kzj: Loop Deletion Mutant of Paracoccus Denitrificans Aztc

The structure of Loop Deletion Mutant of Paracoccus Denitrificans Aztc, PDB code: 5kzj was solved by E.Yukl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.47 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.826, 104.314, 64.320, 90.00, 110.70, 90.00
R / Rfree (%)	15.9 / 20

The binding sites of Zinc atom in the Loop Deletion Mutant of Paracoccus Denitrificans Aztc (pdb code 5kzj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Loop Deletion Mutant of Paracoccus Denitrificans Aztc, PDB code: 5kzj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Loop Deletion Mutant of Paracoccus Denitrificans Aztc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Loop Deletion Mutant of Paracoccus Denitrificans Aztc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:41.2 occ:1.00 NE2 A:HIS138 2.0 39.0 1.0 NE2 A:HIS61 2.0 41.8 1.0 NE2 A:HIS204 2.0 39.2 1.0 OD2 A:ASP279 2.2 39.8 1.0 CE1 A:HIS138 2.9 36.6 1.0 CD2 A:HIS204 3.0 35.6 1.0 CE1 A:HIS61 3.0 44.2 1.0 CD2 A:HIS138 3.0 40.1 1.0 CG A:ASP279 3.0 36.0 1.0 CD2 A:HIS61 3.0 39.1 1.0 CE1 A:HIS204 3.1 36.2 1.0 OD1 A:ASP279 3.2 35.6 1.0 O A:VAL224 3.5 41.4 1.0 ND1 A:HIS138 4.0 36.4 1.0 CB A:ALA206 4.1 38.7 1.0 CG A:HIS138 4.1 34.0 1.0 ND1 A:HIS61 4.1 41.7 1.0 ND1 A:HIS204 4.1 40.5 1.0 CG A:HIS204 4.2 40.4 1.0 CG A:HIS61 4.2 39.5 1.0 O A:HOH543 4.4 40.1 1.0 CE1 A:PHE86 4.4 46.6 1.0 CB A:ASP279 4.5 33.3 1.0 C A:VAL224 4.7 49.3 1.0 CA A:ALA206 4.8 39.8 1.0

Zinc binding site 2 out of 2 in the Loop Deletion Mutant of Paracoccus Denitrificans Aztc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Loop Deletion Mutant of Paracoccus Denitrificans Aztc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:40.3 occ:1.00 NE2 B:HIS61 2.0 34.4 1.0 OD2 B:ASP279 2.0 36.0 1.0 NE2 B:HIS204 2.0 41.5 1.0 NE2 B:HIS138 2.1 37.4 1.0 CG B:ASP279 2.8 33.4 1.0 CD2 B:HIS61 2.9 34.9 1.0 CE1 B:HIS204 3.0 41.2 1.0 OD1 B:ASP279 3.0 30.8 1.0 CE1 B:HIS61 3.0 34.3 1.0 CE1 B:HIS138 3.0 37.1 1.0 CD2 B:HIS204 3.1 36.1 1.0 CD2 B:HIS138 3.1 35.8 1.0 O B:VAL224 3.5 37.3 1.0 ND1 B:HIS61 4.1 32.1 1.0 CG B:HIS61 4.1 30.9 1.0 ND1 B:HIS204 4.1 40.3 1.0 O B:HOH506 4.2 38.5 1.0 ND1 B:HIS138 4.2 34.9 1.0 CB B:ALA206 4.2 32.8 1.0 CG B:HIS204 4.2 41.2 1.0 CB B:ASP279 4.2 32.9 1.0 CG B:HIS138 4.3 36.0 1.0 CE1 B:PHE86 4.3 39.8 1.0 C B:VAL224 4.8 38.2 1.0 CA B:ALA206 4.9 34.8 1.0

D.P.Neupane, D.Avalos, S.Fullam, H.Roychowdhury, E.T.Yukl. Mechanisms of Zinc Binding to the Solute-Binding Protein Aztc and Transfer From the Metallochaperone Aztd. J. Biol. Chem. V. 292 17496 2017.
ISSN: ESSN 1083-351X
PubMed: 28887302
DOI: 10.1074/JBC.M117.804799