Zinc in PDB 6xpn: Z-Loop Deletion Mutant of Aztc From Paracoccus Denitrificans

The structure of Z-Loop Deletion Mutant of Aztc From Paracoccus Denitrificans, PDB code: 6xpn was solved by E.T.Yukl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.54 / 2.26
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.292, 105.042, 64.245, 90.00, 110.77, 90.00
R / Rfree (%)	17.4 / 20.8

The binding sites of Zinc atom in the Z-Loop Deletion Mutant of Aztc From Paracoccus Denitrificans (pdb code 6xpn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Z-Loop Deletion Mutant of Aztc From Paracoccus Denitrificans, PDB code: 6xpn:
Jump to Zinc binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Z-Loop Deletion Mutant of Aztc From Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:54.1 occ:1.00 OD1 B:ASP279 2.0 50.6 1.0 CE1 B:HIS138 2.1 51.3 1.0 NE2 B:HIS61 2.1 52.9 1.0 NE2 B:HIS204 2.2 51.6 1.0 CG B:ASP279 2.9 46.1 1.0 CD2 B:HIS61 3.0 54.0 1.0 ND1 B:HIS138 3.0 49.5 1.0 NE2 B:HIS138 3.0 50.7 1.0 CE1 B:HIS204 3.1 50.1 1.0 OD2 B:ASP279 3.2 49.3 1.0 CD2 B:HIS204 3.2 46.1 1.0 CE1 B:HIS61 3.2 56.4 1.0 CG B:HIS61 4.2 59.9 1.0 CG B:HIS138 4.2 50.4 1.0 CD2 B:HIS138 4.2 44.1 1.0 O B:HOH512 4.2 57.3 1.0 CB B:ALA206 4.2 44.7 1.0 ND1 B:HIS61 4.2 52.1 1.0 ND1 B:HIS204 4.3 53.5 1.0 CB B:ASP279 4.3 45.1 1.0 CG B:HIS204 4.3 54.0 1.0 CE1 B:PHE86 4.4 49.9 1.0 CA B:ALA206 4.8 55.4 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Z-Loop Deletion Mutant of Aztc From Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:53.8 occ:1.00 OD1 A:ASP279 1.9 54.7 1.0 NE2 A:HIS138 2.0 52.8 1.0 NE2 A:HIS61 2.1 49.0 1.0 NE2 A:HIS204 2.3 55.0 1.0 CG A:ASP279 2.9 51.6 1.0 CD2 A:HIS61 2.9 51.2 1.0 CD2 A:HIS138 3.0 49.3 1.0 CE1 A:HIS138 3.1 52.6 1.0 OD2 A:ASP279 3.1 47.0 1.0 CE1 A:HIS61 3.2 47.4 1.0 CD2 A:HIS204 3.2 56.4 1.0 CE1 A:HIS204 3.2 60.3 1.0 CB A:ALA206 4.1 58.3 1.0 CG A:HIS61 4.1 56.2 1.0 CG A:HIS138 4.1 49.6 1.0 ND1 A:HIS138 4.2 51.8 1.0 ND1 A:HIS61 4.2 52.9 1.0 CB A:ASP279 4.3 45.9 1.0 O A:HOH511 4.3 59.3 1.0 ND1 A:HIS204 4.4 58.2 1.0 CG A:HIS204 4.4 59.2 1.0 CE1 A:PHE86 4.4 53.7 1.0 CA A:ALA206 4.8 53.2 1.0

A.Meni, E.T.Yukl. Structural Features Mediating Zinc Binding and Transfer in the Aztabcd Zinc Transporter System. Biomolecules V. 10 2020.
ISSN: ESSN 2218-273X
PubMed: 32781785
DOI: 10.3390/BIOM10081156