Zinc in PDB 6ck1: Crystal Structure of Paracoccus Denitrificans Aztd

The structure of Crystal Structure of Paracoccus Denitrificans Aztd, PDB code: 6ck1 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)	79.74 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.510, 96.380, 175.520, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 23.7

The binding sites of Zinc atom in the Crystal Structure of Paracoccus Denitrificans Aztd (pdb code 6ck1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Paracoccus Denitrificans Aztd, PDB code: 6ck1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Paracoccus Denitrificans Aztd


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 Paracoccus Denitrificans Aztd within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:26.3 occ:0.71 NE2 B:HIS167 2.0 17.0 1.0 NE2 B:HIS124 2.2 38.8 1.0 NE2 B:HIS218 2.3 35.7 1.0 O B:HOH802 2.4 29.0 1.0 CE1 B:HIS167 2.9 15.7 1.0 CD2 B:HIS167 3.1 15.5 1.0 CE1 B:HIS218 3.1 33.7 1.0 CD2 B:HIS124 3.2 39.9 1.0 CE1 B:HIS124 3.2 41.8 1.0 CD2 B:HIS218 3.3 36.2 1.0 ND1 B:HIS167 4.0 15.8 1.0 O B:HOH775 4.1 21.6 1.0 CG B:HIS167 4.2 16.5 1.0 CE1 B:PHE123 4.2 18.0 1.0 ND1 B:HIS218 4.2 31.2 1.0 ND1 B:HIS124 4.3 42.4 1.0 CG B:HIS124 4.3 39.2 1.0 CG B:HIS218 4.4 24.9 1.0 O B:HOH789 4.4 34.6 1.0 CZ B:PHE123 4.7 27.2 1.0 CD1 B:PHE123 4.7 19.3 1.0 O B:HOH807 4.7 37.7 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Paracoccus Denitrificans Aztd


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 Paracoccus Denitrificans Aztd within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:74.4 occ:0.70 OD1 B:ASP104 2.4 95.1 1.0 NE2 B:HIS408 2.5 92.7 1.0 OD2 B:ASP104 2.7 97.7 1.0 CG B:ASP104 2.9 92.3 1.0 NE2 B:HIS102 3.0 1.0 1.0 CE1 B:HIS99 3.1 93.9 1.0 CD2 B:HIS408 3.1 91.6 1.0 NE2 B:HIS99 3.5 94.7 1.0 CE1 B:HIS102 3.5 0.8 1.0 ND1 B:HIS99 3.7 94.9 1.0 CE1 B:HIS408 3.7 92.3 1.0 CD2 B:HIS102 4.1 0.7 1.0 CD2 B:HIS99 4.3 93.6 1.0 CB B:ASP104 4.4 83.2 1.0 CG B:HIS99 4.4 95.2 1.0 CG B:HIS408 4.4 91.3 1.0 ND1 B:HIS408 4.6 92.8 1.0 CB B:VAL406 4.7 75.3 1.0 ND1 B:HIS102 4.7 0.5 1.0 CG1 B:VAL406 4.8 80.1 1.0 CA B:ASP104 4.9 77.9 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Paracoccus Denitrificans Aztd


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 Paracoccus Denitrificans Aztd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:53.3 occ:0.71 NE2 A:HIS167 2.1 53.4 1.0 NE2 A:HIS124 2.1 31.2 0.5 O A:HOH782 2.5 39.8 1.0 CE1 A:HIS124 2.7 26.2 0.5 NE2 A:HIS218 2.7 42.9 1.0 CE1 A:HIS167 2.8 53.8 1.0 CD2 A:HIS124 3.2 29.4 0.5 CD2 A:HIS167 3.2 52.2 1.0 CE1 A:HIS218 3.4 39.2 1.0 CD2 A:HIS218 3.6 43.8 1.0 ND1 A:HIS124 3.8 28.1 0.5 ND1 A:HIS167 4.0 51.2 1.0 O A:HOH725 4.1 37.9 1.0 CG A:HIS124 4.1 27.1 0.5 CE1 A:PHE123 4.2 32.7 1.0 CG A:HIS167 4.2 49.9 1.0 ND1 A:HIS218 4.4 39.8 1.0 CD1 A:PHE123 4.5 34.3 1.0 CG A:HIS218 4.6 37.3 1.0 CZ A:PHE123 4.7 36.0 1.0 O A:HOH775 4.8 44.2 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Paracoccus Denitrificans Aztd


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 Paracoccus Denitrificans Aztd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:98.1 occ:0.81 NE2 A:HIS102 1.9 97.1 1.0 NE2 A:HIS408 2.0 0.0 1.0 OD1 A:ASP104 2.2 86.1 1.0 CE1 A:HIS102 2.2 98.3 1.0 CE1 A:HIS408 2.8 0.3 1.0 CG A:ASP104 3.0 81.2 1.0 CD2 A:HIS408 3.1 0.4 1.0 OD2 A:ASP104 3.1 83.2 1.0 CD2 A:HIS102 3.2 97.8 1.0 ND1 A:HIS102 3.5 97.5 1.0 CB A:HIS99 3.8 0.5 1.0 ND1 A:HIS408 4.0 0.4 1.0 CG A:HIS102 4.0 97.3 1.0 CG A:HIS99 4.1 0.1 1.0 CG A:HIS408 4.2 0.7 1.0 ND1 A:HIS99 4.4 0.5 1.0 CB A:ASP104 4.4 73.4 1.0 CG1 A:VAL406 4.5 67.1 1.0 O A:THR407 4.5 97.4 1.0 CB A:VAL406 4.7 71.4 1.0 CD2 A:HIS99 4.9 0.3 1.0 CA A:ASP104 4.9 66.0 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Paracoccus Denitrificans Aztd


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 Paracoccus Denitrificans Aztd within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:41.5 occ:0.78 NE2 C:HIS167 2.1 24.7 1.0 NE2 C:HIS124 2.2 24.1 0.6 NE2 C:HIS218 2.5 31.3 1.0 O C:HOH776 2.7 34.5 1.0 CE1 C:HIS167 2.9 20.3 1.0 CD2 C:HIS124 3.1 19.5 0.6 CD2 C:HIS167 3.1 20.9 1.0 CE1 C:HIS124 3.2 22.3 0.6 CE1 C:HIS218 3.2 29.8 1.0 CD2 C:HIS218 3.4 32.2 1.0 O C:HOH751 3.8 39.1 1.0 ND1 C:HIS167 4.1 23.9 1.0 CE1 C:PHE123 4.2 19.0 1.0 CG C:HIS167 4.2 23.1 1.0 CG C:HIS124 4.2 23.9 0.6 ND1 C:HIS124 4.3 22.5 0.6 ND1 C:HIS218 4.3 24.9 1.0 CG C:HIS218 4.4 29.7 1.0 O C:HOH754 4.6 36.6 1.0 CZ C:PHE123 4.6 23.2 1.0 O C:HOH773 4.7 48.6 1.0 CD1 C:PHE123 4.7 23.8 1.0 ND1 C:HIS124 4.8 24.6 0.4

Zinc binding site 6 out of 8 in the Crystal Structure of Paracoccus Denitrificans Aztd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Paracoccus Denitrificans Aztd within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:97.6 occ:0.93 OD1 C:ASP104 2.3 89.2 1.0 OD2 C:ASP104 2.5 86.4 1.0 CG C:ASP104 2.7 83.5 1.0 CD2 C:HIS408 2.9 0.0 1.0 NE2 C:HIS408 2.9 0.5 1.0 CB C:ASP104 4.1 72.6 1.0 CE1 C:HIS408 4.1 1.0 1.0 CG C:HIS408 4.1 0.9 1.0 CG1 C:VAL406 4.6 58.7 1.0 ND1 C:HIS408 4.7 1.0 1.0 CB C:VAL406 4.8 69.7 1.0 CA C:ASP104 4.9 61.1 1.0 N C:ASP104 4.9 52.4 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Paracoccus Denitrificans Aztd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Paracoccus Denitrificans Aztd within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:31.2 occ:1.00 NE2 D:HIS408 1.9 30.3 1.0 OD1 D:ASP104 2.0 43.6 1.0 ND1 D:HIS99 2.0 52.2 1.0 NE2 D:HIS102 2.1 45.4 1.0 CG D:ASP104 2.7 33.5 1.0 OD2 D:ASP104 2.8 35.1 1.0 CE1 D:HIS99 2.9 41.1 1.0 CE1 D:HIS408 2.9 31.3 1.0 CD2 D:HIS408 2.9 29.2 1.0 CD2 D:HIS102 3.0 33.4 1.0 CG D:HIS99 3.1 41.8 1.0 CE1 D:HIS102 3.2 39.2 1.0 CB D:HIS99 3.5 32.2 1.0 NE2 D:HIS99 4.0 40.4 1.0 ND1 D:HIS408 4.0 32.5 1.0 CG D:HIS408 4.1 32.4 1.0 CD2 D:HIS99 4.1 40.4 1.0 CB D:ASP104 4.1 25.9 1.0 CG D:HIS102 4.2 35.5 1.0 ND1 D:HIS102 4.3 37.1 1.0 CG1 D:VAL406 4.4 36.7 1.0 CB D:VAL406 4.5 31.6 1.0 CA D:ASP104 4.7 25.6 1.0 N D:ASP104 4.7 30.4 1.0 O D:HIS99 5.0 27.8 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Paracoccus Denitrificans Aztd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Paracoccus Denitrificans Aztd within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:37.0 occ:0.72 NE2 D:HIS167 2.0 27.3 1.0 NE2 D:HIS124 2.2 27.6 0.5 NE2 D:HIS218 2.3 34.6 1.0 O D:HOH815 2.8 33.9 1.0 CE1 D:HIS167 2.9 25.8 1.0 CE1 D:HIS218 3.0 33.6 1.0 CE1 D:HIS124 3.0 22.5 0.5 CD2 D:HIS167 3.1 21.8 1.0 CD2 D:HIS124 3.2 24.1 0.5 CD2 D:HIS218 3.4 34.3 1.0 O D:HOH779 4.1 27.7 1.0 ND1 D:HIS167 4.1 25.4 1.0 CE1 D:PHE123 4.1 19.7 1.0 ND1 D:HIS218 4.1 36.3 1.0 ND1 D:HIS124 4.1 25.0 0.5 CG D:HIS167 4.2 26.5 1.0 CG D:HIS124 4.3 23.3 0.5 CG D:HIS218 4.4 36.7 1.0 CZ D:PHE123 4.4 24.5 1.0 CD1 D:PHE123 4.6 19.1 1.0

D.P.Neupane, S.H.Fullam, K.N.Chacon, E.T.Yukl. Crystal Structures of Aztd Provide Mechanistic Insights Into Direct Zinc Transfer Between Proteins. Commun Biol V. 2 308 2019.
ISSN: ESSN 2399-3642
PubMed: 31428696
DOI: 10.1038/S42003-019-0542-Z