Zinc in PDB 3wi9: Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus

All present enzymatic activity of Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus:
1.7.2.1;

The structure of Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus, PDB code: 3wi9 was solved by Y.Fukuda, M.Nojiri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.90 / 1.30
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	115.069, 115.069, 87.505, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 19.7

The structure of Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus also contains other interesting chemical elements:

Copper	(Cu)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus (pdb code 3wi9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus, PDB code: 3wi9:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus


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 Copper Nitrite Reductase From Geobacillus Kaustophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:27.9 occ:0.25 CE1 A:HIS83 1.7 14.0 0.5 CD2 A:HIS83 2.0 18.6 0.5 ND1 A:HIS83 2.0 14.4 0.5 NE2 A:HIS83 2.1 19.3 0.5 ZN A:ZN404 2.4 15.2 0.8 NE2 A:HIS83 2.8 14.3 0.5 O A:HOH636 2.8 19.4 1.0 CG2 A:VAL36 3.0 19.0 1.0 CG A:HIS83 3.2 15.1 0.5 NE2 A:HIS42 3.2 19.1 1.0 CG A:HIS83 3.2 17.8 0.5 CE1 A:HIS83 3.3 19.4 0.5 CD2 A:HIS42 3.4 18.5 1.0 CD2 A:HIS83 3.5 15.0 0.5 ND1 A:HIS83 3.8 18.8 0.5 OXT A:ACY408 4.1 21.1 1.0 CB A:VAL36 4.1 18.6 1.0 CB A:ASP40 4.3 18.5 1.0 CB A:HIS83 4.3 15.3 0.5 O A:ACY408 4.3 20.9 1.0 CB A:HIS83 4.3 16.6 0.5 CE1 A:HIS42 4.4 20.1 1.0 C A:ACY408 4.6 21.1 1.0 OD1 A:ASP40 4.7 21.2 1.0 CG1 A:VAL36 4.7 20.2 1.0 CG A:HIS42 4.7 18.0 1.0 CG A:ASP40 4.8 19.7 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus


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 Copper Nitrite Reductase From Geobacillus Kaustophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:15.2 occ:0.75 O A:ACY408 2.0 20.9 1.0 ND1 A:HIS83 2.0 14.4 0.5 NE2 A:HIS42 2.1 19.1 1.0 CD2 A:HIS83 2.2 18.6 0.5 ZN A:ZN403 2.4 27.9 0.2 C A:ACY408 2.6 21.1 1.0 OXT A:ACY408 2.6 21.1 1.0 CE1 A:HIS83 2.9 14.0 0.5 CD2 A:HIS42 3.0 18.5 1.0 CE1 A:HIS42 3.0 20.1 1.0 CG A:HIS83 3.1 17.8 0.5 CG A:HIS83 3.1 15.1 0.5 NE2 A:HIS83 3.3 19.3 0.5 CB A:HIS83 3.4 15.3 0.5 CB A:HIS83 3.5 16.6 0.5 CH3 A:ACY408 4.1 21.6 1.0 NE2 A:HIS83 4.1 14.3 0.5 ND1 A:HIS42 4.1 20.0 1.0 CG A:HIS42 4.1 18.0 1.0 O A:HOH629 4.1 26.6 1.0 CD2 A:HIS83 4.2 15.0 0.5 ND1 A:HIS83 4.3 18.8 0.5 CE1 A:HIS83 4.3 19.4 0.5 O A:HOH569 4.7 25.6 1.0 CG2 A:VAL36 4.7 19.0 1.0 O A:HOH636 4.9 19.4 1.0 CA A:HIS83 5.0 15.4 0.5 CA A:HIS83 5.0 16.1 0.5

Zinc binding site 3 out of 3 in the Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus


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 Copper Nitrite Reductase From Geobacillus Kaustophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:26.9 occ:0.75 O A:HOH555 2.1 24.1 1.0 O A:HOH594 2.1 32.7 1.0 O A:HOH668 2.1 32.2 1.0 O A:HOH582 2.2 28.2 1.0 O A:HOH685 2.2 33.5 1.0 OD1 A:ASP167 2.2 19.0 1.0 CG A:ASP167 3.1 20.1 1.0 OD2 A:ASP167 3.3 21.3 1.0 O A:GLY225 4.1 19.4 1.0 O A:GLU165 4.1 20.6 1.0 N A:LYS227 4.2 17.8 1.0 CB A:ASP167 4.5 19.4 1.0 O A:HOH715 4.6 33.9 1.0 CA A:GLU226 4.6 18.5 1.0 CB A:LYS227 4.7 17.9 1.0 C A:GLU226 4.8 18.3 1.0

Y.Fukuda, H.Koteishi, R.Yoneda, T.Tamada, H.Takami, T.Inoue, M.Nojiri. Structural and Functional Characterization of the Geobacillus Copper Nitrite Reductase: Involvement of the Unique N-Terminal Region in the Interprotein Electron Transfer with Its Redox Partner Biochim.Biophys.Acta V.1837 396 2014.
ISSN: ISSN 0006-3002
PubMed: 24440558
DOI: 10.1016/J.BBABIO.2014.01.004