Zinc in PDB 2bo0: Crystal Structure of the C130A Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans

The structure of Crystal Structure of the C130A Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 2bo0 was solved by M.A.Hough, M.J.Ellis, S.Antonyuk, R.W.Strange, G.Sawers, R.R.Eady, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100 / 1.35
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	79.048, 79.048, 99.367, 90.00, 90.00, 120.00
R / Rfree (%)	10.8 / 11.3

The binding sites of Zinc atom in the Crystal Structure of the C130A Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans (pdb code 2bo0). 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 the C130A Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 2bo0:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the C130A Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans


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 C130A Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:9.1 occ:1.00 O A:HOH2479 1.9 13.2 1.0 NE2 A:HIS94 2.0 8.2 1.0 NE2 A:HIS129 2.0 8.7 1.0 CE1 A:HIS94 3.0 8.7 1.0 CD2 A:HIS129 3.0 8.9 1.0 CE1 A:HIS129 3.0 9.6 1.0 CD2 A:HIS94 3.1 8.2 1.0 HE1 A:HIS94 3.1 10.5 1.0 HD2 A:HIS129 3.2 10.7 1.0 HE1 A:HIS129 3.2 11.5 1.0 HD2 A:HIS94 3.3 9.9 1.0 OD2 A:ASP92 3.6 14.7 1.0 ND1 A:HIS94 4.1 8.9 1.0 CG A:ASP92 4.1 13.6 1.0 ND1 A:HIS129 4.1 9.5 1.0 CG A:HIS129 4.2 8.3 1.0 CG A:HIS94 4.2 7.5 1.0 OD1 A:ASP92 4.4 15.4 1.0 HB3 A:ASP92 4.8 13.9 1.0 HD1 A:HIS94 4.9 10.7 1.0 HG11 A:VAL127 4.9 20.3 1.0 O A:HOH2203 4.9 15.2 1.0 HG13 A:VAL127 4.9 20.3 1.0 HD1 A:HIS129 4.9 11.4 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the C130A Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans


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 C130A Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:15.2 occ:0.75 O A:HOH2482 1.9 33.2 0.8 O A:HOH2480 2.0 12.7 0.8 OD2 A:ASP167 2.0 15.8 1.0 NE2 A:HIS165 2.1 20.6 1.0 O A:HOH2481 2.3 37.2 0.8 CG A:ASP167 2.7 14.1 1.0 OD1 A:ASP167 2.8 17.0 1.0 CE1 A:HIS165 3.0 26.6 1.0 HE1 A:HIS165 3.1 31.9 1.0 CD2 A:HIS165 3.2 19.5 1.0 HG1 A:THR234 3.3 21.1 1.0 H A:THR234 3.4 15.0 1.0 HD2 A:HIS165 3.4 23.4 1.0 HA A:GLU233 3.8 16.6 1.0 HB A:THR234 3.8 15.1 1.0 OG1 A:THR234 3.9 14.1 1.0 N A:THR234 4.1 12.5 1.0 O A:GLY232 4.1 16.2 1.0 ND1 A:HIS165 4.1 27.5 1.0 CB A:ASP167 4.2 13.9 1.0 CG A:HIS165 4.3 19.7 1.0 CB A:THR234 4.3 12.6 1.0 HB2 A:ASP167 4.4 16.7 1.0 HB3 A:ASP167 4.6 16.7 1.0 CA A:GLU233 4.7 13.8 1.0 H A:ASP167 4.7 14.9 1.0 C A:GLU233 4.8 12.1 1.0 CA A:THR234 4.8 11.8 1.0 N A:ASP167 4.8 12.4 1.0 HD1 A:HIS165 4.9 33.0 1.0 HG3 A:GLU233 5.0 28.6 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the C130A Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans


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 C130A Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:16.6 occ:0.75 O A:HOH2487 2.0 17.1 0.8 NE2 A:HIS8 2.1 20.1 1.0 O A:HOH2486 2.1 20.5 0.8 O A:HOH2485 2.2 21.8 0.8 O A:HOH2483 2.2 19.7 0.8 O A:HOH2484 2.2 19.0 0.8 CE1 A:HIS8 3.0 22.0 1.0 CD2 A:HIS8 3.1 18.4 1.0 HD2 A:HIS8 3.2 22.1 1.0 HE1 A:HIS8 3.3 26.4 1.0 HA A:ASP4 3.6 24.6 1.0 O A:HOH2010 4.0 35.4 1.0 O A:ASP4 4.0 25.8 1.0 ND1 A:HIS8 4.1 17.8 1.0 CG A:HIS8 4.2 14.8 1.0 O A:LEU6 4.3 15.5 1.0 O A:ALA3 4.3 17.8 1.0 OD1 A:ASP4 4.4 60.5 1.0 HG22 A:VAL32 4.4 21.8 1.0 CA A:ASP4 4.4 20.5 1.0 C A:ASP4 4.5 19.6 1.0 O A:HOH2181 4.5 20.6 1.0 O A:HOH2180 4.7 31.9 1.0 H A:LEU6 4.9 20.9 1.0 HD1 A:HIS8 4.9 21.3 1.0 O A:HOH2007 4.9 38.2 1.0

M.A.Hough, M.J.Ellis, S.Antonyuk, R.W.Strange, G.Sawers, R.R.Eady, S.S.Hasnain. High Resolution Structural Studies of Mutants Provide Insights Into Catalysis and Electron Transfer Processes in Copper Nitrite Reductase J.Mol.Biol. V. 350 300 2005.
ISSN: ISSN 0022-2836
PubMed: 15927201
DOI: 10.1016/J.JMB.2005.04.006