Copper in PDB 2vw4: Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3

All present enzymatic activity of Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3:
1.7.2.1;

The structure of Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3, PDB code: 2vw4 was solved by M.J.Ellis, S.G.Buffey, M.A.Hough, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	96.23 / 1.90
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	89.080, 89.080, 288.303, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 19.7

The structure of Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Copper atom in the Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3 (pdb code 2vw4). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3, PDB code: 2vw4:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu501 b:21.9 occ:1.00 SG A:CYS130 2.1 17.7 1.0 ND1 A:HIS139 2.2 15.2 1.0 ND1 A:HIS89 2.2 15.5 1.0 SD A:MET144 2.5 13.5 0.8 CB A:CYS130 3.1 15.5 1.0 CE1 A:HIS139 3.1 15.3 1.0 CE1 A:HIS89 3.2 16.3 1.0 CG A:HIS89 3.2 17.3 1.0 CE A:MET144 3.2 16.1 0.1 CG A:HIS139 3.2 14.2 1.0 CE A:MET144 3.5 14.9 0.8 CB A:HIS89 3.5 17.7 1.0 CB A:HIS139 3.5 12.8 1.0 CA A:HIS89 3.8 18.5 1.0 CG A:PRO132 3.9 17.8 1.0 CG A:MET144 4.0 15.2 1.0 SD A:MET144 4.0 15.9 0.1 O A:PRO88 4.1 18.1 1.0 NE2 A:HIS139 4.3 15.9 1.0 NE2 A:HIS89 4.3 15.7 1.0 CD2 A:HIS139 4.3 15.1 1.0 CD2 A:HIS89 4.3 15.7 1.0 CD A:PRO132 4.4 16.5 1.0 SD A:MET56 4.4 17.0 0.7 CA A:CYS130 4.5 15.5 1.0 CB A:MET144 4.6 13.5 1.0 SD A:MET56 4.6 16.5 0.3 N A:ASN90 4.7 17.5 1.0 CA A:HIS139 4.7 12.8 1.0 N A:HIS89 4.8 18.6 1.0 C A:HIS89 4.8 18.6 1.0 C A:PRO88 4.9 19.2 1.0

Copper binding site 2 out of 4 in the Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu502 b:16.4 occ:1.00 O A:HOH2135 1.9 16.9 1.0 NE2 A:HIS129 2.0 12.8 1.0 NE2 A:HIS94 2.0 14.0 1.0 CD2 A:HIS129 2.9 12.4 1.0 CE1 A:HIS94 3.0 13.9 1.0 CE1 A:HIS129 3.0 13.8 1.0 CD2 A:HIS94 3.1 12.8 1.0 OD2 A:ASP92 3.6 24.9 1.0 CG A:HIS129 4.1 13.7 1.0 ND1 A:HIS94 4.1 13.7 1.0 ND1 A:HIS129 4.1 12.0 1.0 CG A:HIS94 4.2 12.6 1.0 CG A:ASP92 4.3 20.8 1.0 OD1 A:ASP92 4.5 19.3 1.0 O A:HOH2134 4.9 17.9 1.0

Copper binding site 3 out of 4 in the Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu501 b:22.1 occ:1.00 SG B:CYS130 2.1 17.5 1.0 ND1 B:HIS139 2.2 16.4 1.0 ND1 B:HIS89 2.2 16.0 1.0 SD B:MET144 2.5 14.1 0.8 CE B:MET144 3.1 16.9 0.1 CB B:CYS130 3.1 16.3 1.0 CE1 B:HIS139 3.1 17.3 1.0 CG B:HIS89 3.2 18.2 1.0 CE1 B:HIS89 3.2 17.4 1.0 CG B:HIS139 3.2 15.7 1.0 CE B:MET144 3.3 15.4 0.8 CB B:HIS89 3.4 18.7 1.0 CB B:HIS139 3.6 14.0 1.0 CA B:HIS89 3.8 18.9 1.0 CG B:MET144 4.0 15.2 1.0 CG B:PRO132 4.0 19.0 1.0 SD B:MET144 4.1 17.4 0.1 O B:PRO88 4.2 19.4 1.0 NE2 B:HIS139 4.2 18.0 1.0 NE2 B:HIS89 4.3 18.5 1.0 CD2 B:HIS89 4.3 17.5 1.0 CD2 B:HIS139 4.3 17.6 1.0 SD B:MET56 4.4 16.5 0.7 CD B:PRO132 4.4 17.9 1.0 CB B:MET144 4.5 13.6 1.0 CA B:CYS130 4.5 16.4 1.0 SD B:MET56 4.6 16.5 0.3 N B:ASN90 4.7 18.3 1.0 CA B:HIS139 4.8 13.6 1.0 C B:HIS89 4.8 19.1 1.0 N B:HIS89 4.8 19.4 1.0 C B:PRO88 4.9 19.8 1.0

Copper binding site 4 out of 4 in the Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu502 b:17.6 occ:1.00 O B:HOH2111 1.9 18.3 1.0 NE2 B:HIS129 2.0 14.6 1.0 NE2 B:HIS94 2.0 14.7 1.0 CE1 B:HIS94 2.9 15.3 1.0 CD2 B:HIS129 2.9 15.7 1.0 CE1 B:HIS129 3.0 15.2 1.0 CD2 B:HIS94 3.1 14.9 1.0 OD2 B:ASP92 3.7 27.1 1.0 ND1 B:HIS94 4.1 15.7 1.0 CG B:HIS129 4.1 15.4 1.0 ND1 B:HIS129 4.1 14.1 1.0 CG B:HIS94 4.2 14.8 1.0 CG B:ASP92 4.3 21.1 1.0 OD1 B:ASP92 4.6 21.4 1.0 O B:HOH2112 4.9 19.6 1.0

M.J.Ellis, S.G.Buffey, M.A.Hough, S.S.Hasnain. On-Line Optical and X-Ray Spectroscopies with Crystallography: An Integrated Approach For Determining Metalloprotein Structures in Functionally Well Defined States. J.Synchrotron Radiat. V. 15 433 2008.
ISSN: ISSN 0909-0495
PubMed: 18728313
DOI: 10.1107/S0909049508014945