Copper in PDB 1ndt: Nitrite Reductase From Alcaligenes Xylosoxidans

All present enzymatic activity of Nitrite Reductase From Alcaligenes Xylosoxidans:
1.7.99.3;

The structure of Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 1ndt was solved by F.E.Dodd, J.Vanbeeumen, 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)	20.00 / 2.10
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	81.236, 81.236, 100.034, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 20.8

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

Chlorine

(Cl)

1 atom

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

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu501 b:16.3 occ:1.00 ND1 A:HIS139 1.9 13.6 1.0 ND1 A:HIS89 2.1 16.6 1.0 SG A:CYS130 2.2 16.5 1.0 SD A:MET144 2.6 16.8 1.0 CE1 A:HIS139 2.9 14.4 1.0 CE1 A:HIS89 2.9 16.8 1.0 CG A:HIS139 3.0 15.1 1.0 CG A:HIS89 3.1 18.1 1.0 CB A:CYS130 3.3 14.5 1.0 CB A:HIS139 3.4 13.2 1.0 CE A:MET144 3.5 11.5 1.0 CB A:HIS89 3.6 16.1 1.0 CA A:HIS89 3.9 17.2 1.0 NE2 A:HIS139 4.0 16.9 1.0 NE2 A:HIS89 4.1 18.3 1.0 O A:PRO88 4.1 16.5 1.0 CD2 A:HIS139 4.1 15.8 1.0 CG A:PRO132 4.1 18.8 1.0 CG A:MET144 4.1 12.3 1.0 CD2 A:HIS89 4.2 17.4 1.0 CD A:PRO132 4.5 16.4 1.0 SD A:MET56 4.5 22.5 1.0 CB A:MET144 4.7 10.4 1.0 CA A:CYS130 4.7 13.9 1.0 CA A:HIS139 4.7 12.9 1.0 N A:ASN90 4.8 17.7 1.0 N A:HIS89 4.8 16.9 1.0 C A:PRO88 4.9 19.0 1.0 C A:HIS89 4.9 18.5 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu502 b:14.8 occ:1.00 NE2 A:HIS94 2.0 8.6 1.0 NE2 A:HIS129 2.1 14.6 1.0 CL A:CL503 2.2 21.9 1.0 CE1 A:HIS94 2.9 9.4 1.0 CD2 A:HIS129 3.1 11.8 1.0 CD2 A:HIS94 3.1 8.7 1.0 CE1 A:HIS129 3.1 13.7 1.0 OD2 A:ASP92 3.9 19.4 1.0 ND1 A:HIS94 4.1 8.8 1.0 CG A:HIS94 4.2 10.0 1.0 CG A:HIS129 4.2 11.8 1.0 ND1 A:HIS129 4.2 14.1 1.0 CG A:ASP92 4.6 18.6 1.0 O A:HOH600 4.9 19.6 1.0 OD1 A:ASP92 5.0 17.7 1.0

F.E.Dodd, J.Van Beeumen, R.R.Eady, S.S.Hasnain. X-Ray Structure of A Blue-Copper Nitrite Reductase in Two Crystal Forms. the Nature of the Copper Sites, Mode of Substrate Binding and Recognition By Redox Partner. J.Mol.Biol. V. 282 369 1998.
ISSN: ISSN 0022-2836
PubMed: 9735294
DOI: 10.1006/JMBI.1998.2007