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Copper in PDB 1ndt: Nitrite Reductase From Alcaligenes Xylosoxidans

Enzymatic activity of Nitrite Reductase From Alcaligenes Xylosoxidans

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

Protein crystallography data

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

Other elements in 1ndt:

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

Chlorine (Cl) 1 atom

Copper Binding Sites:

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 1ndt

Go back to Copper Binding Sites List in 1ndt
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 1ndt

Go back to Copper Binding Sites List in 1ndt
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

Reference:

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
Page generated: Wed Oct 28 14:16:08 2020
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