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Copper in PDB 2vn3: Nitrite Reductase From Alcaligenes Xylosoxidans

Protein crystallography data

The structure of Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 2vn3 was solved by K.Sato, S.J.Firbank, C.Li, M.J.Banfield, C.Dennison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.14 / 2.35
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 89.451, 89.451, 144.473, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 21.5

Other elements in 2vn3:

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

Zinc (Zn) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Nitrite Reductase From Alcaligenes Xylosoxidans (pdb code 2vn3). 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: 2vn3:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 2vn3

Go back to Copper Binding Sites List in 2vn3
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:Cu401

b:42.8
occ:1.00
ND1 A:HIS139 2.0 38.2 1.0
SG A:CYS130 2.2 36.0 1.0
ND1 A:HIS89 2.2 39.0 1.0
SD A:MET144 2.5 34.2 1.0
CE1 A:HIS139 2.9 37.6 1.0
CG A:HIS139 3.1 37.1 1.0
CB A:CYS130 3.1 34.8 1.0
CG A:HIS89 3.2 39.8 1.0
CE1 A:HIS89 3.2 36.4 1.0
CE A:MET144 3.4 30.3 1.0
CB A:HIS89 3.5 40.6 1.0
CB A:HIS139 3.5 33.0 1.0
CA A:HIS89 3.8 40.7 1.0
CG A:PRO132 3.9 38.8 1.0
NE2 A:HIS139 4.0 39.6 1.0
CG A:MET144 4.1 32.3 1.0
O A:PRO88 4.1 42.0 1.0
CD2 A:HIS139 4.2 38.5 1.0
NE2 A:HIS89 4.3 40.7 1.0
CD2 A:HIS89 4.3 40.0 1.0
CD A:PRO132 4.4 37.7 1.0
CA A:CYS130 4.6 35.1 1.0
CB A:MET144 4.6 31.0 1.0
SD A:MET56 4.6 37.2 1.0
CA A:HIS139 4.7 32.7 1.0
N A:ASN90 4.8 40.0 1.0
N A:HIS89 4.8 41.8 1.0
C A:PRO88 4.9 42.6 1.0
C A:HIS89 4.9 40.4 1.0

Copper binding site 2 out of 2 in 2vn3

Go back to Copper Binding Sites List in 2vn3
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:Cu402

b:36.1
occ:1.00
O A:HOH2052 1.8 47.8 1.0
NE2 A:HIS129 2.0 32.8 1.0
NE2 A:HIS94 2.1 29.6 1.0
CD2 A:HIS129 2.9 32.3 1.0
CE1 A:HIS94 3.0 30.9 1.0
CE1 A:HIS129 3.0 33.4 1.0
CD2 A:HIS94 3.2 28.9 1.0
OD2 A:ASP92 3.7 35.0 1.0
CG A:HIS129 4.1 31.1 1.0
ND1 A:HIS129 4.1 35.0 1.0
ND1 A:HIS94 4.1 31.9 1.0
CG A:HIS94 4.3 31.9 1.0
CG A:ASP92 4.4 35.5 1.0
OD1 A:ASP92 4.8 35.5 1.0

Reference:

K.Sato, S.J.Firbank, C.Li, M.J.Banfield, C.Dennison. The Importance of the Long Type 1 Copper-Binding Loop of Nitrite Reductase For Structure and Function. Chemistry V. 14 5820 2008.
ISSN: ISSN 0947-6539
PubMed: 18491346
DOI: 10.1002/CHEM.200701997
Page generated: Sun Dec 13 11:07:10 2020

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