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Copper in PDB 2dws: Cu-Containing Nitrite Reductase at pH 8.4 with Bound Nitrite

Enzymatic activity of Cu-Containing Nitrite Reductase at pH 8.4 with Bound Nitrite

All present enzymatic activity of Cu-Containing Nitrite Reductase at pH 8.4 with Bound Nitrite:
1.7.2.1;

Protein crystallography data

The structure of Cu-Containing Nitrite Reductase at pH 8.4 with Bound Nitrite, PDB code: 2dws was solved by F.Jacobson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.46 / 1.85
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 82.204, 82.204, 146.152, 90.00, 90.00, 120.00
R / Rfree (%) 16.8 / 19.9

Copper Binding Sites:

The binding sites of Copper atom in the Cu-Containing Nitrite Reductase at pH 8.4 with Bound Nitrite (pdb code 2dws). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Cu-Containing Nitrite Reductase at pH 8.4 with Bound Nitrite, PDB code: 2dws:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 2dws

Go back to Copper Binding Sites List in 2dws
Copper binding site 1 out of 2 in the Cu-Containing Nitrite Reductase at pH 8.4 with Bound Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cu-Containing Nitrite Reductase at pH 8.4 with Bound Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:25.7
occ:1.00
ND1 A:HIS177 2.0 22.6 1.0
ND1 A:HIS126 2.1 23.7 1.0
SG A:CYS167 2.2 25.5 1.0
SD A:MET182 2.4 24.9 1.0
CE1 A:HIS177 3.0 26.0 1.0
CE1 A:HIS126 3.1 28.0 1.0
CG A:HIS126 3.1 27.2 1.0
CG A:HIS177 3.1 22.0 1.0
CB A:CYS167 3.1 22.9 1.0
CE A:MET182 3.2 24.1 1.0
CB A:HIS126 3.4 25.9 1.0
CB A:HIS177 3.5 20.0 1.0
CG A:MET182 3.8 25.3 1.0
CA A:HIS126 3.9 25.8 1.0
NE2 A:HIS177 4.1 25.5 1.0
CD2 A:HIS177 4.2 22.7 1.0
NE2 A:HIS126 4.2 23.6 1.0
CD2 A:HIS126 4.2 25.1 1.0
CG A:PRO169 4.3 26.1 1.0
CB A:MET182 4.4 20.3 1.0
O A:PRO125 4.4 26.4 1.0
SD A:MET93 4.5 23.1 0.5
CA A:CYS167 4.6 22.7 1.0
N A:ASN127 4.7 24.4 1.0
CA A:HIS177 4.8 19.8 1.0
CD A:PRO169 4.8 25.5 1.0
C A:HIS126 4.8 25.7 1.0
N A:HIS126 4.9 27.3 1.0
CB A:MET93 4.9 23.1 0.5

Copper binding site 2 out of 2 in 2dws

Go back to Copper Binding Sites List in 2dws
Copper binding site 2 out of 2 in the Cu-Containing Nitrite Reductase at pH 8.4 with Bound Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cu-Containing Nitrite Reductase at pH 8.4 with Bound Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:25.8
occ:1.00
NE2 A:HIS131 2.0 22.4 1.0
NE2 A:HIS166 2.1 21.4 1.0
CE1 A:HIS131 2.9 20.9 1.0
CD2 A:HIS166 3.0 22.4 1.0
CD2 A:HIS131 3.1 20.8 1.0
CE1 A:HIS166 3.1 23.1 1.0
OD2 A:ASP129 3.6 33.9 1.0
ND1 A:HIS131 4.0 20.0 1.0
CG A:HIS131 4.2 18.6 1.0
CG A:HIS166 4.2 22.6 1.0
ND1 A:HIS166 4.2 22.4 1.0
CG A:ASP129 4.3 29.6 1.0
OD1 A:ASP129 4.6 27.6 1.0
O A:HOH582 4.7 27.7 1.0

Reference:

F.Jacobson, A.Pistorius, D.Farkas, W.De Grip, O.Hansson, L.Sjolin, R.Neutze. pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase J.Biol.Chem. V. 282 6347 2007.
ISSN: ISSN 0021-9258
PubMed: 17148448
DOI: 10.1074/JBC.M605746200
Page generated: Wed Oct 28 14:19:09 2020
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