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Copper in PDB 2dwt: Cu-Containing Nitrite Reductase at pH 6.0 with Bound Nitrite

Enzymatic activity of Cu-Containing Nitrite Reductase at pH 6.0 with Bound Nitrite

All present enzymatic activity of Cu-Containing Nitrite Reductase at pH 6.0 with Bound Nitrite:
1.7.2.1;

Protein crystallography data

The structure of Cu-Containing Nitrite Reductase at pH 6.0 with Bound Nitrite, PDB code: 2dwt was solved by F.Jacobson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.71 / 1.90
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 74.740, 74.740, 153.146, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 23.5

Copper Binding Sites:

The binding sites of Copper atom in the Cu-Containing Nitrite Reductase at pH 6.0 with Bound Nitrite (pdb code 2dwt). 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 6.0 with Bound Nitrite, PDB code: 2dwt:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 2dwt

Go back to Copper Binding Sites List in 2dwt
Copper binding site 1 out of 2 in the Cu-Containing Nitrite Reductase at pH 6.0 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 6.0 with Bound Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:36.1
occ:1.00
ND1 A:HIS177 2.1 35.4 1.0
SG A:CYS167 2.2 29.8 1.0
ND1 A:HIS126 2.3 34.6 1.0
SD A:MET182 2.6 35.9 1.0
CE1 A:HIS177 2.9 37.9 1.0
CB A:CYS167 3.1 29.7 1.0
CG A:HIS177 3.2 33.8 1.0
CE1 A:HIS126 3.3 37.4 1.0
CG A:HIS126 3.3 34.3 1.0
CE A:MET182 3.3 33.0 1.0
CB A:HIS126 3.6 34.0 1.0
CB A:HIS177 3.7 29.0 1.0
CA A:HIS126 3.8 34.9 1.0
CG A:MET182 4.0 32.3 1.0
NE2 A:HIS177 4.1 35.6 1.0
CG A:PRO169 4.2 33.2 1.0
CD2 A:HIS177 4.3 34.9 1.0
O A:PRO125 4.3 37.4 1.0
NE2 A:HIS126 4.4 35.4 1.0
CD2 A:HIS126 4.4 34.0 1.0
CB A:MET182 4.4 30.9 1.0
SD A:MET93 4.6 42.5 1.0
CA A:CYS167 4.6 29.5 1.0
N A:ASN127 4.6 32.9 1.0
CD A:PRO169 4.8 32.2 1.0
C A:HIS126 4.8 34.7 1.0
CA A:HIS177 4.9 28.7 1.0
CB A:MET93 4.9 37.6 1.0
N A:HIS126 4.9 36.2 1.0

Copper binding site 2 out of 2 in 2dwt

Go back to Copper Binding Sites List in 2dwt
Copper binding site 2 out of 2 in the Cu-Containing Nitrite Reductase at pH 6.0 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 6.0 with Bound Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:27.2
occ:1.00
NE2 A:HIS166 2.0 26.0 1.0
NE2 A:HIS131 2.0 19.2 1.0
CE1 A:HIS131 2.8 21.6 1.0
CE1 A:HIS166 2.9 26.4 1.0
CD2 A:HIS166 3.1 29.5 1.0
CD2 A:HIS131 3.2 21.5 1.0
OD2 A:ASP129 3.7 29.7 1.0
ND1 A:HIS131 4.1 22.9 1.0
ND1 A:HIS166 4.1 26.0 1.0
CG A:HIS166 4.2 26.8 1.0
CG A:HIS131 4.2 18.7 1.0
CG A:ASP129 4.4 30.6 1.0
OD1 A:ASP129 4.8 27.0 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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