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Copper in PDB 2dy2: Nitrite Reductase pH 6.0

Enzymatic activity of Nitrite Reductase pH 6.0

All present enzymatic activity of Nitrite Reductase pH 6.0:
1.7.2.1;

Protein crystallography data

The structure of Nitrite Reductase pH 6.0, PDB code: 2dy2 was solved by F.Jacobson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.77 / 2.26
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 74.996, 74.996, 153.611, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 24.1

Copper Binding Sites:

The binding sites of Copper atom in the Nitrite Reductase pH 6.0 (pdb code 2dy2). 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 pH 6.0, PDB code: 2dy2:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 2dy2

Go back to Copper Binding Sites List in 2dy2
Copper binding site 1 out of 2 in the Nitrite Reductase pH 6.0


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Nitrite Reductase pH 6.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:40.9
occ:1.00
ND1 A:HIS177 2.0 37.8 1.0
SG A:CYS167 2.2 39.6 1.0
ND1 A:HIS126 2.3 44.0 1.0
SD A:MET182 2.5 40.3 1.0
CE1 A:HIS177 2.9 39.5 1.0
CG A:HIS177 3.1 39.6 1.0
CG A:HIS126 3.2 43.2 1.0
CB A:CYS167 3.2 39.3 1.0
CE1 A:HIS126 3.3 42.4 1.0
CB A:HIS126 3.4 44.1 1.0
CB A:HIS177 3.5 38.1 1.0
CE A:MET182 3.5 39.8 1.0
CA A:HIS126 3.8 44.2 1.0
CG A:MET182 3.9 37.0 1.0
CG A:PRO169 4.1 43.2 1.0
NE2 A:HIS177 4.1 38.5 1.0
CD2 A:HIS177 4.2 38.0 1.0
O A:PRO125 4.2 45.7 1.0
CD2 A:HIS126 4.4 44.0 1.0
CB A:MET182 4.4 35.0 1.0
NE2 A:HIS126 4.4 45.3 1.0
CA A:CYS167 4.6 39.1 1.0
SD A:MET93 4.6 48.5 1.0
N A:ASN127 4.7 43.0 1.0
CA A:HIS177 4.7 37.5 1.0
CD A:PRO169 4.7 42.0 1.0
C A:HIS126 4.8 43.8 1.0
N A:HIS126 4.9 44.8 1.0
C A:PRO125 5.0 46.1 1.0
C A:CYS167 5.0 39.6 1.0

Copper binding site 2 out of 2 in 2dy2

Go back to Copper Binding Sites List in 2dy2
Copper binding site 2 out of 2 in the Nitrite Reductase pH 6.0


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Nitrite Reductase pH 6.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:35.3
occ:1.00
O A:HOH474 2.1 45.0 1.0
NE2 A:HIS338 2.2 23.3 1.0
CD2 A:HIS338 3.0 25.2 1.0
CE1 A:HIS338 3.2 25.6 1.0
NE2 A:HIS287 4.0 31.7 1.0
CG A:HIS338 4.2 24.1 1.0
ND1 A:HIS338 4.3 25.8 1.0
CD2 A:HIS287 4.3 29.4 1.0
CE1 A:HIS287 4.4 33.4 1.0
CG A:HIS287 4.9 31.0 1.0
ND1 A:HIS287 4.9 32.0 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: Thu Sep 3 16:34:45 2020
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