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Copper in PDB 2e86: Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6

Enzymatic activity of Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6

All present enzymatic activity of Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6:
1.7.2.1;

Protein crystallography data

The structure of Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6, PDB code: 2e86 was solved by E.I.Tocheva, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.750, 102.582, 146.000, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 17.9

Copper Binding Sites:

The binding sites of Copper atom in the Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6 (pdb code 2e86). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6, PDB code: 2e86:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2e86

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Copper binding site 1 out of 6 in the Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:8.7
occ:1.00
ND1 A:HIS145 2.1 8.0 1.0
ND1 A:HIS95 2.1 7.0 1.0
SG A:CYS136 2.2 8.1 1.0
SD A:MET150 2.5 7.6 1.0
CE1 A:HIS145 2.9 8.3 1.0
CE1 A:HIS95 3.0 7.5 1.0
CG A:HIS95 3.1 8.1 1.0
CG A:HIS145 3.1 7.5 1.0
CB A:CYS136 3.2 7.5 1.0
CE A:MET150 3.2 8.6 1.0
CB A:HIS95 3.5 7.9 1.0
CB A:HIS145 3.5 7.2 1.0
CG A:MET150 3.8 7.2 1.0
CA A:HIS95 3.9 8.0 1.0
NE2 A:HIS145 4.1 8.4 1.0
NE2 A:HIS95 4.2 7.8 1.0
CD2 A:HIS145 4.2 8.3 1.0
CD2 A:HIS95 4.2 7.5 1.0
CB A:MET150 4.3 6.8 1.0
CG A:PRO138 4.3 9.0 1.0
O A:MET94 4.3 8.9 1.0
SD A:MET62 4.4 9.8 1.0
CA A:CYS136 4.6 7.4 1.0
CD A:PRO138 4.6 8.5 1.0
N A:ASN96 4.7 8.1 1.0
CB A:MET62 4.7 9.3 1.0
CA A:HIS145 4.8 7.2 1.0
C A:HIS95 4.9 8.1 1.0
N A:HIS95 4.9 8.1 1.0

Copper binding site 2 out of 6 in 2e86

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Copper binding site 2 out of 6 in the Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:8.7
occ:1.00
N3 A:AZI503 2.0 24.0 1.0
NE2 A:HIS100 2.0 6.5 1.0
NE2 A:HIS135 2.0 7.2 1.0
NE2 B:HIS306 2.1 7.5 1.0
N2 A:AZI503 2.7 24.0 1.0
CE1 A:HIS100 2.9 6.5 1.0
CD2 A:HIS135 3.0 6.4 1.0
CE1 B:HIS306 3.0 7.4 1.0
CE1 A:HIS135 3.1 6.8 1.0
CD2 A:HIS100 3.1 6.9 1.0
CD2 B:HIS306 3.1 7.7 1.0
OD1 A:ASP98 3.6 13.8 1.0
N1 A:AZI503 3.7 24.1 1.0
ND1 A:HIS100 4.1 6.7 1.0
ND1 B:HIS306 4.1 7.1 1.0
CG A:HIS135 4.1 6.6 1.0
ND1 A:HIS135 4.1 6.7 1.0
NE2 B:HIS255 4.2 9.9 1.0
CG A:HIS100 4.2 7.2 1.0
CG B:HIS306 4.2 7.4 1.0
CG A:ASP98 4.3 10.0 1.0
CE1 B:HIS255 4.4 10.3 1.0
CD2 B:HIS255 4.6 9.7 1.0
OD2 A:ASP98 4.7 10.5 1.0
ND1 B:HIS255 4.8 10.1 1.0
CD2 B:LEU308 4.8 7.9 1.0
O B:HOH2233 4.9 10.6 1.0
CG B:HIS255 4.9 8.7 1.0
CD1 B:LEU308 5.0 8.0 1.0

Copper binding site 3 out of 6 in 2e86

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Copper binding site 3 out of 6 in the Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:10.4
occ:1.00
ND1 B:HIS95 2.1 9.2 1.0
ND1 B:HIS145 2.1 10.2 1.0
SG B:CYS136 2.2 9.6 1.0
SD B:MET150 2.5 8.8 1.0
CE1 B:HIS95 3.0 9.5 1.0
CE1 B:HIS145 3.0 10.1 1.0
CG B:HIS95 3.1 10.3 1.0
CB B:CYS136 3.1 9.6 1.0
CG B:HIS145 3.2 9.5 1.0
CE B:MET150 3.2 9.9 1.0
CB B:HIS95 3.5 10.8 1.0
CB B:HIS145 3.6 9.5 1.0
CA B:HIS95 3.9 10.8 1.0
CG B:MET150 3.9 8.2 1.0
NE2 B:HIS95 4.1 9.6 1.0
NE2 B:HIS145 4.1 10.8 1.0
CG B:PRO138 4.2 11.3 1.0
CD2 B:HIS95 4.2 10.0 1.0
CD2 B:HIS145 4.3 10.4 1.0
O B:MET94 4.3 11.3 1.0
SD B:MET62 4.4 11.4 1.0
CB B:MET150 4.4 8.2 1.0
CA B:CYS136 4.6 9.3 1.0
CD B:PRO138 4.6 11.1 1.0
N B:ASN96 4.7 10.8 1.0
CB B:MET62 4.8 10.4 1.0
CA B:HIS145 4.8 9.4 1.0
C B:HIS95 4.9 10.9 1.0
N B:HIS95 4.9 10.9 1.0
C B:MET94 5.0 11.3 1.0

Copper binding site 4 out of 6 in 2e86

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Copper binding site 4 out of 6 in the Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:10.6
occ:1.00
NE2 B:HIS135 2.0 8.9 1.0
NE2 B:HIS100 2.0 8.6 1.0
NE2 C:HIS306 2.1 8.4 1.0
N3 C:AZI2013 2.1 31.3 1.0
N2 C:AZI2013 2.8 31.3 1.0
CE1 B:HIS100 2.9 8.7 1.0
CD2 B:HIS135 3.0 8.9 1.0
CE1 C:HIS306 3.0 8.7 1.0
CE1 B:HIS135 3.1 8.9 1.0
CD2 B:HIS100 3.1 8.8 1.0
CD2 C:HIS306 3.1 8.4 1.0
OD1 B:ASP98 3.6 15.1 1.0
N1 C:AZI2013 3.8 31.6 1.0
ND1 B:HIS100 4.1 8.2 1.0
NE2 C:HIS255 4.1 11.6 1.0
CG B:HIS135 4.1 8.5 1.0
ND1 C:HIS306 4.1 8.1 1.0
ND1 B:HIS135 4.1 8.7 1.0
CG B:HIS100 4.2 9.3 1.0
CG C:HIS306 4.2 8.4 1.0
CG B:ASP98 4.3 12.0 1.0
CE1 C:HIS255 4.4 11.9 1.0
CD2 C:HIS255 4.5 11.8 1.0
O B:HOH2397 4.6 30.8 1.0
OD2 B:ASP98 4.8 12.4 1.0
ND1 C:HIS255 4.8 12.1 1.0
O C:HOH2206 4.9 11.8 1.0
CG C:HIS255 4.9 10.4 1.0
CD2 C:LEU308 5.0 8.9 1.0
CD1 C:LEU308 5.0 9.7 1.0

Copper binding site 5 out of 6 in 2e86

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Copper binding site 5 out of 6 in the Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:13.9
occ:1.00
ND1 C:HIS95 2.1 13.6 1.0
ND1 C:HIS145 2.1 13.9 1.0
SG C:CYS136 2.2 12.5 1.0
SD C:MET150 2.5 12.3 1.0
CE1 C:HIS145 3.0 13.5 1.0
CE1 C:HIS95 3.0 14.0 1.0
CG C:HIS95 3.1 14.2 1.0
CB C:CYS136 3.1 11.8 1.0
CG C:HIS145 3.2 12.8 1.0
CE C:MET150 3.3 13.1 1.0
CB C:HIS95 3.5 14.3 1.0
CB C:HIS145 3.5 12.0 1.0
CA C:HIS95 3.9 14.2 1.0
CG C:MET150 3.9 12.0 1.0
NE2 C:HIS145 4.2 14.2 1.0
NE2 C:HIS95 4.2 13.5 1.0
CD2 C:HIS95 4.2 14.2 1.0
CD2 C:HIS145 4.2 13.4 1.0
CG C:PRO138 4.2 13.6 1.0
O C:MET94 4.3 15.4 1.0
CB C:MET150 4.4 11.6 1.0
SD C:MET62 4.4 14.0 1.0
CA C:CYS136 4.6 11.8 1.0
CD C:PRO138 4.6 13.2 1.0
N C:ASN96 4.7 13.7 1.0
CB C:MET62 4.7 13.9 1.0
CA C:HIS145 4.8 11.8 1.0
C C:HIS95 4.8 14.2 1.0
N C:HIS95 4.9 14.8 1.0
C C:MET94 5.0 15.5 1.0

Copper binding site 6 out of 6 in 2e86

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Copper binding site 6 out of 6 in the Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:11.6
occ:1.00
NE2 C:HIS100 2.0 11.6 1.0
NE2 C:HIS135 2.0 10.6 1.0
NE2 A:HIS306 2.1 8.7 1.0
N3 C:AZI503 2.1 26.7 1.0
CE1 C:HIS100 2.9 11.1 1.0
N2 C:AZI503 2.9 26.9 1.0
CD2 C:HIS135 3.0 10.6 1.0
CE1 A:HIS306 3.0 9.6 1.0
CE1 C:HIS135 3.1 10.5 1.0
CD2 C:HIS100 3.1 10.7 1.0
CD2 A:HIS306 3.2 9.7 1.0
OD1 C:ASP98 3.6 16.7 1.0
N1 C:AZI503 3.9 26.6 1.0
ND1 C:HIS100 4.1 10.6 1.0
ND1 A:HIS306 4.1 9.3 1.0
NE2 A:HIS255 4.1 11.5 1.0
CG C:HIS135 4.1 10.4 1.0
ND1 C:HIS135 4.1 10.6 1.0
CG C:HIS100 4.2 10.7 1.0
CG A:HIS306 4.2 9.1 1.0
CE1 A:HIS255 4.3 12.3 1.0
CG C:ASP98 4.4 13.9 1.0
O C:HOH2336 4.5 31.5 1.0
CD2 A:HIS255 4.5 11.5 1.0
ND1 A:HIS255 4.8 11.6 1.0
OD2 C:ASP98 4.9 14.8 1.0
O A:HOH2247 4.9 13.3 1.0
CG A:HIS255 4.9 10.4 1.0
CD2 A:LEU308 4.9 10.5 1.0
CD1 A:LEU308 4.9 11.2 1.0

Reference:

E.I.Tocheva, L.D.Eltis, M.E.P.Murphy. Conserved Active Site Residues Limit Inhibition of A Copper-Containing Nitrite Reductase By Small Molecules. Biochemistry V. 47 4452 2008.
ISSN: ISSN 0006-2960
PubMed: 18358002
DOI: 10.1021/BI7020537
Page generated: Thu Sep 3 16:35:49 2020
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