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Copper in PDB 1l9p: Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6

Enzymatic activity of Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6

All present enzymatic activity of Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6:
1.7.99.3;

Protein crystallography data

The structure of Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6, PDB code: 1l9p was solved by M.J.Boulanger, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.61 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.050, 102.450, 146.210, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.4

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6 (pdb code 1l9p). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6, PDB code: 1l9p:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1l9p

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Copper binding site 1 out of 6 in the Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:16.1
occ:1.00
 ND1 A:HIS145 2.0 12.4 1.0
ND1 A:HIS95 2.0 13.2 1.0
SG A:CYS136 2.2 13.1 1.0
SD A:MET150 2.5 13.9 1.0
CE1 A:HIS145 2.9 13.7 1.0
CE1 A:HIS95 3.0 12.8 1.0
CG A:HIS95 3.1 13.4 1.0
CG A:HIS145 3.1 14.9 1.0
CB A:CYS136 3.2 12.4 1.0
CE A:MET150 3.3 14.5 1.0
CB A:HIS95 3.5 10.6 1.0
CB A:HIS145 3.5 11.6 1.0
CG A:MET150 3.8 10.7 1.0
CA A:HIS95 3.8 12.2 1.0
NE2 A:HIS145 4.1 14.6 1.0
NE2 A:HIS95 4.1 14.9 1.0
CD2 A:HIS95 4.2 14.1 1.0
CD2 A:HIS145 4.2 14.5 1.0
CB A:MET150 4.3 11.0 1.0
SD A:MET62 4.3 14.9 1.0
CG A:PRO138 4.3 14.5 1.0
O A:MET94 4.4 14.4 1.0
CA A:CYS136 4.6 12.6 1.0
N A:ASN96 4.7 12.8 1.0
CB A:MET62 4.7 15.2 1.0
CA A:HIS145 4.7 12.2 1.0
CD A:PRO138 4.8 14.1 1.0
C A:HIS95 4.8 12.5 1.0
N A:HIS95 4.9 12.9 1.0

Copper binding site 2 out of 6 in 1l9p

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Copper binding site 2 out of 6 in the Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:17.5
occ:1.00
 O2 A:NO21504 2.0 11.2 0.3
NE2 A:HIS100 2.1 12.9 1.0
O1 A:NO21504 2.1 29.1 0.7
NE2 B:HIS306 2.1 13.9 1.0
NE2 A:HIS135 2.1 14.6 1.0
O1 A:NO21504 2.1 12.9 0.3
N A:NO21504 2.3 13.6 0.3
CE1 A:HIS100 3.0 14.5 1.0
CE1 B:HIS306 3.1 12.7 1.0
CE1 A:HIS135 3.1 15.6 1.0
CD2 A:HIS135 3.1 14.3 1.0
CD2 B:HIS306 3.1 12.2 1.0
CD2 A:HIS100 3.1 13.3 1.0
N A:NO21504 3.3 29.4 0.7
O2 A:NO21504 3.7 27.8 0.7
NE2 B:HIS255 3.8 15.7 1.0
OD2 A:ASP98 3.8 22.5 1.0
CD2 B:HIS255 3.9 16.8 1.0
ND1 A:HIS100 4.1 13.2 1.0
ND1 B:HIS306 4.2 12.2 1.0
ND1 A:HIS135 4.2 11.5 1.0
CG A:HIS100 4.2 11.6 1.0
CG B:HIS306 4.2 12.4 1.0
CG A:HIS135 4.2 12.9 1.0
CG A:ASP98 4.4 17.5 1.0
CE1 B:HIS255 4.4 17.3 1.0
CG B:HIS255 4.6 16.1 1.0
OD1 A:ASP98 4.6 19.0 1.0
O B:HOH6002 4.7 15.4 1.0
ND1 B:HIS255 4.8 16.6 1.0
CD2 B:LEU308 5.0 14.0 1.0

Copper binding site 3 out of 6 in 1l9p

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Copper binding site 3 out of 6 in the Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:20.3
occ:1.00
 ND1 B:HIS145 2.0 17.3 1.0
ND1 B:HIS95 2.1 15.3 1.0
SG B:CYS136 2.2 17.6 1.0
SD B:MET150 2.5 15.8 1.0
CE1 B:HIS145 2.9 18.8 1.0
CE1 B:HIS95 3.0 15.5 1.0
CG B:HIS95 3.1 16.2 1.0
CG B:HIS145 3.1 19.1 1.0
CB B:CYS136 3.2 16.2 1.0
CE B:MET150 3.3 15.4 1.0
CB B:HIS95 3.4 16.8 1.0
CB B:HIS145 3.6 16.3 1.0
CA B:HIS95 3.8 16.2 1.0
CG B:MET150 3.9 14.5 1.0
NE2 B:HIS145 4.0 17.3 1.0
NE2 B:HIS95 4.1 15.3 1.0
CD2 B:HIS145 4.2 19.0 1.0
CD2 B:HIS95 4.2 15.7 1.0
CG B:PRO138 4.2 19.3 1.0
SD B:MET62 4.3 17.4 1.0
O B:MET94 4.3 18.4 1.0
CB B:MET150 4.4 14.9 1.0
CA B:CYS136 4.6 16.9 1.0
CD B:PRO138 4.7 18.4 1.0
N B:ASN96 4.7 16.5 1.0
CB B:MET62 4.8 15.1 1.0
CA B:HIS145 4.8 16.2 1.0
C B:HIS95 4.8 17.5 1.0
N B:HIS95 4.9 17.7 1.0

Copper binding site 4 out of 6 in 1l9p

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Copper binding site 4 out of 6 in the Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:20.9
occ:1.00
 NE2 B:HIS100 2.0 14.8 1.0
O2 B:NO22504 2.0 23.7 0.7
O1 B:NO22504 2.1 21.7 0.3
NE2 B:HIS135 2.1 17.2 1.0
NE2 C:HIS306 2.1 14.7 1.0
O1 B:NO22504 2.3 25.3 0.7
N B:NO22504 2.3 26.4 0.7
CE1 B:HIS100 2.9 16.5 1.0
CD2 C:HIS306 3.0 16.1 1.0
CD2 B:HIS135 3.1 17.5 1.0
CE1 B:HIS135 3.1 17.5 1.0
CD2 B:HIS100 3.1 13.7 1.0
CE1 C:HIS306 3.2 15.9 1.0
N B:NO22504 3.3 22.1 0.3
NE2 C:HIS255 3.7 21.8 1.0
CD2 C:HIS255 3.9 21.7 1.0
O2 B:NO22504 3.9 21.9 0.3
OD2 B:ASP98 3.9 25.2 1.0
ND1 B:HIS100 4.1 15.2 1.0
ND1 B:HIS135 4.2 16.1 1.0
CG B:HIS100 4.2 12.6 1.0
CG B:HIS135 4.2 16.5 1.0
CG C:HIS306 4.2 14.8 1.0
ND1 C:HIS306 4.3 14.5 1.0
CG B:ASP98 4.4 21.1 1.0
CE1 C:HIS255 4.4 21.2 1.0
CG C:HIS255 4.6 20.6 1.0
OD1 B:ASP98 4.6 19.5 1.0
O B:HOH6003 4.8 22.5 1.0
ND1 C:HIS255 4.9 23.0 1.0

Copper binding site 5 out of 6 in 1l9p

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Copper binding site 5 out of 6 in the Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:23.9
occ:1.00
 ND1 C:HIS145 2.0 22.4 1.0
ND1 C:HIS95 2.1 20.3 1.0
SG C:CYS136 2.2 21.9 1.0
SD C:MET150 2.4 20.7 1.0
CE1 C:HIS145 2.8 24.4 1.0
CG C:HIS145 3.1 21.9 1.0
CE1 C:HIS95 3.1 20.9 1.0
CG C:HIS95 3.1 21.1 1.0
CB C:CYS136 3.2 18.9 1.0
CE C:MET150 3.3 20.9 1.0
CB C:HIS95 3.5 21.0 1.0
CB C:HIS145 3.5 18.9 1.0
CG C:MET150 3.8 20.5 1.0
CA C:HIS95 3.8 21.3 1.0
NE2 C:HIS145 4.0 21.9 1.0
CD2 C:HIS145 4.1 23.3 1.0
CG C:PRO138 4.2 22.3 1.0
NE2 C:HIS95 4.2 19.2 1.0
CD2 C:HIS95 4.3 20.3 1.0
O C:MET94 4.3 22.9 1.0
CB C:MET150 4.3 19.1 1.0
SD C:MET62 4.4 21.3 1.0
CA C:CYS136 4.6 18.7 1.0
N C:ASN96 4.6 20.3 1.0
CB C:MET62 4.7 21.4 1.0
CD C:PRO138 4.7 21.0 1.0
CA C:HIS145 4.7 18.6 1.0
C C:HIS95 4.8 21.1 1.0
N C:HIS95 4.9 21.2 1.0

Copper binding site 6 out of 6 in 1l9p

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Copper binding site 6 out of 6 in the Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Nitrite Soaked I257G Variant of the Copper-Containing Nitrite Reductase From Alcaligenes Faecalies S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:22.2
occ:1.00
 O1 C:NO23504 2.0 28.9 0.7
O2 C:NO23504 2.0 11.7 0.3
NE2 C:HIS100 2.0 16.8 1.0
NE2 A:HIS306 2.1 14.6 1.0
NE2 C:HIS135 2.2 19.0 1.0
N C:NO23504 2.3 10.9 0.3
O1 C:NO23504 2.3 11.9 0.3
CE1 C:HIS100 2.9 19.6 1.0
CD2 C:HIS135 3.0 17.9 1.0
CE1 A:HIS306 3.1 15.7 1.0
CD2 A:HIS306 3.1 15.7 1.0
CD2 C:HIS100 3.1 18.6 1.0
N C:NO23504 3.2 29.8 0.7
CE1 C:HIS135 3.2 19.4 1.0
NE2 A:HIS255 3.7 24.0 1.0
O2 C:NO23504 3.7 28.3 0.7
CD2 A:HIS255 3.9 22.6 1.0
OD2 C:ASP98 3.9 26.7 1.0
ND1 C:HIS100 4.1 17.9 1.0
CG C:HIS100 4.2 17.8 1.0
ND1 A:HIS306 4.2 15.4 1.0
CG C:HIS135 4.2 17.7 1.0
CG A:HIS306 4.3 14.7 1.0
ND1 C:HIS135 4.3 18.6 1.0
CE1 A:HIS255 4.4 22.9 1.0
CG C:ASP98 4.5 24.6 1.0
CG A:HIS255 4.6 21.9 1.0
OD1 C:ASP98 4.7 22.9 1.0
O A:HOH6005 4.8 21.4 1.0
ND1 A:HIS255 4.9 22.4 1.0

Reference:

M.J.Boulanger, M.E.P.Murphy. Directing the Mode of Nitrite Binding to A Copper-Containing Nitrite Reductase From Alcaligenes Faecalis S-6: Characterization of An Active Site Isoleucine Protein Sci. V. 12 248 2003.
ISSN: ISSN 0961-8368
PubMed: 12538888
DOI: 10.1110/PS.0224503
Page generated: Tue Jul 30 22:12:50 2024

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