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Copper in PDB 1l9t: Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6

Enzymatic activity of Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6

All present enzymatic activity of Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6:
1.7.99.3;

Protein crystallography data

The structure of Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6, PDB code: 1l9t 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) 50.00 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.730, 102.340, 145.900, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 20.8

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 (pdb code 1l9t). 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 the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6, PDB code: 1l9t:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1l9t

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Copper binding site 1 out of 6 in the Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes 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 Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:20.4
occ:1.00
 ND1 A:HIS145 2.0 16.9 1.0
ND1 A:HIS95 2.1 18.6 1.0
SG A:CYS136 2.2 17.2 1.0
SD A:MET150 2.4 17.5 1.0
CE1 A:HIS145 2.9 16.9 1.0
CE1 A:HIS95 3.0 19.5 1.0
CG A:HIS145 3.1 15.3 1.0
CG A:HIS95 3.1 18.6 1.0
CB A:CYS136 3.2 17.4 1.0
CE A:MET150 3.3 16.3 1.0
CB A:HIS95 3.5 16.1 1.0
CB A:HIS145 3.6 15.5 1.0
CG A:MET150 3.8 16.2 1.0
CA A:HIS95 3.9 17.9 1.0
NE2 A:HIS145 4.1 17.7 1.0
NE2 A:HIS95 4.2 19.4 1.0
CD2 A:HIS145 4.2 18.1 1.0
CD2 A:HIS95 4.2 18.5 1.0
CB A:MET150 4.3 16.0 1.0
SD A:MET62 4.3 19.5 1.0
CG A:PRO138 4.3 19.7 1.0
O A:MET94 4.4 18.1 1.0
CA A:CYS136 4.6 17.1 1.0
N A:ASN96 4.7 17.4 1.0
CB A:MET62 4.7 18.3 1.0
CD A:PRO138 4.7 17.6 1.0
CA A:HIS145 4.7 16.0 1.0
C A:HIS95 4.9 17.5 1.0
N A:HIS95 5.0 18.2 1.0

Copper binding site 2 out of 6 in 1l9t

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Copper binding site 2 out of 6 in the Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes 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 Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:21.1
occ:1.00
 O2 B:NO2504 2.0 35.6 1.0
NE2 A:HIS100 2.1 16.6 1.0
NE2 B:HIS306 2.1 17.7 1.0
N B:NO2504 2.1 35.4 1.0
NE2 A:HIS135 2.1 18.7 1.0
O1 B:NO2504 2.3 30.9 1.0
CE1 A:HIS100 3.0 18.5 1.0
CE1 B:HIS306 3.0 16.6 1.0
CE1 A:HIS135 3.1 17.3 1.0
CD2 A:HIS135 3.1 18.1 1.0
CD2 A:HIS100 3.1 17.4 1.0
CD2 B:HIS306 3.1 17.2 1.0
OD2 A:ASP98 3.5 26.9 1.0
NE2 B:HIS255 4.0 20.6 1.0
ND1 A:HIS100 4.1 16.7 1.0
ND1 B:HIS306 4.2 15.6 1.0
O A:HOH5296 4.2 45.1 1.0
ND1 A:HIS135 4.2 16.0 1.0
CG A:HIS100 4.2 15.6 1.0
CG A:HIS135 4.2 18.1 1.0
CG B:HIS306 4.3 16.7 1.0
CD2 B:HIS255 4.3 21.2 1.0
CG A:ASP98 4.3 23.2 1.0
CE1 B:HIS255 4.4 23.9 1.0
CG B:HIS255 4.8 20.6 1.0
ND1 B:HIS255 4.8 22.8 1.0
OD1 A:ASP98 4.9 23.7 1.0
O B:HOH6001 4.9 19.6 1.0
CD2 B:LEU308 4.9 17.1 1.0

Copper binding site 3 out of 6 in 1l9t

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Copper binding site 3 out of 6 in the Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes 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 Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:22.9
occ:1.00
 ND1 B:HIS145 2.0 20.6 1.0
ND1 B:HIS95 2.0 18.5 1.0
SG B:CYS136 2.2 20.4 1.0
SD B:MET150 2.5 19.3 1.0
CE1 B:HIS145 2.9 23.3 1.0
CE1 B:HIS95 3.0 19.9 1.0
CG B:HIS95 3.1 19.7 1.0
CG B:HIS145 3.1 21.8 1.0
CB B:CYS136 3.2 18.5 1.0
CE B:MET150 3.3 21.6 1.0
CB B:HIS95 3.4 20.3 1.0
CB B:HIS145 3.5 20.4 1.0
CG B:MET150 3.8 17.8 1.0
CA B:HIS95 3.9 21.3 1.0
NE2 B:HIS145 4.1 22.9 1.0
NE2 B:HIS95 4.1 18.6 1.0
CD2 B:HIS95 4.2 18.8 1.0
CD2 B:HIS145 4.2 22.2 1.0
CG B:PRO138 4.2 20.8 1.0
SD B:MET62 4.3 21.9 1.0
O B:MET94 4.3 22.3 1.0
CB B:MET150 4.4 17.4 1.0
CA B:CYS136 4.6 19.7 1.0
CD B:PRO138 4.6 19.1 1.0
N B:ASN96 4.7 20.6 1.0
CA B:HIS145 4.8 19.5 1.0
CB B:MET62 4.8 20.7 1.0
C B:HIS95 4.9 21.7 1.0
N B:HIS95 4.9 21.5 1.0

Copper binding site 4 out of 6 in 1l9t

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Copper binding site 4 out of 6 in the Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes 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 Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:23.9
occ:1.00
 O2 C:NO2604 1.9 37.3 1.0
NE2 B:HIS100 2.1 19.0 1.0
NE2 B:HIS135 2.1 20.5 1.0
NE2 C:HIS306 2.1 18.4 1.0
N C:NO2604 2.2 35.8 1.0
O1 C:NO2604 2.4 34.2 1.0
CE1 B:HIS100 2.9 19.4 1.0
CE1 B:HIS135 3.1 19.7 1.0
CE1 C:HIS306 3.1 19.3 1.0
CD2 B:HIS135 3.1 19.5 1.0
CD2 C:HIS306 3.1 21.1 1.0
CD2 B:HIS100 3.2 19.7 1.0
OD2 B:ASP98 3.6 28.4 1.0
NE2 C:HIS255 3.9 26.0 1.0
ND1 B:HIS100 4.1 18.4 1.0
O B:HOH6004 4.1 39.9 1.0
ND1 B:HIS135 4.2 18.7 1.0
ND1 C:HIS306 4.2 18.9 1.0
CG B:HIS135 4.2 19.0 1.0
CD2 C:HIS255 4.2 25.0 1.0
CG B:HIS100 4.2 19.2 1.0
CG C:HIS306 4.3 19.4 1.0
CE1 C:HIS255 4.3 25.0 1.0
CG B:ASP98 4.4 24.7 1.0
CG C:HIS255 4.8 23.1 1.0
ND1 C:HIS255 4.8 25.6 1.0
OD1 B:ASP98 4.8 22.9 1.0
O C:HOH6003 4.9 21.7 1.0

Copper binding site 5 out of 6 in 1l9t

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Copper binding site 5 out of 6 in the Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes 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 Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:27.2
occ:1.00
 ND1 C:HIS145 2.0 25.1 1.0
ND1 C:HIS95 2.1 24.8 1.0
SG C:CYS136 2.2 24.6 1.0
SD C:MET150 2.5 23.4 1.0
CE1 C:HIS145 2.8 26.4 1.0
CE1 C:HIS95 3.1 24.3 1.0
CG C:HIS145 3.1 25.1 1.0
CG C:HIS95 3.1 23.2 1.0
CB C:CYS136 3.2 23.3 1.0
CE C:MET150 3.3 22.5 1.0
CB C:HIS95 3.4 24.9 1.0
CB C:HIS145 3.5 23.4 1.0
CA C:HIS95 3.8 25.6 1.0
CG C:MET150 3.8 23.0 1.0
NE2 C:HIS145 4.0 24.5 1.0
CD2 C:HIS145 4.1 25.9 1.0
CG C:PRO138 4.2 27.1 1.0
NE2 C:HIS95 4.2 22.6 1.0
CD2 C:HIS95 4.2 24.2 1.0
O C:MET94 4.3 25.9 1.0
SD C:MET62 4.3 24.4 1.0
CB C:MET150 4.4 23.2 1.0
CA C:CYS136 4.6 23.7 1.0
CD C:PRO138 4.6 24.8 1.0
N C:ASN96 4.7 24.9 1.0
CB C:MET62 4.7 24.8 1.0
CA C:HIS145 4.8 23.1 1.0
C C:HIS95 4.8 26.2 1.0
N C:HIS95 4.9 25.6 1.0

Copper binding site 6 out of 6 in 1l9t

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Copper binding site 6 out of 6 in the Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes 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 Crystal Structure of the I257V Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:25.0
occ:1.00
 O2 A:NO2704 2.0 39.4 1.0
NE2 C:HIS100 2.1 19.7 1.0
NE2 A:HIS306 2.1 20.4 1.0
NE2 C:HIS135 2.2 22.1 1.0
N A:NO2704 2.2 38.0 1.0
O1 A:NO2704 2.4 34.5 1.0
CE1 C:HIS100 2.9 21.0 1.0
CE1 A:HIS306 3.0 19.6 1.0
CD2 C:HIS135 3.1 21.5 1.0
CD2 A:HIS306 3.1 20.4 1.0
CD2 C:HIS100 3.2 20.7 1.0
CE1 C:HIS135 3.2 22.6 1.0
OD2 C:ASP98 3.6 30.8 1.0
NE2 A:HIS255 3.8 28.0 1.0
O C:HOH5309 4.0 44.6 1.0
ND1 C:HIS100 4.1 18.6 1.0
CD2 A:HIS255 4.1 26.9 1.0
ND1 A:HIS306 4.2 18.2 1.0
CG C:HIS100 4.2 18.8 1.0
CG C:HIS135 4.2 21.0 1.0
CG A:HIS306 4.3 18.8 1.0
ND1 C:HIS135 4.3 21.9 1.0
CE1 A:HIS255 4.3 26.7 1.0
CG C:ASP98 4.4 28.2 1.0
CG A:HIS255 4.7 24.8 1.0
ND1 A:HIS255 4.9 27.4 1.0
O A:HOH5326 4.9 47.4 1.0
OD1 C:ASP98 4.9 29.2 1.0
CD2 A:LEU308 5.0 20.0 1.0
CD1 A:LEU308 5.0 20.7 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: Mon Jul 14 00:03:09 2025

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