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Copper in PDB 1l9r: Crystal Structure of the I257M Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6

Enzymatic activity of Crystal Structure of the I257M Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6

All present enzymatic activity of Crystal Structure of the I257M 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 I257M Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6, PDB code: 1l9r 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) 25.60 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.770, 102.380, 146.000, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 19.7

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of the I257M Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 (pdb code 1l9r). 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 I257M Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6, PDB code: 1l9r:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1l9r

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Copper binding site 1 out of 6 in the Crystal Structure of the I257M 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 I257M 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:19.3
occ:1.00
 ND1 A:HIS145 2.0 15.3 1.0
ND1 A:HIS95 2.1 15.6 1.0
SG A:CYS136 2.2 15.9 1.0
SD A:MET150 2.5 16.0 1.0
CE1 A:HIS145 2.9 15.9 1.0
CE1 A:HIS95 3.0 17.1 1.0
CG A:HIS95 3.1 17.0 1.0
CG A:HIS145 3.1 15.8 1.0
CB A:CYS136 3.2 15.2 1.0
CE A:MET150 3.3 14.9 1.0
CB A:HIS95 3.5 13.2 1.0
CB A:HIS145 3.6 13.2 1.0
CG A:MET150 3.8 13.2 1.0
CA A:HIS95 3.9 15.9 1.0
NE2 A:HIS145 4.0 17.3 1.0
NE2 A:HIS95 4.1 18.2 1.0
CD2 A:HIS145 4.2 18.3 1.0
CD2 A:HIS95 4.2 16.3 1.0
CG A:PRO138 4.3 18.1 1.0
CB A:MET150 4.3 13.6 1.0
SD A:MET62 4.3 18.5 1.0
O A:MET94 4.4 16.1 1.0
CA A:CYS136 4.6 15.1 1.0
N A:ASN96 4.7 16.3 1.0
CD A:PRO138 4.7 17.6 1.0
CB A:MET62 4.7 16.5 1.0
CA A:HIS145 4.8 13.4 1.0
C A:HIS95 4.9 16.1 1.0
N A:HIS95 4.9 15.8 1.0

Copper binding site 2 out of 6 in 1l9r

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Copper binding site 2 out of 6 in the Crystal Structure of the I257M 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 I257M 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:21.5
occ:1.00
 O1 B:NO2504 1.8 39.3 1.0
NE2 A:HIS100 2.1 14.1 1.0
NE2 A:HIS135 2.1 18.2 1.0
NE2 B:HIS306 2.2 17.3 1.0
O B:HOH6003 2.2 32.8 1.0
CE1 A:HIS100 2.9 16.1 1.0
CD2 A:HIS135 3.1 16.7 1.0
CE1 A:HIS135 3.1 16.7 1.0
CE1 B:HIS306 3.1 16.9 1.0
CD2 A:HIS100 3.1 14.9 1.0
CD2 B:HIS306 3.2 17.1 1.0
N B:NO2504 3.2 42.1 1.0
NE2 B:HIS255 3.8 22.8 1.0
OD2 A:ASP98 3.8 27.5 1.0
CD2 B:HIS255 4.1 21.9 1.0
ND1 A:HIS100 4.1 13.2 1.0
O2 B:NO2504 4.1 42.4 1.0
ND1 A:HIS135 4.2 14.7 1.0
CG A:HIS100 4.2 12.3 1.0
CG A:HIS135 4.2 15.7 1.0
ND1 B:HIS306 4.2 16.0 1.0
CE1 B:HIS255 4.3 22.3 1.0
CG B:HIS306 4.3 17.7 1.0
CE B:MET257 4.4 45.7 1.0
CG A:ASP98 4.4 22.5 1.0
CG B:HIS255 4.7 20.8 1.0
OD1 A:ASP98 4.7 22.8 1.0
ND1 B:HIS255 4.8 21.7 1.0
O B:HOH6001 4.9 22.3 1.0
CD2 B:LEU308 4.9 15.8 1.0

Copper binding site 3 out of 6 in 1l9r

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Copper binding site 3 out of 6 in the Crystal Structure of the I257M 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 I257M 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:22.4
occ:1.00
 ND1 B:HIS95 2.0 16.9 1.0
ND1 B:HIS145 2.1 19.6 1.0
SG B:CYS136 2.2 21.4 1.0
SD B:MET150 2.5 18.7 1.0
CE1 B:HIS145 3.0 19.9 1.0
CE1 B:HIS95 3.0 18.2 1.0
CG B:HIS95 3.1 18.3 1.0
CG B:HIS145 3.1 20.1 1.0
CB B:CYS136 3.2 18.8 1.0
CE B:MET150 3.2 17.1 1.0
CB B:HIS95 3.5 19.5 1.0
CB B:HIS145 3.6 18.4 1.0
CA B:HIS95 3.9 21.0 1.0
CG B:MET150 3.9 16.4 1.0
CG B:PRO138 4.1 23.8 1.0
NE2 B:HIS95 4.1 18.4 1.0
NE2 B:HIS145 4.1 21.2 1.0
CD2 B:HIS95 4.2 17.7 1.0
CD2 B:HIS145 4.2 21.1 1.0
SD B:MET62 4.3 20.4 1.0
O B:MET94 4.3 21.7 1.0
CB B:MET150 4.4 15.0 1.0
CD B:PRO138 4.6 22.6 1.0
CA B:CYS136 4.6 19.0 1.0
N B:ASN96 4.6 20.5 1.0
CA B:HIS145 4.8 18.6 1.0
CB B:MET62 4.8 19.9 1.0
C B:HIS95 4.8 20.6 1.0
N B:HIS95 4.9 21.9 1.0

Copper binding site 4 out of 6 in 1l9r

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Copper binding site 4 out of 6 in the Crystal Structure of the I257M 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 I257M 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:24.1
occ:1.00
 NE2 B:HIS100 2.0 16.4 1.0
NE2 B:HIS135 2.0 19.8 1.0
NE2 C:HIS306 2.1 17.2 1.0
O1 C:NO2604 2.1 44.7 1.0
O C:HOH6006 2.3 38.7 1.0
CE1 B:HIS100 2.9 17.0 1.0
CE1 B:HIS135 3.0 19.6 1.0
CD2 B:HIS135 3.0 17.6 1.0
N C:NO2604 3.1 45.2 1.0
CD2 C:HIS306 3.1 19.8 1.0
CE1 C:HIS306 3.1 17.6 1.0
O2 C:NO2604 3.1 47.1 1.0
CD2 B:HIS100 3.1 16.3 1.0
NE2 C:HIS255 3.8 26.2 1.0
OD2 B:ASP98 3.9 26.2 1.0
CD2 C:HIS255 4.0 25.8 1.0
ND1 B:HIS100 4.1 17.3 1.0
ND1 B:HIS135 4.1 18.0 1.0
CG B:HIS135 4.2 17.4 1.0
CG B:HIS100 4.2 17.1 1.0
ND1 C:HIS306 4.2 17.7 1.0
CG C:HIS306 4.2 19.3 1.0
CE1 C:HIS255 4.3 25.0 1.0
CE C:MET257 4.4 42.9 1.0
CG B:ASP98 4.4 23.4 1.0
CG C:HIS255 4.7 23.2 1.0
OD1 B:ASP98 4.7 21.6 1.0
ND1 C:HIS255 4.8 25.5 1.0
O B:HOH6004 4.9 23.4 1.0

Copper binding site 5 out of 6 in 1l9r

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Copper binding site 5 out of 6 in the Crystal Structure of the I257M 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 I257M 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:26.9
occ:1.00
 ND1 C:HIS145 2.1 25.6 1.0
ND1 C:HIS95 2.2 24.5 1.0
SG C:CYS136 2.2 23.6 1.0
SD C:MET150 2.5 23.3 1.0
CE1 C:HIS145 3.0 26.8 1.0
CE1 C:HIS95 3.1 25.1 1.0
CG C:HIS145 3.1 24.6 1.0
CB C:CYS136 3.1 23.8 1.0
CG C:HIS95 3.2 23.7 1.0
CE C:MET150 3.2 23.4 1.0
CB C:HIS95 3.5 25.1 1.0
CB C:HIS145 3.5 22.1 1.0
CG C:MET150 3.8 21.4 1.0
CA C:HIS95 3.9 25.2 1.0
NE2 C:HIS145 4.1 25.1 1.0
CG C:PRO138 4.1 28.8 1.0
CD2 C:HIS145 4.2 24.7 1.0
NE2 C:HIS95 4.2 23.2 1.0
CD2 C:HIS95 4.3 24.6 1.0
O C:MET94 4.3 27.8 1.0
SD C:MET62 4.3 24.7 1.0
CB C:MET150 4.4 20.9 1.0
CA C:CYS136 4.6 23.8 1.0
CD C:PRO138 4.7 25.1 1.0
N C:ASN96 4.7 24.2 1.0
CB C:MET62 4.7 24.6 1.0
CA C:HIS145 4.8 22.6 1.0
C C:HIS95 4.9 25.1 1.0
N C:HIS95 4.9 25.1 1.0

Copper binding site 6 out of 6 in 1l9r

Go back to Copper Binding Sites List in 1l9r
Copper binding site 6 out of 6 in the Crystal Structure of the I257M 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 I257M 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:25.5
occ:1.00
 O1 A:NO2704 1.9 42.4 1.0
NE2 C:HIS100 2.0 18.4 1.0
NE2 C:HIS135 2.1 21.0 1.0
NE2 A:HIS306 2.2 19.3 1.0
CE1 C:HIS100 2.9 19.8 1.0
CD2 C:HIS135 3.0 20.0 1.0
CE1 A:HIS306 3.1 18.8 1.0
N A:NO2704 3.1 43.7 1.0
CD2 C:HIS100 3.1 19.1 1.0
CD2 A:HIS306 3.2 21.2 1.0
CE1 C:HIS135 3.2 21.2 1.0
O2 A:NO2704 3.6 45.7 1.0
NE2 A:HIS255 3.7 28.7 1.0
OD2 C:ASP98 3.8 33.6 1.0
CD2 A:HIS255 3.9 27.2 1.0
ND1 C:HIS100 4.1 18.4 1.0
CG C:HIS135 4.2 19.4 1.0
CG C:HIS100 4.2 18.6 1.0
ND1 A:HIS306 4.2 19.7 1.0
ND1 C:HIS135 4.3 20.9 1.0
CG A:HIS306 4.3 18.6 1.0
CE A:MET257 4.4 41.8 1.0
CE1 A:HIS255 4.4 27.5 1.0
CG C:ASP98 4.5 28.9 1.0
CG A:HIS255 4.7 25.0 1.0
OD1 C:ASP98 4.8 28.8 1.0
ND1 A:HIS255 4.9 27.0 1.0
O A:HOH6007 4.9 24.0 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 22:13:00 2024

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