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Copper in PDB 1as8: Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature

Enzymatic activity of Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature

All present enzymatic activity of Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature:
1.7.99.3;

Protein crystallography data

The structure of Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature, PDB code: 1as8 was solved by M.E.P.Murphy, E.T.Adman, S.Turley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.100, 102.800, 146.300, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / n/a

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature (pdb code 1as8). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature, PDB code: 1as8:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1as8

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Copper binding site 1 out of 6 in the Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:17.3
occ:1.00
 SG A:CYS136 2.1 11.2 1.0
ND1 A:HIS145 2.1 12.2 1.0
ND1 A:HIS95 2.1 8.9 1.0
SD A:MET150 2.6 17.7 1.0
CE1 A:HIS95 3.0 7.2 1.0
CE1 A:HIS145 3.0 11.3 1.0
CB A:CYS136 3.1 10.0 1.0
CG A:HIS145 3.1 12.9 1.0
CG A:HIS95 3.1 6.4 1.0
CE A:MET150 3.3 13.4 1.0
CB A:HIS145 3.5 10.4 1.0
CB A:HIS95 3.5 8.1 1.0
CG A:MET150 3.8 16.9 1.0
CA A:HIS95 3.9 10.8 1.0
H A:ASN96 4.0 0.0 1.0
CG A:PRO138 4.2 10.8 1.0
NE2 A:HIS95 4.2 8.6 1.0
NE2 A:HIS145 4.2 12.4 1.0
CD2 A:HIS145 4.2 13.3 1.0
CD2 A:HIS95 4.2 9.2 1.0
CB A:MET150 4.3 9.8 1.0
O A:MET94 4.3 11.5 1.0
CD A:PRO138 4.4 11.1 1.0
SD A:MET62 4.5 17.5 1.0
CA A:CYS136 4.5 9.5 1.0
CA A:HIS145 4.7 9.4 1.0
N A:ASN96 4.8 11.5 1.0
CB A:MET62 4.9 14.2 1.0
C A:HIS95 4.9 11.7 1.0
N A:HIS95 4.9 11.4 1.0

Copper binding site 2 out of 6 in 1as8

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Copper binding site 2 out of 6 in the Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:14.4
occ:1.00
 NE2 A:HIS135 1.9 10.1 1.0
NE2 A:HIS100 2.0 8.1 1.0
NE2 B:HIS306 2.1 10.3 1.0
O2 A:NO2503 2.2 16.2 0.5
N A:NO2503 2.5 16.6 0.5
O1 A:NO2503 2.7 16.1 0.5
CE1 A:HIS135 2.8 9.7 1.0
CE1 A:HIS100 2.9 7.7 1.0
CE1 B:HIS306 2.9 8.0 1.0
CD2 A:HIS135 3.0 10.1 1.0
CD2 A:HIS100 3.1 6.1 1.0
CD2 B:HIS306 3.3 9.1 1.0
H2 A:HOH754 3.6 0.0 1.0
OD1 A:ASP98 3.6 19.3 1.0
HE2 B:HIS255 3.8 0.0 1.0
ND1 A:HIS135 4.0 10.8 1.0
ND1 A:HIS100 4.1 7.8 1.0
NE2 B:HIS255 4.1 13.0 1.0
CG A:HIS135 4.1 11.7 1.0
ND1 B:HIS306 4.2 11.1 1.0
CG A:HIS100 4.2 7.2 1.0
CG B:HIS306 4.3 11.1 1.0
CG A:ASP98 4.4 12.9 1.0
CD2 B:HIS255 4.4 15.1 1.0
CE1 B:HIS255 4.5 14.3 1.0
O A:HOH754 4.6 48.1 1.0
H1 A:HOH754 4.9 0.0 1.0
HD1 A:HIS135 4.9 0.0 1.0
OD2 A:ASP98 4.9 14.6 1.0
HD1 A:HIS100 4.9 0.0 1.0
CG B:HIS255 4.9 11.4 1.0
ND1 B:HIS255 4.9 14.4 1.0
HD1 B:HIS306 5.0 0.0 1.0

Copper binding site 3 out of 6 in 1as8

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Copper binding site 3 out of 6 in the Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:19.3
occ:1.00
 ND1 B:HIS145 2.0 13.7 1.0
ND1 B:HIS95 2.1 15.7 1.0
SG B:CYS136 2.2 15.5 1.0
SD B:MET150 2.7 14.9 1.0
CE1 B:HIS145 2.9 14.1 1.0
CE1 B:HIS95 3.1 14.6 1.0
CG B:HIS95 3.1 16.5 1.0
CG B:HIS145 3.1 13.3 1.0
CB B:CYS136 3.2 14.3 1.0
CE B:MET150 3.4 11.1 1.0
CB B:HIS95 3.4 17.9 1.0
CB B:HIS145 3.6 13.0 1.0
CA B:HIS95 3.8 16.5 1.0
H B:ASN96 3.9 0.0 1.0
CG B:PRO138 4.0 17.6 1.0
CG B:MET150 4.0 13.9 1.0
NE2 B:HIS145 4.1 15.1 1.0
CD2 B:HIS145 4.2 14.6 1.0
NE2 B:HIS95 4.2 16.3 1.0
CD2 B:HIS95 4.2 14.2 1.0
O B:MET94 4.3 16.7 1.0
SD B:MET62 4.4 18.4 1.0
CB B:MET150 4.4 12.2 1.0
CD B:PRO138 4.5 17.7 1.0
CA B:CYS136 4.6 14.5 1.0
N B:ASN96 4.7 14.0 1.0
CA B:HIS145 4.8 14.9 1.0
N B:HIS95 4.8 16.5 1.0
C B:HIS95 4.8 16.8 1.0
HE2 B:HIS145 4.9 0.0 1.0
C B:MET94 4.9 16.3 1.0
CB B:MET62 5.0 13.7 1.0

Copper binding site 4 out of 6 in 1as8

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Copper binding site 4 out of 6 in the Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:16.2
occ:1.00
 NE2 B:HIS100 1.9 11.3 1.0
NE2 B:HIS135 2.0 13.7 1.0
NE2 C:HIS306 2.1 15.7 1.0
O1 B:NO2503 2.2 26.5 0.5
O2 B:NO2503 2.4 29.5 0.5
N B:NO2503 2.5 29.8 0.5
CE1 B:HIS100 2.7 11.9 1.0
CE1 C:HIS306 3.0 14.6 1.0
CD2 B:HIS135 3.0 12.8 1.0
CE1 B:HIS135 3.0 12.9 1.0
CD2 B:HIS100 3.1 10.0 1.0
CD2 C:HIS306 3.3 12.8 1.0
OD1 B:ASP98 3.5 18.7 1.0
HE2 C:HIS255 3.7 0.0 1.0
ND1 B:HIS100 4.0 8.9 1.0
NE2 C:HIS255 4.0 19.3 1.0
ND1 B:HIS135 4.2 11.7 1.0
CG B:HIS135 4.2 12.0 1.0
CG B:HIS100 4.2 9.6 1.0
ND1 C:HIS306 4.2 12.5 1.0
CD2 C:HIS255 4.3 14.8 1.0
H2 B:HOH640 4.3 0.0 1.0
CG C:HIS306 4.4 13.3 1.0
CG B:ASP98 4.4 16.6 1.0
CE1 C:HIS255 4.5 18.5 1.0
O B:HOH728 4.6 29.2 1.0
HD1 B:HIS100 4.8 0.0 1.0
H1 B:HOH728 4.8 0.0 1.0
CG C:HIS255 4.9 15.3 1.0
OD2 B:ASP98 4.9 18.6 1.0

Copper binding site 5 out of 6 in 1as8

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Copper binding site 5 out of 6 in the Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:19.9
occ:1.00
 ND1 C:HIS145 2.0 16.4 1.0
ND1 C:HIS95 2.2 19.6 1.0
SG C:CYS136 2.2 17.4 1.0
SD C:MET150 2.5 16.9 1.0
CE1 C:HIS145 3.0 17.2 1.0
CE1 C:HIS95 3.1 18.7 1.0
CG C:HIS145 3.1 16.4 1.0
CB C:CYS136 3.2 15.4 1.0
CG C:HIS95 3.2 18.4 1.0
CE C:MET150 3.4 14.3 1.0
CB C:HIS145 3.5 17.3 1.0
CB C:HIS95 3.6 14.9 1.0
CG C:MET150 3.9 13.9 1.0
CA C:HIS95 3.9 16.4 1.0
H C:ASN96 3.9 0.0 1.0
CG C:PRO138 4.0 20.4 1.0
NE2 C:HIS145 4.2 15.4 1.0
CD2 C:HIS145 4.2 14.9 1.0
O C:MET94 4.3 14.6 1.0
NE2 C:HIS95 4.3 19.6 1.0
CD2 C:HIS95 4.3 17.5 1.0
SD C:MET62 4.4 17.8 1.0
CB C:MET150 4.4 13.5 1.0
CD C:PRO138 4.5 19.4 1.0
CA C:CYS136 4.6 15.4 1.0
CB C:MET62 4.7 17.8 1.0
N C:ASN96 4.7 17.9 1.0
CA C:HIS145 4.8 16.5 1.0
C C:HIS95 4.9 16.9 1.0
N C:HIS95 4.9 16.4 1.0

Copper binding site 6 out of 6 in 1as8

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Copper binding site 6 out of 6 in the Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase at Cryo Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:16.6
occ:1.00
 NE2 C:HIS100 1.8 9.6 1.0
NE2 A:HIS306 2.1 16.7 1.0
NE2 C:HIS135 2.1 13.7 1.0
O2 C:NO2503 2.3 28.0 0.5
O1 C:NO2503 2.4 26.9 0.5
N C:NO2503 2.6 26.5 0.5
CE1 C:HIS100 2.6 11.5 1.0
CE1 A:HIS306 2.9 12.7 1.0
CD2 C:HIS100 3.1 9.8 1.0
CE1 C:HIS135 3.1 13.5 1.0
CD2 C:HIS135 3.2 16.1 1.0
CD2 A:HIS306 3.3 16.3 1.0
OD1 C:ASP98 3.7 22.1 1.0
ND1 C:HIS100 3.8 10.2 1.0
CG C:HIS100 4.1 10.1 1.0
HE2 A:HIS255 4.1 0.0 1.0
ND1 A:HIS306 4.1 16.8 1.0
NE2 A:HIS255 4.2 16.5 1.0
H1 A:HOH544 4.2 0.0 1.0
ND1 C:HIS135 4.3 16.1 1.0
CG C:HIS135 4.3 15.8 1.0
H2 C:HOH638 4.3 0.0 1.0
CG A:HIS306 4.3 13.9 1.0
H2 C:HOH737 4.4 0.0 1.0
CE1 A:HIS255 4.5 19.0 1.0
CG C:ASP98 4.5 18.1 1.0
CD2 A:HIS255 4.5 15.6 1.0
HD1 C:HIS100 4.6 0.0 1.0
ND1 A:HIS255 4.9 15.5 1.0
OD2 C:ASP98 4.9 19.9 1.0
CG A:HIS255 4.9 16.0 1.0
HD1 A:HIS306 5.0 0.0 1.0
CD1 A:LEU308 5.0 10.4 1.0

Reference:

M.E.Murphy, S.Turley, E.T.Adman. Structure of Nitrite Bound to Copper-Containing Nitrite Reductase From Alcaligenes Faecalis. Mechanistic Implications. J.Biol.Chem. V. 272 28455 1997.
ISSN: ISSN 0021-9258
PubMed: 9353305
DOI: 10.1074/JBC.272.45.28455
Page generated: Tue Jul 30 21:31:29 2024

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