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Copper in PDB 2b08: Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis

Enzymatic activity of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis

All present enzymatic activity of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis:
1.7.2.1;

Protein crystallography data

The structure of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis, PDB code: 2b08 was solved by H.J.Wijma, I.S.Macpherson, O.Farver, E.I.Tocheva, I.Pecht, M.Ph.Verbeet, M.E.P.Murphy, G.W.Canters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.52 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.972, 102.047, 146.423, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 22

Copper Binding Sites:

The binding sites of Copper atom in the Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis (pdb code 2b08). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis, PDB code: 2b08:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 2b08

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Copper binding site 1 out of 9 in the Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1501

b:30.0
occ:1.00
 ND1 A:HIS145 2.1 19.4 1.0
ND1 A:HIS95 2.2 19.5 1.0
SG A:CYS136 2.3 20.6 1.0
SD A:MET62 2.3 27.5 1.0
CE1 A:HIS145 3.0 21.1 1.0
CE A:MET62 3.0 25.3 1.0
CE1 A:HIS95 3.1 20.6 1.0
CG A:MET62 3.2 25.8 1.0
CG A:HIS145 3.2 19.7 1.0
CG A:HIS95 3.2 19.6 1.0
CB A:CYS136 3.2 19.4 1.0
CB A:HIS95 3.6 20.3 1.0
CB A:HIS145 3.6 17.0 1.0
CA A:HIS95 4.1 19.9 1.0
NE2 A:HIS145 4.1 21.4 1.0
CB A:MET62 4.2 22.6 1.0
NE2 A:HIS95 4.2 21.0 1.0
CD2 A:HIS145 4.3 18.4 1.0
CD2 A:HIS95 4.3 18.9 1.0
CG A:PRO138 4.4 19.6 1.0
O A:MET94 4.4 19.9 1.0
CA A:CYS136 4.7 19.2 1.0
CA A:HIS145 4.7 17.7 1.0
CD A:PRO138 4.7 19.6 1.0
O A:ACM1503 4.8 34.4 1.0
C2 A:ACM1503 4.9 33.0 1.0
N A:ASN96 5.0 19.5 1.0

Copper binding site 2 out of 9 in 2b08

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Copper binding site 2 out of 9 in the Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1502

b:21.0
occ:1.00
 NE2 A:HIS135 2.0 20.9 1.0
NE2 B:HIS306 2.0 18.7 1.0
NE2 A:HIS100 2.1 18.3 1.0
CD2 A:HIS135 2.9 18.1 1.0
CE1 B:HIS306 2.9 15.1 1.0
CE1 A:HIS100 2.9 19.7 1.0
CE1 A:HIS135 3.1 20.2 1.0
CD2 B:HIS306 3.2 17.4 1.0
CD2 A:HIS100 3.2 17.8 1.0
OD1 A:ASP98 3.7 24.7 1.0
CG A:HIS135 4.1 20.0 1.0
ND1 B:HIS306 4.1 16.0 1.0
ND1 A:HIS100 4.1 20.0 1.0
ND1 A:HIS135 4.1 18.8 1.0
CG B:HIS306 4.2 17.6 1.0
NE2 B:HIS255 4.2 20.0 1.0
CG A:HIS100 4.2 16.9 1.0
CE1 B:HIS255 4.3 18.8 1.0
CG A:ASP98 4.4 18.7 1.0
O A:HOH1808 4.4 28.4 1.0
CD2 B:HIS255 4.7 20.5 1.0
ND1 B:HIS255 4.8 21.4 1.0
OD2 A:ASP98 4.8 20.9 1.0
CD2 B:LEU308 4.8 17.3 1.0
CG B:HIS255 5.0 19.4 1.0

Copper binding site 3 out of 9 in 2b08

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Copper binding site 3 out of 9 in the Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1506

b:37.0
occ:0.30
 O A:HOH1655 2.0 24.4 1.0
NE2 A:HIS145 2.0 21.4 1.0
SD A:MET141 2.7 31.4 1.0
CE A:MET141 2.9 31.0 1.0
CD2 A:HIS145 3.0 18.4 1.0
CE1 A:HIS145 3.0 21.1 1.0
CB A:MET141 3.5 22.9 1.0
CG A:MET141 3.8 25.9 1.0
CZ3 A:TRP144 3.9 23.5 1.0
CE3 A:TRP144 4.1 20.2 1.0
CG A:PRO138 4.1 19.6 1.0
CG A:HIS145 4.1 19.7 1.0
ND1 A:HIS145 4.1 19.4 1.0
CB A:PRO138 4.2 19.8 1.0
O A:HOH1542 4.3 23.1 1.0
O A:MET94 4.3 19.9 1.0
CD2 A:LEU93 4.3 23.1 1.0
CB A:LEU93 4.6 22.7 1.0
CD1 A:LEU93 4.6 22.8 1.0
CG A:LEU93 4.7 23.0 1.0
O A:MET141 4.9 19.5 1.0
CA A:MET141 5.0 23.1 1.0

Copper binding site 4 out of 9 in 2b08

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Copper binding site 4 out of 9 in the Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2501

b:35.5
occ:1.00
 CU B:CU12505 2.1 33.7 0.3
ND1 B:HIS95 2.2 27.2 1.0
SD B:MET62 2.2 33.3 1.0
SG B:CYS136 2.3 25.1 1.0
ND1 B:HIS145 2.5 28.0 1.0
CE1 B:HIS95 3.1 25.7 1.0
CB B:CYS136 3.1 23.7 1.0
CG B:HIS95 3.2 26.3 1.0
CE B:MET62 3.2 29.5 1.0
CG B:MET62 3.2 30.1 1.0
CE1 B:HIS145 3.3 29.9 1.0
CG B:HIS145 3.5 26.8 1.0
CB B:HIS95 3.5 26.8 1.0
O B:ACM2503 3.8 48.1 1.0
CB B:HIS145 3.8 24.7 1.0
CA B:HIS95 4.0 26.7 1.0
NE2 B:HIS95 4.2 26.4 1.0
CB B:MET62 4.3 27.7 1.0
CD2 B:HIS95 4.3 26.5 1.0
O B:MET94 4.4 26.0 1.0
CG B:PRO138 4.5 30.4 1.0
NE2 B:HIS145 4.5 28.4 1.0
CA B:CYS136 4.6 24.1 1.0
CD2 B:HIS145 4.6 28.8 1.0
CD B:PRO138 4.8 29.6 1.0
CA B:HIS145 4.9 24.6 1.0
N B:ASN96 4.9 26.3 1.0
C1 B:ACM2503 5.0 47.8 1.0

Copper binding site 5 out of 9 in 2b08

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Copper binding site 5 out of 9 in the Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2502

b:26.0
occ:1.00
 NE2 B:HIS135 2.0 21.9 1.0
NE2 B:HIS100 2.0 21.2 1.0
NE2 C:HIS306 2.1 21.4 1.0
CE1 B:HIS100 2.8 21.9 1.0
CD2 B:HIS135 2.9 20.4 1.0
CE1 C:HIS306 3.0 20.6 1.0
CD2 C:HIS306 3.1 20.4 1.0
CE1 B:HIS135 3.1 22.2 1.0
CD2 B:HIS100 3.2 21.0 1.0
OD1 B:ASP98 3.8 25.8 1.0
ND1 B:HIS100 4.0 22.8 1.0
CG B:HIS135 4.1 21.4 1.0
ND1 B:HIS135 4.1 22.7 1.0
ND1 C:HIS306 4.1 19.8 1.0
CG B:HIS100 4.2 21.0 1.0
CG C:HIS306 4.2 21.3 1.0
NE2 C:HIS255 4.2 24.3 1.0
CG B:ASP98 4.3 24.7 1.0
CE1 C:HIS255 4.4 24.6 1.0
CD2 C:HIS255 4.6 23.1 1.0
O B:HOH2649 4.6 41.5 1.0
OD2 B:ASP98 4.8 25.6 1.0
ND1 C:HIS255 4.8 25.9 1.0
CD2 C:LEU308 4.9 20.9 1.0
CG C:HIS255 5.0 22.3 1.0
O B:HOH2709 5.0 23.3 1.0
CG1 C:ILE257 5.0 26.7 1.0

Copper binding site 6 out of 9 in 2b08

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Copper binding site 6 out of 9 in the Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2505

b:33.7
occ:0.30
 ND1 B:HIS145 2.0 28.0 1.0
SG B:CYS136 2.0 25.1 1.0
CU B:CU12501 2.1 35.5 1.0
CG B:PRO138 2.4 30.4 1.0
CG B:HIS145 2.7 26.8 1.0
CD B:PRO138 2.8 29.6 1.0
CE1 B:HIS145 2.8 29.9 1.0
CB B:HIS145 3.2 24.7 1.0
CB B:CYS136 3.3 23.7 1.0
CD2 B:HIS145 3.5 28.8 1.0
NE2 B:HIS145 3.6 28.4 1.0
ND1 B:HIS95 3.6 27.2 1.0
CB B:PRO138 3.9 30.1 1.0
O B:MET94 3.9 26.0 1.0
N B:PRO138 4.0 29.3 1.0
CA B:HIS95 4.0 26.7 1.0
SD B:MET62 4.1 33.3 1.0
CB B:HIS95 4.2 26.8 1.0
CA B:CYS136 4.3 24.1 1.0
N B:ALA137 4.3 25.9 1.0
CG B:HIS95 4.3 26.3 1.0
C B:CYS136 4.3 24.9 1.0
OD1 B:ASN96 4.4 27.1 1.0
CE1 B:HIS95 4.5 25.7 1.0
N B:ASN96 4.5 26.3 1.0
CA B:PRO138 4.6 30.0 1.0
CA B:HIS145 4.6 24.6 1.0
O B:ACM2503 4.7 48.1 1.0
C B:MET94 4.8 27.4 1.0
C B:HIS95 4.8 26.7 1.0
O B:HOH2648 4.9 43.7 1.0
C B:ALA137 4.9 28.4 1.0
N B:HIS95 4.9 26.9 1.0
CA B:ALA137 4.9 27.2 1.0
O B:CYS136 5.0 24.9 1.0

Copper binding site 7 out of 9 in 2b08

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Copper binding site 7 out of 9 in the Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu3501

b:42.9
occ:1.00
 CU C:CU13505 1.9 44.3 0.4
SD C:MET62 2.1 40.6 1.0
ND1 C:HIS95 2.3 34.2 1.0
ND1 C:HIS145 2.3 32.2 1.0
SG C:CYS136 2.3 32.8 1.0
CE1 C:HIS145 3.2 34.0 1.0
CE1 C:HIS95 3.2 32.8 1.0
CG C:MET62 3.2 38.9 1.0
CB C:CYS136 3.3 30.5 1.0
CE C:MET62 3.3 41.8 1.0
CG C:HIS95 3.3 33.0 1.0
CG C:HIS145 3.3 29.8 1.0
CB C:HIS95 3.6 32.6 1.0
CB C:HIS145 3.7 27.9 1.0
CA C:HIS95 4.0 31.9 1.0
CB C:MET62 4.3 36.5 1.0
NE2 C:HIS95 4.3 32.8 1.0
NE2 C:HIS145 4.3 33.4 1.0
O C:MET94 4.3 33.0 1.0
CD2 C:HIS95 4.4 33.7 1.0
CD2 C:HIS145 4.4 31.1 1.0
CG C:PRO138 4.6 33.5 1.0
CA C:CYS136 4.7 30.4 1.0
CA C:HIS145 4.8 27.7 1.0
CD C:PRO138 4.8 33.2 1.0
N C:ASN96 4.9 30.8 1.0
N C:HIS95 5.0 32.3 1.0

Copper binding site 8 out of 9 in 2b08

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Copper binding site 8 out of 9 in the Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu3502

b:26.8
occ:1.00
 NE2 C:HIS100 2.1 23.7 1.0
NE2 C:HIS135 2.1 25.9 1.0
NE2 A:HIS306 2.1 24.2 1.0
CD2 C:HIS135 2.9 26.4 1.0
CE1 A:HIS306 3.0 25.3 1.0
CE1 C:HIS100 3.0 22.8 1.0
CD2 C:HIS100 3.1 24.3 1.0
CD2 A:HIS306 3.2 23.8 1.0
CE1 C:HIS135 3.3 25.0 1.0
OD1 C:ASP98 3.7 29.8 1.0
CG C:HIS135 4.1 26.6 1.0
ND1 C:HIS100 4.1 24.1 1.0
ND1 A:HIS306 4.1 23.8 1.0
NE2 A:HIS255 4.2 24.1 1.0
CG C:HIS100 4.2 24.0 1.0
ND1 C:HIS135 4.3 24.7 1.0
CG A:HIS306 4.3 23.2 1.0
CE1 A:HIS255 4.3 24.5 1.0
CG C:ASP98 4.3 26.7 1.0
O C:HOH3636 4.5 34.3 1.0
CD2 A:HIS255 4.6 22.8 1.0
ND1 A:HIS255 4.7 22.7 1.0
OD2 C:ASP98 4.7 24.2 1.0
CG1 A:ILE257 4.8 23.0 1.0
CG A:HIS255 4.9 22.5 1.0
O A:HOH1543 5.0 24.9 1.0

Copper binding site 9 out of 9 in 2b08

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Copper binding site 9 out of 9 in the Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu3505

b:44.3
occ:0.40
 CU C:CU13501 1.9 42.9 1.0
SG C:CYS136 2.0 32.8 1.0
ND1 C:HIS145 2.0 32.2 1.0
CG C:PRO138 2.7 33.5 1.0
CG C:HIS145 2.7 29.8 1.0
CE1 C:HIS145 2.8 34.0 1.0
CD C:PRO138 3.0 33.2 1.0
CB C:HIS145 3.2 27.9 1.0
CB C:CYS136 3.2 30.5 1.0
ND1 C:HIS95 3.6 34.2 1.0
CD2 C:HIS145 3.6 31.1 1.0
NE2 C:HIS145 3.6 33.4 1.0
O C:MET94 3.8 33.0 1.0
SD C:MET62 3.8 40.6 1.0
CA C:HIS95 3.8 31.9 1.0
CB C:PRO138 3.9 34.0 1.0
N C:PRO138 4.1 33.0 1.0
CB C:HIS95 4.2 32.6 1.0
N C:ALA137 4.3 30.8 1.0
CG C:HIS95 4.3 33.0 1.0
CA C:CYS136 4.3 30.4 1.0
C C:CYS136 4.4 31.1 1.0
OD1 C:ASN96 4.4 28.3 1.0
N C:ASN96 4.4 30.8 1.0
CE1 C:HIS95 4.5 32.8 1.0
C C:HIS95 4.7 31.8 1.0
CA C:HIS145 4.7 27.7 1.0
C C:MET94 4.7 32.6 1.0
CA C:PRO138 4.7 33.7 1.0
N C:HIS95 4.8 32.3 1.0
CE C:MET62 4.9 41.8 1.0
C C:ALA137 5.0 32.3 1.0

Reference:

H.J.Wijma, I.Macpherson, O.Farver, E.I.Tocheva, I.Pecht, M.P.Verbeet, M.E.P.Murphy, G.W.Canters. Effect of the Methionine Ligand on the Reorganization Energy of the Type-1 Copper Site of Nitrite Reductase. J.Am.Chem.Soc. V. 129 519 2007.
ISSN: ISSN 0002-7863
PubMed: 17227014
DOI: 10.1021/JA064763J
Page generated: Tue Jul 30 23:13:48 2024

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