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Copper in PDB 2ppc: Oxidized Wild Type Afnir Exposed to No (Nitrite Bound)

Enzymatic activity of Oxidized Wild Type Afnir Exposed to No (Nitrite Bound)

All present enzymatic activity of Oxidized Wild Type Afnir Exposed to No (Nitrite Bound):
1.7.2.1;

Protein crystallography data

The structure of Oxidized Wild Type Afnir Exposed to No (Nitrite Bound), PDB code: 2ppc was solved by E.I.Tocheva, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.111, 101.833, 145.508, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 18.2

Copper Binding Sites:

The binding sites of Copper atom in the Oxidized Wild Type Afnir Exposed to No (Nitrite Bound) (pdb code 2ppc). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Oxidized Wild Type Afnir Exposed to No (Nitrite Bound), PDB code: 2ppc:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2ppc

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Copper binding site 1 out of 6 in the Oxidized Wild Type Afnir Exposed to No (Nitrite Bound)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Oxidized Wild Type Afnir Exposed to No (Nitrite Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:14.5
occ:1.00
ND1 A:HIS95 2.0 12.0 1.0
ND1 A:HIS145 2.1 12.6 1.0
SG A:CYS136 2.2 13.8 1.0
SD A:MET150 2.4 13.7 1.0
CE1 A:HIS145 2.9 14.0 1.0
CE1 A:HIS95 3.0 14.0 1.0
CG A:HIS95 3.1 14.5 1.0
CG A:HIS145 3.1 12.5 1.0
CB A:CYS136 3.2 13.7 1.0
CE A:MET150 3.2 14.0 1.0
CB A:HIS95 3.5 13.7 1.0
CB A:HIS145 3.6 12.3 1.0
CG A:MET150 3.8 13.6 1.0
CA A:HIS95 3.9 13.9 1.0
NE2 A:HIS145 4.1 13.9 1.0
NE2 A:HIS95 4.1 14.0 1.0
CD2 A:HIS95 4.2 13.6 1.0
CD2 A:HIS145 4.2 12.5 1.0
CB A:MET150 4.3 11.9 1.0
CG A:PRO138 4.3 13.4 1.0
O A:MET94 4.4 14.9 1.0
SD A:MET62 4.4 17.1 1.0
CA A:CYS136 4.6 12.7 1.0
N A:ASN96 4.6 13.6 1.0
CD A:PRO138 4.7 14.7 1.0
CB A:MET62 4.7 14.6 1.0
CA A:HIS145 4.8 12.7 1.0
C A:HIS95 4.8 13.7 1.0
N A:HIS95 4.9 13.8 1.0

Copper binding site 2 out of 6 in 2ppc

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Copper binding site 2 out of 6 in the Oxidized Wild Type Afnir Exposed to No (Nitrite Bound)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Oxidized Wild Type Afnir Exposed to No (Nitrite Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:13.9
occ:1.00
O2 A:NO2503 2.0 35.8 1.0
NE2 B:HIS306 2.0 13.3 1.0
NE2 A:HIS100 2.0 11.3 1.0
NE2 A:HIS135 2.0 12.4 1.0
O1 A:NO2503 2.4 34.3 1.0
N A:NO2503 2.4 35.3 1.0
CE1 A:HIS100 2.9 10.5 1.0
CE1 B:HIS306 2.9 10.6 1.0
CD2 A:HIS135 3.0 12.2 1.0
CE1 A:HIS135 3.0 13.6 1.0
CD2 B:HIS306 3.1 13.5 1.0
CD2 A:HIS100 3.1 13.6 1.0
OD1 A:ASP98 3.8 27.6 1.0
ND1 B:HIS306 4.1 11.6 1.0
ND1 A:HIS100 4.1 11.5 1.0
NE2 B:HIS255 4.1 15.5 1.0
ND1 A:HIS135 4.1 11.8 1.0
CG A:HIS135 4.2 12.9 1.0
CG B:HIS306 4.2 12.1 1.0
CG A:HIS100 4.2 11.2 1.0
CE1 B:HIS255 4.3 15.8 1.0
CG A:ASP98 4.4 20.9 1.0
CD2 B:HIS255 4.6 15.1 1.0
OD2 A:ASP98 4.7 24.6 1.0
ND1 B:HIS255 4.8 15.6 1.0
CD2 B:LEU308 4.8 13.8 1.0
CG B:HIS255 4.9 13.7 1.0

Copper binding site 3 out of 6 in 2ppc

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Copper binding site 3 out of 6 in the Oxidized Wild Type Afnir Exposed to No (Nitrite Bound)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Oxidized Wild Type Afnir Exposed to No (Nitrite Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:16.6
occ:1.00
ND1 B:HIS95 2.1 15.5 1.0
ND1 B:HIS145 2.1 13.7 1.0
SG B:CYS136 2.3 16.0 1.0
SD B:MET150 2.4 15.2 1.0
CE1 B:HIS145 3.0 17.1 1.0
CE1 B:HIS95 3.0 14.7 1.0
CG B:HIS95 3.1 15.6 1.0
CB B:CYS136 3.2 14.4 1.0
CG B:HIS145 3.2 14.6 1.0
CE B:MET150 3.2 17.0 1.0
CB B:HIS95 3.5 15.5 1.0
CB B:HIS145 3.6 14.9 1.0
CA B:HIS95 3.8 16.1 1.0
CG B:MET150 3.8 15.1 1.0
NE2 B:HIS145 4.1 15.6 1.0
NE2 B:HIS95 4.1 15.1 1.0
CD2 B:HIS95 4.2 16.1 1.0
CG B:PRO138 4.2 16.4 1.0
CD2 B:HIS145 4.2 15.8 1.0
O B:MET94 4.3 17.3 1.0
SD B:MET62 4.3 17.8 1.0
CB B:MET150 4.4 14.1 1.0
CA B:CYS136 4.6 14.5 1.0
CD B:PRO138 4.6 15.7 1.0
N B:ASN96 4.7 16.5 1.0
CA B:HIS145 4.8 14.7 1.0
CB B:MET62 4.8 15.7 1.0
C B:HIS95 4.8 16.2 1.0
N B:HIS95 4.9 16.4 1.0
C B:MET94 5.0 16.9 1.0

Copper binding site 4 out of 6 in 2ppc

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Copper binding site 4 out of 6 in the Oxidized Wild Type Afnir Exposed to No (Nitrite Bound)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Oxidized Wild Type Afnir Exposed to No (Nitrite Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:15.9
occ:1.00
NE2 B:HIS100 2.0 12.6 1.0
O2 B:NO2503 2.0 21.8 0.5
NE2 B:HIS135 2.0 16.4 1.0
NE2 C:HIS306 2.0 13.4 1.0
OXT B:ACT504 2.1 20.8 0.5
O1 B:NO2503 2.2 20.7 0.5
O B:ACT504 2.3 20.0 0.5
C B:ACT504 2.5 20.1 0.5
N B:NO2503 2.5 21.4 0.5
CE1 B:HIS100 2.9 14.1 1.0
CE1 C:HIS306 3.0 13.6 1.0
CD2 B:HIS135 3.0 13.9 1.0
CE1 B:HIS135 3.0 14.7 1.0
CD2 C:HIS306 3.1 14.0 1.0
CD2 B:HIS100 3.1 15.1 1.0
OD1 B:ASP98 3.8 18.9 0.5
CH3 B:ACT504 3.9 19.8 0.5
ND1 B:HIS100 4.0 14.5 1.0
ND1 C:HIS306 4.1 12.5 1.0
ND1 B:HIS135 4.1 14.1 1.0
CG B:HIS135 4.2 13.8 1.0
CG B:HIS100 4.2 14.3 1.0
CG C:HIS306 4.2 12.6 1.0
NE2 C:HIS255 4.2 18.2 1.0
O B:HOH1799 4.3 19.6 0.5
CE1 C:HIS255 4.4 17.9 1.0
CG B:ASP98 4.4 17.4 0.5
CD2 C:HIS255 4.6 17.0 1.0
OD2 B:ASP98 4.7 15.7 0.5
ND1 C:HIS255 4.8 16.4 1.0
CD2 C:LEU308 4.9 14.7 1.0
O C:HOH1700 4.9 19.7 1.0
CG C:HIS255 5.0 16.5 1.0

Copper binding site 5 out of 6 in 2ppc

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Copper binding site 5 out of 6 in the Oxidized Wild Type Afnir Exposed to No (Nitrite Bound)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Oxidized Wild Type Afnir Exposed to No (Nitrite Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:19.1
occ:1.00
ND1 C:HIS145 2.1 18.4 1.0
ND1 C:HIS95 2.1 16.4 1.0
SG C:CYS136 2.3 16.8 1.0
SD C:MET150 2.4 17.5 1.0
CE1 C:HIS145 2.9 18.1 1.0
CE1 C:HIS95 3.0 18.2 1.0
CG C:HIS145 3.1 17.9 1.0
CG C:HIS95 3.1 18.6 1.0
CB C:CYS136 3.2 17.3 1.0
CE C:MET150 3.3 18.6 1.0
CB C:HIS95 3.5 19.6 1.0
CB C:HIS145 3.5 17.0 1.0
CG C:MET150 3.8 15.5 1.0
CA C:HIS95 3.9 19.3 1.0
NE2 C:HIS145 4.1 17.3 1.0
NE2 C:HIS95 4.2 17.3 1.0
CD2 C:HIS145 4.2 18.0 1.0
CG C:PRO138 4.2 18.6 1.0
CD2 C:HIS95 4.2 18.8 1.0
O C:MET94 4.3 20.6 1.0
CB C:MET150 4.3 16.1 1.0
SD C:MET62 4.4 19.0 1.0
CA C:CYS136 4.6 16.5 1.0
CD C:PRO138 4.6 18.6 1.0
N C:ASN96 4.7 18.4 1.0
CB C:MET62 4.7 19.0 1.0
CA C:HIS145 4.8 16.7 1.0
C C:HIS95 4.8 19.4 1.0
N C:HIS95 4.9 20.0 1.0
C C:MET94 5.0 20.4 1.0

Copper binding site 6 out of 6 in 2ppc

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Copper binding site 6 out of 6 in the Oxidized Wild Type Afnir Exposed to No (Nitrite Bound)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Oxidized Wild Type Afnir Exposed to No (Nitrite Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:16.9
occ:1.00
O1 C:NO2503 2.0 20.6 0.5
NE2 C:HIS100 2.0 14.2 1.0
NE2 C:HIS135 2.0 15.2 1.0
NE2 A:HIS306 2.0 14.3 1.0
O C:ACT504 2.1 20.2 0.5
OXT C:ACT504 2.3 19.1 0.5
O2 C:NO2503 2.3 19.0 0.5
C C:ACT504 2.5 19.4 0.5
N C:NO2503 2.5 19.8 0.5
CE1 C:HIS100 2.9 15.6 1.0
CE1 A:HIS306 2.9 11.8 1.0
CD2 C:HIS135 3.0 14.0 1.0
CE1 C:HIS135 3.1 16.6 1.0
CD2 C:HIS100 3.1 17.1 1.0
CD2 A:HIS306 3.1 13.8 1.0
CH3 C:ACT504 3.8 19.3 0.5
OD1 C:ASP98 3.9 23.0 0.5
ND1 C:HIS100 4.1 15.7 1.0
ND1 A:HIS306 4.1 12.9 1.0
CG C:HIS135 4.1 14.7 1.0
ND1 C:HIS135 4.2 16.0 1.0
CG C:HIS100 4.2 14.9 1.0
CG A:HIS306 4.2 13.1 1.0
NE2 A:HIS255 4.2 18.0 1.0
O C:HOH1753 4.3 18.2 0.5
CE1 A:HIS255 4.3 17.5 1.0
CG C:ASP98 4.5 19.7 0.5
CD2 A:HIS255 4.6 16.9 1.0
OD2 C:ASP98 4.8 19.4 0.5
ND1 A:HIS255 4.8 16.5 1.0
CG A:HIS255 5.0 15.2 1.0
CD2 A:LEU308 5.0 15.9 1.0

Reference:

E.I.Tocheva, F.I.Rosell, A.G.Mauk, M.E.Murphy. Stable Copper-Nitrosyl Formation By Nitrite Reductase in Either Oxidation State. Biochemistry V. 46 12366 2007.
ISSN: ISSN 0006-2960
PubMed: 17924665
DOI: 10.1021/BI701205J
Page generated: Thu Sep 3 16:48:25 2020
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