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Copper in PDB 2ppf: Reduced Mutant D98N of Afnir Exposed to Nitric Oxide

Enzymatic activity of Reduced Mutant D98N of Afnir Exposed to Nitric Oxide

All present enzymatic activity of Reduced Mutant D98N of Afnir Exposed to Nitric Oxide:
1.7.2.1;

Protein crystallography data

The structure of Reduced Mutant D98N of Afnir Exposed to Nitric Oxide, PDB code: 2ppf 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) 83.92 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.423, 102.422, 146.123, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 17

Copper Binding Sites:

The binding sites of Copper atom in the Reduced Mutant D98N of Afnir Exposed to Nitric Oxide (pdb code 2ppf). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Reduced Mutant D98N of Afnir Exposed to Nitric Oxide, PDB code: 2ppf:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 2ppf

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Copper binding site 1 out of 8 in the Reduced Mutant D98N of Afnir Exposed to Nitric Oxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Reduced Mutant D98N of Afnir Exposed to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:15.7
occ:1.00
ND1 A:HIS95 2.1 12.2 1.0
ND1 A:HIS145 2.1 12.7 1.0
SG A:CYS136 2.2 12.8 1.0
SD A:MET150 2.4 13.6 1.0
CE1 A:HIS145 3.0 13.5 1.0
CE1 A:HIS95 3.1 13.5 1.0
CB A:CYS136 3.1 12.7 1.0
CG A:HIS95 3.2 12.7 1.0
CG A:HIS145 3.2 12.5 1.0
CE A:MET150 3.3 13.6 1.0
CB A:HIS95 3.5 12.8 1.0
CB A:HIS145 3.6 13.1 1.0
CA A:HIS95 3.8 13.1 1.0
CG A:MET150 3.9 12.2 1.0
NE2 A:HIS145 4.2 13.4 1.0
NE2 A:HIS95 4.2 12.4 1.0
CD2 A:HIS145 4.3 13.5 1.0
CD2 A:HIS95 4.3 13.8 1.0
O A:MET94 4.3 13.9 1.0
CB A:MET150 4.3 10.4 1.0
CG A:PRO138 4.3 15.2 1.0
SD A:MET62 4.5 15.9 1.0
CA A:CYS136 4.6 11.3 1.0
N A:ASN96 4.6 12.5 1.0
CD A:PRO138 4.7 14.8 1.0
CB A:MET62 4.8 14.5 1.0
CA A:HIS145 4.8 12.0 1.0
C A:HIS95 4.8 12.6 1.0
N A:HIS95 4.9 12.9 1.0

Copper binding site 2 out of 8 in 2ppf

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Copper binding site 2 out of 8 in the Reduced Mutant D98N of Afnir Exposed to Nitric Oxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Reduced Mutant D98N of Afnir Exposed to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:12.9
occ:1.00
NE2 B:HIS306 2.0 10.8 1.0
NE2 A:HIS100 2.0 9.7 1.0
NE2 A:HIS135 2.1 11.1 1.0
N A:NO1511 2.2 26.4 1.0
O A:NO1511 2.4 26.8 1.0
CE1 A:HIS100 2.9 10.0 1.0
CE1 B:HIS306 3.0 10.5 1.0
CD2 A:HIS135 3.1 10.3 1.0
CD2 B:HIS306 3.1 11.2 1.0
CE1 A:HIS135 3.1 12.9 1.0
CD2 A:HIS100 3.1 11.9 1.0
ND1 A:HIS100 4.1 10.9 1.0
ND1 B:HIS306 4.1 9.6 1.0
ND1 A:HIS135 4.2 11.2 1.0
CG B:HIS306 4.2 10.3 1.0
CG A:HIS100 4.2 10.2 1.0
CG A:HIS135 4.2 10.7 1.0
NE2 B:HIS255 4.3 15.2 1.0
O A:HOH1512 4.3 23.7 1.0
CE1 B:HIS255 4.4 15.0 1.0
CD2 B:HIS255 4.7 14.0 1.0
ND1 B:HIS255 4.8 13.9 1.0
CD2 B:LEU308 4.9 12.0 1.0
CG1 B:ILE257 5.0 14.6 1.0

Copper binding site 3 out of 8 in 2ppf

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Copper binding site 3 out of 8 in the Reduced Mutant D98N of Afnir Exposed to Nitric Oxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Reduced Mutant D98N of Afnir Exposed to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:17.8
occ:1.00
ND1 B:HIS95 2.1 13.3 1.0
CU B:CU1504 2.2 20.3 0.3
SG B:CYS136 2.2 14.4 1.0
ND1 B:HIS145 2.3 18.4 1.0
SD B:MET150 2.5 13.8 1.0
CE1 B:HIS95 3.0 14.7 1.0
CB B:CYS136 3.1 14.5 1.0
CG B:HIS95 3.1 14.3 1.0
CE1 B:HIS145 3.2 19.6 1.0
CE B:MET150 3.2 14.3 1.0
CG B:HIS145 3.4 17.2 1.0
CB B:HIS95 3.5 14.7 1.0
CB B:HIS145 3.7 14.9 1.0
CA B:HIS95 3.8 15.1 1.0
CG B:MET150 3.9 11.8 1.0
NE2 B:HIS95 4.2 13.4 1.0
CD2 B:HIS95 4.2 14.6 1.0
O B:MET94 4.3 16.7 1.0
NE2 B:HIS145 4.3 19.3 1.0
CG B:PRO138 4.3 19.4 1.0
CB B:MET150 4.4 12.5 1.0
CD2 B:HIS145 4.4 18.2 1.0
SD B:MET62 4.4 16.2 1.0
CA B:CYS136 4.5 13.3 1.0
N B:ASN96 4.6 14.4 1.0
CD B:PRO138 4.7 18.6 1.0
C B:HIS95 4.8 15.1 1.0
N B:HIS95 4.9 15.6 1.0
CB B:MET62 4.9 14.5 1.0
CA B:HIS145 5.0 14.6 1.0

Copper binding site 4 out of 8 in 2ppf

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Copper binding site 4 out of 8 in the Reduced Mutant D98N of Afnir Exposed to Nitric Oxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Reduced Mutant D98N of Afnir Exposed to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:14.4
occ:1.00
NE2 B:HIS135 2.0 12.9 1.0
NE2 B:HIS100 2.0 10.6 1.0
NE2 C:HIS306 2.1 12.0 1.0
N B:NO503 2.1 30.6 1.0
O B:NO503 2.4 30.2 1.0
CE1 B:HIS100 2.9 10.9 1.0
CE1 C:HIS306 3.0 13.2 1.0
CE1 B:HIS135 3.0 14.4 1.0
CD2 B:HIS135 3.0 14.4 1.0
CD2 B:HIS100 3.1 13.1 1.0
CD2 C:HIS306 3.1 12.6 1.0
ND1 B:HIS100 4.1 11.2 1.0
ND1 B:HIS135 4.1 12.8 1.0
ND1 C:HIS306 4.2 12.2 1.0
CG B:HIS135 4.2 12.2 1.0
CG B:HIS100 4.2 11.8 1.0
CG C:HIS306 4.2 11.7 1.0
O B:HOH1849 4.3 14.3 0.5
NE2 C:HIS255 4.3 17.1 1.0
CE1 C:HIS255 4.4 16.9 1.0
CD2 C:HIS255 4.8 17.6 1.0
ND1 C:HIS255 4.8 17.0 1.0
CD2 C:LEU308 5.0 14.5 1.0

Copper binding site 5 out of 8 in 2ppf

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Copper binding site 5 out of 8 in the Reduced Mutant D98N of Afnir Exposed to Nitric Oxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Reduced Mutant D98N of Afnir Exposed to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu504

b:20.3
occ:0.30
ND1 B:HIS145 2.0 18.4 1.0
SG B:CYS136 2.0 14.4 1.0
CU B:CU1501 2.2 17.8 1.0
CG B:PRO138 2.3 19.4 1.0
CG B:HIS145 2.5 17.2 1.0
CD B:PRO138 2.5 18.6 1.0
CE1 B:HIS145 2.7 19.6 1.0
CB B:HIS145 3.0 14.9 1.0
CD2 B:HIS145 3.3 18.2 1.0
CB B:CYS136 3.4 14.5 1.0
NE2 B:HIS145 3.4 19.3 1.0
N B:PRO138 3.7 18.3 1.0
ND1 B:HIS95 3.8 13.3 1.0
CB B:PRO138 3.8 18.6 1.0
N B:ALA137 4.1 14.7 1.0
O B:MET94 4.2 16.7 1.0
C B:CYS136 4.2 14.3 1.0
CA B:HIS95 4.3 15.1 1.0
CA B:CYS136 4.3 13.3 1.0
CA B:PRO138 4.5 19.0 1.0
SD B:MET150 4.5 13.8 1.0
CA B:HIS145 4.5 14.6 1.0
C B:ALA137 4.6 17.4 1.0
CE1 B:HIS95 4.6 14.7 1.0
CA B:ALA137 4.6 16.3 1.0
CG B:HIS95 4.7 14.3 1.0
O B:CYS136 4.7 13.4 1.0
CB B:HIS95 4.7 14.7 1.0
N B:ASN96 4.8 14.4 1.0
OD1 B:ASN96 4.9 16.6 1.0
O B:HOH1632 5.0 34.0 1.0

Copper binding site 6 out of 8 in 2ppf

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Copper binding site 6 out of 8 in the Reduced Mutant D98N of Afnir Exposed to Nitric Oxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Reduced Mutant D98N of Afnir Exposed to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:19.5
occ:1.00
ND1 C:HIS95 2.1 16.3 1.0
SG C:CYS136 2.2 17.3 1.0
CU C:CU1504 2.2 33.6 0.4
ND1 C:HIS145 2.3 23.4 1.0
SD C:MET150 2.5 16.4 1.0
CE1 C:HIS95 3.0 18.0 1.0
CE1 C:HIS145 3.1 22.8 1.0
CB C:CYS136 3.1 17.1 1.0
CG C:HIS95 3.1 18.2 1.0
CE C:MET150 3.2 17.0 1.0
CG C:HIS145 3.3 20.3 1.0
CB C:HIS95 3.5 18.4 1.0
CB C:HIS145 3.7 18.3 1.0
CA C:HIS95 3.8 18.5 1.0
CG C:MET150 3.9 14.7 1.0
NE2 C:HIS95 4.2 16.5 1.0
CD2 C:HIS95 4.3 18.6 1.0
O C:MET94 4.3 20.6 1.0
NE2 C:HIS145 4.3 23.0 1.0
CD2 C:HIS145 4.4 22.4 1.0
CG C:PRO138 4.4 22.2 1.0
CB C:MET150 4.4 14.9 1.0
SD C:MET62 4.5 20.3 1.0
CA C:CYS136 4.6 16.4 1.0
N C:ASN96 4.6 17.7 1.0
C C:HIS95 4.8 18.2 1.0
CD C:PRO138 4.8 21.3 1.0
CB C:MET62 4.8 19.3 1.0
N C:HIS95 4.8 19.5 1.0
C C:MET94 5.0 20.4 1.0
CA C:HIS145 5.0 17.3 1.0

Copper binding site 7 out of 8 in 2ppf

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Copper binding site 7 out of 8 in the Reduced Mutant D98N of Afnir Exposed to Nitric Oxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Reduced Mutant D98N of Afnir Exposed to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:15.7
occ:1.00
NE2 C:HIS100 2.0 14.0 1.0
NE2 A:HIS306 2.1 13.0 1.0
NE2 C:HIS135 2.1 13.7 1.0
N C:NO505 2.2 19.1 0.5
O C:NO505 2.3 18.4 0.5
N A:NO503 2.6 21.3 0.5
CE1 C:HIS100 2.9 13.0 1.0
CE1 A:HIS306 3.0 13.9 1.0
CD2 C:HIS135 3.0 14.4 1.0
CD2 C:HIS100 3.1 14.7 1.0
CD2 A:HIS306 3.1 14.9 1.0
CE1 C:HIS135 3.2 16.0 1.0
O A:NO503 3.4 21.5 0.5
ND1 C:HIS100 4.1 13.4 1.0
ND1 A:HIS306 4.1 13.1 1.0
CG C:HIS100 4.2 13.1 1.0
CG C:HIS135 4.2 14.2 1.0
CG A:HIS306 4.2 11.9 1.0
ND1 C:HIS135 4.3 14.9 1.0
O C:HOH1510 4.3 28.1 1.0
NE2 A:HIS255 4.4 17.7 1.0
CE1 A:HIS255 4.5 17.6 1.0
CD2 A:HIS255 4.7 16.9 1.0
ND1 A:HIS255 4.9 16.7 1.0
CG1 A:ILE257 5.0 18.0 1.0
CD1 A:LEU308 5.0 13.5 1.0

Copper binding site 8 out of 8 in 2ppf

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Copper binding site 8 out of 8 in the Reduced Mutant D98N of Afnir Exposed to Nitric Oxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Reduced Mutant D98N of Afnir Exposed to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu504

b:33.6
occ:0.40
SG C:CYS136 1.9 17.3 1.0
ND1 C:HIS145 2.2 23.4 1.0
CU C:CU1501 2.2 19.5 1.0
CG C:PRO138 2.3 22.2 1.0
CD C:PRO138 2.6 21.3 1.0
CG C:HIS145 2.6 20.3 1.0
CE1 C:HIS145 2.9 22.8 1.0
CB C:HIS145 3.1 18.3 1.0
CB C:CYS136 3.3 17.1 1.0
CD2 C:HIS145 3.4 22.4 1.0
NE2 C:HIS145 3.5 23.0 1.0
N C:PRO138 3.7 21.5 1.0
CB C:PRO138 3.8 22.1 1.0
ND1 C:HIS95 3.9 16.3 1.0
N C:ALA137 4.0 18.2 1.0
C C:CYS136 4.1 17.5 1.0
O C:MET94 4.1 20.6 1.0
CA C:HIS95 4.2 18.5 1.0
CA C:CYS136 4.3 16.4 1.0
CA C:PRO138 4.4 22.5 1.0
CA C:ALA137 4.5 19.4 1.0
C C:ALA137 4.5 20.5 1.0
SD C:MET150 4.5 16.4 1.0
N C:ASN96 4.6 17.7 1.0
CA C:HIS145 4.6 17.3 1.0
OD1 C:ASN96 4.6 18.9 1.0
O C:CYS136 4.7 17.0 1.0
CB C:HIS95 4.7 18.4 1.0
CG C:HIS95 4.7 18.2 1.0
CE1 C:HIS95 4.7 18.0 1.0
C C:HIS95 4.9 18.2 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: Wed Oct 28 14:21:34 2020
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