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Copper in PDB 2ppd: Oxidized H145A Mutant of Afnir Bound to Nitric Oxide

Enzymatic activity of Oxidized H145A Mutant of Afnir Bound to Nitric Oxide

All present enzymatic activity of Oxidized H145A Mutant of Afnir Bound to Nitric Oxide:
1.7.2.1;

Protein crystallography data

The structure of Oxidized H145A Mutant of Afnir Bound to Nitric Oxide, PDB code: 2ppd 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) 83.62 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.957, 102.062, 145.797, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 21.2

Copper Binding Sites:

The binding sites of Copper atom in the Oxidized H145A Mutant of Afnir Bound to Nitric Oxide (pdb code 2ppd). 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 H145A Mutant of Afnir Bound to Nitric Oxide, PDB code: 2ppd:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2ppd

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Copper binding site 1 out of 6 in the Oxidized H145A Mutant of Afnir Bound 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 Oxidized H145A Mutant of Afnir Bound to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:33.3
occ:1.00
ND1 A:HIS95 2.1 22.2 1.0
SG A:CYS136 2.2 21.3 1.0
SD A:MET150 2.5 23.5 1.0
CG A:HIS95 3.0 20.8 1.0
CE A:MET150 3.0 24.0 1.0
CE1 A:HIS95 3.1 22.2 1.0
CB A:CYS136 3.1 19.7 1.0
CB A:HIS95 3.2 19.1 1.0
CA A:HIS95 3.6 19.5 1.0
CG A:MET150 3.8 21.5 1.0
CD2 A:HIS95 4.1 20.9 1.0
NE2 A:HIS95 4.2 21.7 1.0
CB A:ALA145 4.3 17.7 1.0
N A:ASN96 4.3 18.3 1.0
O A:MET94 4.4 20.2 1.0
CB A:MET150 4.4 19.3 1.0
SD A:MET62 4.5 27.6 1.0
CA A:CYS136 4.5 18.8 1.0
C A:HIS95 4.5 18.8 1.0
CG A:PRO138 4.7 22.8 1.0
N A:HIS95 4.7 20.4 1.0
O A:ASN96 4.8 17.2 1.0
CB A:MET62 4.8 23.1 1.0
CD A:PRO138 4.9 21.7 1.0
C A:MET94 5.0 20.4 1.0

Copper binding site 2 out of 6 in 2ppd

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Copper binding site 2 out of 6 in the Oxidized H145A Mutant of Afnir Bound 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 Oxidized H145A Mutant of Afnir Bound to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:19.1
occ:1.00
N A:NO503 2.0 36.8 1.0
NE2 A:HIS135 2.0 19.1 1.0
NE2 B:HIS306 2.1 18.6 1.0
NE2 A:HIS100 2.1 16.5 1.0
O A:NO503 2.2 37.0 1.0
CE1 B:HIS306 3.0 17.1 1.0
CE1 A:HIS100 3.0 18.0 1.0
CD2 A:HIS135 3.0 17.3 1.0
CE1 A:HIS135 3.0 17.7 1.0
CD2 B:HIS306 3.1 16.2 1.0
CD2 A:HIS100 3.1 16.2 1.0
NE2 B:HIS255 3.9 20.1 1.0
OD1 A:ASP98 4.0 28.7 1.0
ND1 B:HIS306 4.1 15.6 1.0
ND1 A:HIS100 4.1 15.9 1.0
ND1 A:HIS135 4.1 18.1 1.0
CG A:HIS135 4.2 16.9 1.0
CG B:HIS306 4.2 17.4 1.0
CG A:HIS100 4.2 16.7 1.0
CE1 B:HIS255 4.3 19.5 1.0
CG A:ASP98 4.3 24.1 1.0
CD2 B:HIS255 4.3 20.0 1.0
OD2 A:ASP98 4.5 24.8 1.0
ND1 B:HIS255 4.8 20.8 1.0
CG B:HIS255 4.9 18.3 1.0
CD2 B:LEU308 4.9 17.4 1.0
O B:HOH1696 4.9 21.9 1.0

Copper binding site 3 out of 6 in 2ppd

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Copper binding site 3 out of 6 in the Oxidized H145A Mutant of Afnir Bound 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 Oxidized H145A Mutant of Afnir Bound to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:34.8
occ:1.00
ND1 B:HIS95 2.0 28.8 1.0
SG B:CYS136 2.2 26.7 1.0
SD B:MET150 2.4 27.2 1.0
CE B:MET150 2.9 27.0 1.0
CG B:HIS95 3.0 27.1 1.0
CE1 B:HIS95 3.0 29.9 1.0
CB B:CYS136 3.1 25.1 1.0
CB B:HIS95 3.3 27.0 1.0
CA B:HIS95 3.7 26.9 1.0
CG B:MET150 3.8 24.8 1.0
CD2 B:HIS95 4.1 27.9 1.0
NE2 B:HIS95 4.1 26.1 1.0
CB B:ALA145 4.3 24.9 1.0
N B:ASN96 4.4 25.9 1.0
O B:MET94 4.4 27.7 1.0
CG B:PRO138 4.4 28.4 1.0
CB B:MET150 4.4 22.9 1.0
CA B:CYS136 4.5 24.8 1.0
SD B:MET62 4.5 28.9 1.0
C B:HIS95 4.6 26.6 1.0
O B:ASN96 4.7 25.2 1.0
N B:HIS95 4.8 27.7 1.0
CD B:PRO138 4.9 27.6 1.0
CB B:MET62 4.9 25.1 1.0

Copper binding site 4 out of 6 in 2ppd

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Copper binding site 4 out of 6 in the Oxidized H145A Mutant of Afnir Bound 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 Oxidized H145A Mutant of Afnir Bound to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:25.3
occ:1.00
O B:NO503 2.0 29.2 1.0
NE2 B:HIS135 2.0 22.9 1.0
N B:NO503 2.0 27.9 1.0
NE2 B:HIS100 2.0 23.6 1.0
NE2 C:HIS306 2.0 23.2 1.0
CE1 B:HIS100 2.9 21.8 1.0
CE1 C:HIS306 3.0 23.1 1.0
CD2 B:HIS135 3.0 21.4 1.0
CE1 B:HIS135 3.0 23.7 1.0
CD2 C:HIS306 3.1 23.6 1.0
CD2 B:HIS100 3.1 23.6 1.0
OD1 B:ASP98 3.9 33.7 1.0
NE2 C:HIS255 4.0 24.9 1.0
ND1 B:HIS100 4.1 21.5 1.0
ND1 C:HIS306 4.1 22.2 1.0
ND1 B:HIS135 4.1 21.2 1.0
CG B:HIS135 4.1 21.8 1.0
CG B:HIS100 4.2 23.1 1.0
CG C:HIS306 4.2 22.3 1.0
CE1 C:HIS255 4.4 24.3 1.0
CD2 C:HIS255 4.4 23.0 1.0
CG B:ASP98 4.4 29.2 1.0
OD2 B:ASP98 4.7 30.7 1.0
O B:HOH1698 4.8 25.7 1.0
ND1 C:HIS255 4.9 24.6 1.0
CG C:HIS255 4.9 23.3 1.0
CD2 C:LEU308 4.9 24.4 1.0

Copper binding site 5 out of 6 in 2ppd

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Copper binding site 5 out of 6 in the Oxidized H145A Mutant of Afnir Bound 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 Oxidized H145A Mutant of Afnir Bound to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:45.5
occ:1.00
ND1 C:HIS95 2.0 42.8 1.0
SG C:CYS136 2.3 36.4 1.0
SD C:MET150 2.3 37.2 1.0
CE C:MET150 2.9 36.2 1.0
CG C:HIS95 3.0 41.5 1.0
CE1 C:HIS95 3.0 41.8 1.0
CB C:CYS136 3.1 34.0 1.0
CB C:HIS95 3.3 40.6 1.0
CA C:HIS95 3.7 40.8 1.0
CG C:MET150 3.8 34.3 1.0
NE2 C:HIS95 4.1 42.0 1.0
CD2 C:HIS95 4.1 42.1 1.0
CB C:ALA145 4.3 30.8 1.0
CB C:MET150 4.3 33.1 1.0
N C:ASN96 4.4 38.9 1.0
O C:MET94 4.4 42.9 1.0
CG C:PRO138 4.5 36.7 1.0
CA C:CYS136 4.6 33.8 1.0
SD C:MET62 4.6 40.3 1.0
C C:HIS95 4.6 39.9 1.0
CB C:MET62 4.8 38.8 1.0
N C:HIS95 4.8 41.6 1.0
O C:ASN96 4.8 37.1 1.0
CD C:PRO138 5.0 36.1 1.0

Copper binding site 6 out of 6 in 2ppd

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Copper binding site 6 out of 6 in the Oxidized H145A Mutant of Afnir Bound 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 Oxidized H145A Mutant of Afnir Bound to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:28.0
occ:1.00
NE2 C:HIS100 2.0 25.6 1.0
O C:HOH503 2.0 43.8 1.0
NE2 C:HIS135 2.0 27.0 1.0
NE2 A:HIS306 2.0 26.4 1.0
CE1 C:HIS100 2.9 26.4 1.0
CD2 C:HIS135 2.9 27.3 1.0
CE1 A:HIS306 3.0 25.6 1.0
CD2 A:HIS306 3.1 25.1 1.0
CD2 C:HIS100 3.1 26.8 1.0
CE1 C:HIS135 3.1 27.9 1.0
OD1 C:ASP98 3.8 38.3 1.0
NE2 A:HIS255 4.0 26.1 1.0
ND1 C:HIS100 4.0 26.4 1.0
CG C:HIS135 4.1 28.3 1.0
ND1 A:HIS306 4.1 24.8 1.0
ND1 C:HIS135 4.1 27.9 1.0
CG C:HIS100 4.2 26.6 1.0
CG A:HIS306 4.2 23.0 1.0
CE1 A:HIS255 4.2 24.4 1.0
CG C:ASP98 4.3 34.9 1.0
CD2 A:HIS255 4.4 24.8 1.0
OD2 C:ASP98 4.7 35.9 1.0
ND1 A:HIS255 4.8 23.3 1.0
CG A:HIS255 4.9 23.5 1.0
CG1 A:ILE257 5.0 24.9 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 16:48:24 2020
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