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Copper in PDB 2ppa: Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide

Enzymatic activity of Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide

All present enzymatic activity of Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide:
1.7.2.1;

Protein crystallography data

The structure of Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide, PDB code: 2ppa 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 / 1.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.650, 101.623, 146.042, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22.4

Copper Binding Sites:

The binding sites of Copper atom in the Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide (pdb code 2ppa). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide, PDB code: 2ppa:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2ppa

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Copper binding site 1 out of 6 in the Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:18.1
occ:1.00
 ND1 A:HIS145 2.0 16.4 1.0
ND1 A:HIS95 2.1 16.4 1.0
SG A:CYS136 2.2 17.2 1.0
SD A:MET150 2.5 18.5 1.0
CE1 A:HIS145 2.9 18.1 1.0
CE1 A:HIS95 3.0 17.6 1.0
CG A:HIS145 3.1 16.3 1.0
CG A:HIS95 3.1 15.9 1.0
CB A:CYS136 3.2 17.8 1.0
CE A:MET150 3.2 18.1 1.0
CB A:HIS95 3.5 15.7 1.0
CB A:HIS145 3.5 16.5 1.0
CG A:MET150 3.8 17.1 1.0
CA A:HIS95 3.9 16.3 1.0
NE2 A:HIS145 4.0 16.3 1.0
CD2 A:HIS145 4.1 16.8 1.0
NE2 A:HIS95 4.2 15.8 1.0
CD2 A:HIS95 4.2 17.3 1.0
CB A:MET150 4.3 16.2 1.0
CG A:PRO138 4.3 18.3 1.0
SD A:MET62 4.3 20.5 1.0
O A:MET94 4.3 17.1 1.0
CA A:CYS136 4.6 17.3 1.0
CD A:PRO138 4.7 18.5 1.0
N A:ASN96 4.7 16.2 1.0
CA A:HIS145 4.7 16.7 1.0
CB A:MET62 4.7 18.7 1.0
C A:HIS95 4.9 16.6 1.0
N A:HIS95 4.9 16.2 1.0

Copper binding site 2 out of 6 in 2ppa

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Copper binding site 2 out of 6 in the Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:18.5
occ:1.00
 NE2 B:HIS306 2.0 16.9 1.0
NE2 A:HIS100 2.0 16.3 1.0
NE2 A:HIS135 2.1 15.2 1.0
O3 A:N2O503 2.2 32.1 1.0
N2 A:N2O503 2.2 32.1 1.0
N1 A:N2O503 2.7 31.7 1.0
CE1 B:HIS306 2.9 14.9 1.0
CE1 A:HIS100 2.9 14.7 1.0
CD2 A:HIS135 3.0 15.9 1.0
CD2 B:HIS306 3.1 16.8 1.0
CD2 A:HIS100 3.1 17.2 1.0
CE1 A:HIS135 3.1 18.3 1.0
ND1 B:HIS306 4.1 16.0 1.0
ND1 A:HIS100 4.1 17.2 1.0
CG B:HIS306 4.2 15.8 1.0
NE2 B:HIS255 4.2 19.2 1.0
CG A:HIS100 4.2 15.4 1.0
CG A:HIS135 4.2 17.1 1.0
ND1 A:HIS135 4.2 17.1 1.0
O A:HOH1601 4.3 26.8 1.0
CE1 B:HIS255 4.4 18.4 1.0
CD2 B:HIS255 4.6 18.3 1.0
ND1 B:HIS255 4.8 18.2 1.0
CD2 B:LEU308 4.8 16.7 1.0
CD1 B:LEU308 5.0 18.2 1.0

Copper binding site 3 out of 6 in 2ppa

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Copper binding site 3 out of 6 in the Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:21.2
occ:1.00
 ND1 B:HIS95 2.1 20.9 1.0
ND1 B:HIS145 2.1 18.4 1.0
SG B:CYS136 2.2 19.9 1.0
SD B:MET150 2.5 20.1 1.0
CE1 B:HIS145 2.9 21.8 1.0
CE1 B:HIS95 3.0 18.9 1.0
CG B:HIS95 3.1 20.4 1.0
CG B:HIS145 3.1 20.2 1.0
CB B:CYS136 3.1 19.0 1.0
CE B:MET150 3.2 21.3 1.0
CB B:HIS95 3.5 20.6 1.0
CB B:HIS145 3.6 20.0 1.0
CA B:HIS95 3.8 20.8 1.0
CG B:MET150 3.9 19.1 1.0
NE2 B:HIS145 4.1 20.7 1.0
NE2 B:HIS95 4.1 17.8 1.0
CD2 B:HIS145 4.2 20.5 1.0
CD2 B:HIS95 4.2 20.8 1.0
CG B:PRO138 4.2 21.9 1.0
O B:MET94 4.3 22.2 1.0
SD B:MET62 4.3 21.3 1.0
CB B:MET150 4.4 18.8 1.0
CD B:PRO138 4.6 21.3 1.0
CA B:CYS136 4.6 19.2 1.0
N B:ASN96 4.6 20.6 1.0
CA B:HIS145 4.8 20.2 1.0
C B:HIS95 4.8 20.8 1.0
CB B:MET62 4.8 19.6 1.0
N B:HIS95 4.9 21.4 1.0
C B:MET94 5.0 22.4 1.0

Copper binding site 4 out of 6 in 2ppa

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Copper binding site 4 out of 6 in the Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:19.6
occ:1.00
 NE2 B:HIS100 2.0 14.1 1.0
NE2 C:HIS306 2.0 16.5 1.0
O3 B:N2O503 2.1 32.0 1.0
NE2 B:HIS135 2.1 20.4 1.0
N2 B:N2O503 2.1 31.6 1.0
N1 B:N2O503 2.5 31.5 1.0
CE1 B:HIS100 2.9 17.2 1.0
CE1 C:HIS306 3.0 18.7 1.0
CE1 B:HIS135 3.0 20.1 1.0
CD2 C:HIS306 3.1 17.4 1.0
CD2 B:HIS135 3.1 18.0 1.0
CD2 B:HIS100 3.1 19.6 1.0
ND1 B:HIS100 4.0 18.2 1.0
ND1 C:HIS306 4.1 17.1 1.0
ND1 B:HIS135 4.2 18.5 1.0
CG B:HIS100 4.2 16.3 1.0
CG C:HIS306 4.2 17.7 1.0
CG B:HIS135 4.2 19.1 1.0
O B:HOH1556 4.3 24.8 1.0
CE1 C:HIS255 4.4 20.5 1.0
NE2 C:HIS255 4.4 21.3 1.0
ND1 C:HIS255 4.8 20.0 1.0
CD2 C:HIS255 4.8 20.3 1.0
CD2 C:LEU308 4.9 17.2 1.0
CD1 C:LEU308 5.0 18.5 1.0

Copper binding site 5 out of 6 in 2ppa

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Copper binding site 5 out of 6 in the Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:22.5
occ:1.00
 ND1 C:HIS145 2.1 19.9 1.0
ND1 C:HIS95 2.1 22.2 1.0
SG C:CYS136 2.2 21.0 1.0
SD C:MET150 2.5 20.9 1.0
CE1 C:HIS145 3.0 22.6 1.0
CE1 C:HIS95 3.0 21.9 1.0
CG C:HIS145 3.1 20.1 1.0
CB C:CYS136 3.1 20.9 1.0
CG C:HIS95 3.1 21.8 1.0
CE C:MET150 3.4 20.5 1.0
CB C:HIS145 3.5 19.8 1.0
CB C:HIS95 3.5 21.6 1.0
CA C:HIS95 3.8 21.6 1.0
CG C:MET150 3.9 19.3 1.0
NE2 C:HIS145 4.1 21.3 1.0
NE2 C:HIS95 4.1 19.8 1.0
CG C:PRO138 4.2 21.9 1.0
CD2 C:HIS145 4.2 21.3 1.0
CD2 C:HIS95 4.2 21.9 1.0
O C:MET94 4.3 23.0 1.0
CB C:MET150 4.4 19.1 1.0
SD C:MET62 4.4 22.3 1.0
CD C:PRO138 4.5 22.3 1.0
CA C:CYS136 4.5 20.6 1.0
N C:ASN96 4.7 20.6 1.0
CA C:HIS145 4.7 19.2 1.0
CB C:MET62 4.7 21.4 1.0
C C:HIS95 4.8 20.9 1.0
N C:HIS95 4.9 21.9 1.0
C C:MET94 5.0 22.7 1.0

Copper binding site 6 out of 6 in 2ppa

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Copper binding site 6 out of 6 in the Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Anaerobically Manipulated Wild Type Oxidized Afnir Bound to Nitrous Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:20.9
occ:1.00
 NE2 C:HIS100 2.0 15.2 1.0
NE2 A:HIS306 2.1 18.3 1.0
O C:ACT503 2.1 31.6 1.0
NE2 C:HIS135 2.1 18.2 1.0
OXT C:ACT503 2.4 32.2 1.0
C C:ACT503 2.6 32.0 1.0
CE1 C:HIS100 2.9 17.8 1.0
CE1 A:HIS306 2.9 17.7 1.0
CD2 C:HIS135 3.0 19.0 1.0
CE1 C:HIS135 3.1 20.5 1.0
CD2 C:HIS100 3.1 18.4 1.0
CD2 A:HIS306 3.1 17.9 1.0
CH3 C:ACT503 3.9 30.6 1.0
ND1 C:HIS100 4.1 17.2 1.0
ND1 A:HIS306 4.1 18.5 1.0
CG C:HIS135 4.2 19.3 1.0
CG C:HIS100 4.2 17.7 1.0
ND1 C:HIS135 4.2 18.9 1.0
CG A:HIS306 4.2 17.8 1.0
NE2 A:HIS255 4.3 18.7 1.0
CE1 A:HIS255 4.4 18.5 1.0
O C:HOH1593 4.4 31.6 1.0
CD2 A:HIS255 4.7 19.0 1.0
ND1 A:HIS255 4.8 18.8 1.0
CG1 A:ILE257 4.9 20.2 1.0
CD1 A:LEU308 4.9 21.0 1.0
CD2 A:LEU308 5.0 21.5 1.0
CG A:HIS255 5.0 18.9 1.0

Reference:

E.I.Tocheva, L.D.Eltis, M.E.Murphy. Conserved Active Site Residues Limit Inhibition of A Copper-Containing Nitrite Reductase By Small Molecules. Biochemistry V. 47 4452 2008.
ISSN: ISSN 0006-2960
PubMed: 18358002
DOI: 10.1021/BI7020537
Page generated: Tue Jul 30 23:55:48 2024

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