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Copper in PDB 2pp9: Nitrate Bound Wild Type Oxidized Afnir

Enzymatic activity of Nitrate Bound Wild Type Oxidized Afnir

All present enzymatic activity of Nitrate Bound Wild Type Oxidized Afnir:
1.7.2.1;

Protein crystallography data

The structure of Nitrate Bound Wild Type Oxidized Afnir, PDB code: 2pp9 was solved by M.E.P.Murphy, E.I.Tocheva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.910, 102.084, 145.830, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.5

Copper Binding Sites:

The binding sites of Copper atom in the Nitrate Bound Wild Type Oxidized Afnir (pdb code 2pp9). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Nitrate Bound Wild Type Oxidized Afnir, PDB code: 2pp9:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2pp9

Go back to Copper Binding Sites List in 2pp9
Copper binding site 1 out of 6 in the Nitrate Bound Wild Type Oxidized Afnir


Mono view


Stereo pair view

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

b:18.0
occ:1.00
ND1 A:HIS145 2.0 13.5 1.0
ND1 A:HIS95 2.1 15.3 1.0
SG A:CYS136 2.2 14.7 1.0
SD A:MET150 2.5 13.8 1.0
CE1 A:HIS145 3.0 13.7 1.0
CG A:HIS145 3.1 12.8 1.0
CE1 A:HIS95 3.1 16.2 1.0
CG A:HIS95 3.1 16.4 1.0
CB A:CYS136 3.2 14.1 1.0
CE A:MET150 3.2 11.6 1.0
CB A:HIS95 3.4 15.1 1.0
CB A:HIS145 3.5 12.7 1.0
CG A:MET150 3.8 12.5 1.0
CA A:HIS95 3.8 15.9 1.0
NE2 A:HIS145 4.1 15.1 1.0
CD2 A:HIS145 4.2 13.3 1.0
NE2 A:HIS95 4.2 17.7 1.0
CD2 A:HIS95 4.2 15.1 1.0
SD A:MET62 4.3 16.3 1.0
CB A:MET150 4.3 11.8 1.0
CG A:PRO138 4.3 17.6 1.0
O A:MET94 4.3 15.6 1.0
CA A:CYS136 4.6 13.8 1.0
N A:ASN96 4.6 14.6 1.0
CD A:PRO138 4.6 16.9 1.0
CA A:HIS145 4.7 12.9 1.0
CB A:MET62 4.8 14.4 1.0
C A:HIS95 4.8 15.7 1.0
N A:HIS95 4.9 15.6 1.0

Copper binding site 2 out of 6 in 2pp9

Go back to Copper Binding Sites List in 2pp9
Copper binding site 2 out of 6 in the Nitrate Bound Wild Type Oxidized Afnir


Mono view


Stereo pair view

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

b:17.7
occ:1.00
NE2 A:HIS100 2.0 14.2 1.0
NE2 B:HIS306 2.0 14.7 1.0
NE2 A:HIS135 2.1 14.6 1.0
O2 A:NO3503 2.2 31.0 1.0
O1 A:NO3503 2.2 29.5 1.0
N A:NO3503 2.5 31.2 1.0
CE1 A:HIS100 2.9 15.4 1.0
CE1 B:HIS306 3.0 12.2 1.0
CD2 B:HIS306 3.0 13.2 1.0
CD2 A:HIS100 3.1 13.6 1.0
CE1 A:HIS135 3.1 15.9 1.0
CD2 A:HIS135 3.1 13.7 1.0
O3 A:NO3503 3.9 33.0 1.0
ND1 A:HIS100 4.0 14.5 1.0
ND1 B:HIS306 4.1 12.2 1.0
CG A:HIS100 4.1 13.3 1.0
CG B:HIS306 4.2 14.5 1.0
NE2 B:HIS255 4.2 13.5 1.0
ND1 A:HIS135 4.2 13.4 1.0
CE1 B:HIS255 4.3 15.3 1.0
CG A:HIS135 4.3 14.4 1.0
O A:HOH2244 4.4 23.5 1.0
CD2 B:HIS255 4.7 13.8 1.0
ND1 B:HIS255 4.7 15.3 1.0
CD2 B:LEU308 4.8 13.5 1.0
CG1 B:ILE257 4.8 17.3 1.0
CG B:HIS255 5.0 13.8 1.0

Copper binding site 3 out of 6 in 2pp9

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Copper binding site 3 out of 6 in the Nitrate Bound Wild Type Oxidized Afnir


Mono view


Stereo pair view

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

b:20.4
occ:1.00
ND1 B:HIS145 2.1 17.2 1.0
ND1 B:HIS95 2.1 16.7 1.0
SG B:CYS136 2.2 16.7 1.0
SD B:MET150 2.5 16.7 1.0
CE1 B:HIS145 2.9 15.4 1.0
CE1 B:HIS95 3.0 16.7 1.0
CG B:HIS145 3.1 15.9 1.0
CG B:HIS95 3.1 17.0 1.0
CB B:CYS136 3.2 15.0 1.0
CE B:MET150 3.2 15.8 1.0
CB B:HIS95 3.5 17.5 1.0
CB B:HIS145 3.5 15.0 1.0
CG B:MET150 3.8 15.6 1.0
CA B:HIS95 3.9 18.0 1.0
NE2 B:HIS145 4.1 16.9 1.0
NE2 B:HIS95 4.2 15.1 1.0
CD2 B:HIS145 4.2 18.0 1.0
CG B:PRO138 4.2 17.5 1.0
CD2 B:HIS95 4.2 16.9 1.0
SD B:MET62 4.3 17.7 1.0
O B:MET94 4.3 20.0 1.0
CB B:MET150 4.4 15.1 1.0
CA B:CYS136 4.6 15.3 1.0
N B:ASN96 4.6 17.6 1.0
CD B:PRO138 4.6 16.9 1.0
CA B:HIS145 4.8 15.4 1.0
CB B:MET62 4.8 16.3 1.0
C B:HIS95 4.8 18.1 1.0
N B:HIS95 4.9 19.2 1.0

Copper binding site 4 out of 6 in 2pp9

Go back to Copper Binding Sites List in 2pp9
Copper binding site 4 out of 6 in the Nitrate Bound Wild Type Oxidized Afnir


Mono view


Stereo pair view

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

b:20.1
occ:1.00
NE2 B:HIS100 2.0 13.2 1.0
O2 B:NO3503 2.1 29.2 1.0
NE2 B:HIS135 2.1 15.8 1.0
NE2 C:HIS306 2.1 14.8 1.0
O1 B:NO3503 2.3 29.1 1.0
N B:NO3503 2.5 29.9 1.0
CE1 B:HIS100 2.9 14.5 1.0
CE1 B:HIS135 3.0 17.8 1.0
CE1 C:HIS306 3.0 14.2 1.0
CD2 B:HIS100 3.1 13.6 1.0
CD2 C:HIS306 3.1 14.5 1.0
CD2 B:HIS135 3.1 15.4 1.0
O3 B:NO3503 3.8 30.6 1.0
ND1 B:HIS100 4.1 14.7 1.0
ND1 B:HIS135 4.1 15.5 1.0
ND1 C:HIS306 4.2 14.0 1.0
CG B:HIS100 4.2 14.4 1.0
NE2 C:HIS255 4.2 19.3 1.0
CG B:HIS135 4.2 14.4 1.0
CG C:HIS306 4.3 16.1 1.0
O B:HOH2227 4.3 26.1 1.0
CE1 C:HIS255 4.4 19.0 1.0
CD2 C:HIS255 4.6 17.1 1.0
ND1 C:HIS255 4.8 17.9 1.0
CG1 C:ILE257 4.8 18.6 1.0
CD2 C:LEU308 4.8 16.4 1.0
O C:HOH2204 4.9 20.2 1.0
CG C:HIS255 5.0 17.5 1.0
CD1 C:LEU308 5.0 18.9 1.0

Copper binding site 5 out of 6 in 2pp9

Go back to Copper Binding Sites List in 2pp9
Copper binding site 5 out of 6 in the Nitrate Bound Wild Type Oxidized Afnir


Mono view


Stereo pair view

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

b:23.1
occ:1.00
ND1 C:HIS145 2.1 19.9 1.0
SG C:CYS136 2.2 19.8 1.0
ND1 C:HIS95 2.2 20.6 1.0
SD C:MET150 2.5 19.3 1.0
CE1 C:HIS145 3.0 20.6 1.0
CG C:HIS145 3.1 19.0 1.0
CE1 C:HIS95 3.1 21.2 1.0
CB C:CYS136 3.1 18.6 1.0
CG C:HIS95 3.2 21.5 1.0
CE C:MET150 3.4 17.9 1.0
CB C:HIS95 3.4 21.2 1.0
CB C:HIS145 3.5 17.4 1.0
CA C:HIS95 3.8 21.6 1.0
CG C:MET150 3.8 17.1 1.0
NE2 C:HIS145 4.1 19.5 1.0
CD2 C:HIS145 4.2 19.5 1.0
NE2 C:HIS95 4.3 19.3 1.0
CG C:PRO138 4.3 21.5 1.0
O C:MET94 4.3 22.7 1.0
CB C:MET150 4.3 17.7 1.0
CD2 C:HIS95 4.3 19.9 1.0
SD C:MET62 4.4 19.8 1.0
N C:ASN96 4.6 20.6 1.0
CA C:CYS136 4.6 18.5 1.0
CD C:PRO138 4.7 20.2 1.0
CA C:HIS145 4.7 17.3 1.0
CB C:MET62 4.7 19.0 1.0
C C:HIS95 4.8 21.4 1.0
N C:HIS95 4.8 22.2 1.0
C C:MET94 5.0 22.8 1.0

Copper binding site 6 out of 6 in 2pp9

Go back to Copper Binding Sites List in 2pp9
Copper binding site 6 out of 6 in the Nitrate Bound Wild Type Oxidized Afnir


Mono view


Stereo pair view

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

b:20.9
occ:1.00
NE2 C:HIS100 1.9 16.1 1.0
NE2 A:HIS306 2.1 12.5 1.0
O1 C:NO3503 2.2 33.2 1.0
NE2 C:HIS135 2.2 15.6 1.0
O2 C:NO3503 2.3 33.9 1.0
N C:NO3503 2.5 34.3 1.0
CE1 C:HIS100 2.8 16.6 1.0
CD2 C:HIS100 3.0 17.2 1.0
CE1 A:HIS306 3.0 15.9 1.0
CD2 C:HIS135 3.1 16.0 1.0
CD2 A:HIS306 3.1 14.3 1.0
CE1 C:HIS135 3.2 16.4 1.0
O3 C:NO3503 3.9 35.1 1.0
ND1 C:HIS100 3.9 15.5 1.0
CG C:HIS100 4.1 17.5 1.0
ND1 A:HIS306 4.1 15.2 1.0
CG A:HIS306 4.2 13.6 1.0
CG C:HIS135 4.3 16.4 1.0
NE2 A:HIS255 4.3 19.2 1.0
ND1 C:HIS135 4.3 14.8 1.0
CE1 A:HIS255 4.4 20.1 1.0
O C:HOH2225 4.4 29.5 1.0
CD2 A:HIS255 4.7 18.2 1.0
ND1 A:HIS255 4.7 18.8 1.0
CG1 A:ILE257 4.8 16.6 1.0
CD1 A:LEU308 4.9 13.9 1.0
CG A:HIS255 4.9 17.0 1.0
CD2 A:LEU308 5.0 14.2 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: Sun Dec 13 11:06:44 2020

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