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Copper in PDB 2pp8: Formate Bound to Oxidized Wild Type Afnir

Enzymatic activity of Formate Bound to Oxidized Wild Type Afnir

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

Protein crystallography data

The structure of Formate Bound to Oxidized Wild Type Afnir, PDB code: 2pp8 was solved by E.I.Tocheva, L.D.Eltis, 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 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.334, 102.453, 146.179, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 20.1

Copper Binding Sites:

The binding sites of Copper atom in the Formate Bound to Oxidized Wild Type Afnir (pdb code 2pp8). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Formate Bound to Oxidized Wild Type Afnir, PDB code: 2pp8:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2pp8

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Copper binding site 1 out of 6 in the Formate Bound to Oxidized Wild Type Afnir


Mono view


Stereo pair view

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

b:11.2
occ:1.00
ND1 A:HIS145 2.0 10.0 1.0
ND1 A:HIS95 2.1 11.1 1.0
SG A:CYS136 2.2 10.9 1.0
SD A:MET150 2.5 10.4 1.0
CE1 A:HIS145 2.9 9.8 1.0
CE1 A:HIS95 3.1 10.8 1.0
CG A:HIS145 3.1 9.9 1.0
CB A:CYS136 3.1 9.9 1.0
CG A:HIS95 3.2 10.8 1.0
CE A:MET150 3.2 10.6 1.0
CB A:HIS95 3.5 10.9 1.0
CB A:HIS145 3.5 9.6 1.0
CA A:HIS95 3.9 11.0 1.0
CG A:MET150 3.9 10.0 1.0
NE2 A:HIS145 4.1 9.8 1.0
CD2 A:HIS145 4.2 10.4 1.0
NE2 A:HIS95 4.2 10.5 1.0
CG A:PRO138 4.2 11.9 1.0
CD2 A:HIS95 4.3 10.2 1.0
CB A:MET150 4.3 8.8 1.0
O A:MET94 4.3 11.6 1.0
SD A:MET62 4.4 12.4 1.0
CA A:CYS136 4.6 9.3 1.0
CD A:PRO138 4.6 10.6 1.0
N A:ASN96 4.6 9.9 1.0
CA A:HIS145 4.8 9.2 1.0
CB A:MET62 4.8 11.3 1.0
C A:HIS95 4.8 10.6 1.0
N A:HIS95 4.9 11.6 1.0

Copper binding site 2 out of 6 in 2pp8

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Copper binding site 2 out of 6 in the Formate Bound to Oxidized Wild Type Afnir


Mono view


Stereo pair view

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

b:11.6
occ:1.00
NE2 A:HIS100 2.0 10.4 1.0
NE2 B:HIS306 2.1 10.3 1.0
NE2 A:HIS135 2.1 12.1 1.0
O2 A:FMT401 2.2 30.8 1.0
O1 A:FMT401 2.4 30.1 1.0
C A:FMT401 2.5 30.6 1.0
CE1 A:HIS100 2.9 9.8 1.0
CE1 B:HIS306 2.9 7.2 1.0
CD2 A:HIS135 3.0 10.2 1.0
CD2 A:HIS100 3.1 9.6 1.0
CE1 A:HIS135 3.1 10.8 1.0
CD2 B:HIS306 3.2 9.5 1.0
ND1 A:HIS100 4.1 10.8 1.0
ND1 B:HIS306 4.1 8.1 1.0
OD1 A:ASP98 4.1 16.2 0.5
CG A:HIS100 4.2 9.3 1.0
CG A:HIS135 4.2 9.4 1.0
ND1 A:HIS135 4.2 8.8 1.0
NE2 B:HIS255 4.2 14.2 1.0
O A:HOH1910 4.2 21.3 1.0
CG B:HIS306 4.2 8.2 1.0
CE1 B:HIS255 4.4 14.3 1.0
CG A:ASP98 4.5 13.8 0.5
CD2 B:HIS255 4.6 13.0 1.0
OD2 A:ASP98 4.7 15.8 0.5
CD2 B:LEU308 4.8 10.8 1.0
ND1 B:HIS255 4.9 13.0 1.0
CG1 B:ILE257 4.9 14.6 1.0

Copper binding site 3 out of 6 in 2pp8

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


Mono view


Stereo pair view

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

b:14.8
occ:1.00
ND1 B:HIS95 2.0 13.9 1.0
ND1 B:HIS145 2.1 14.6 1.0
SG B:CYS136 2.3 13.7 1.0
SD B:MET150 2.5 13.2 1.0
CE1 B:HIS145 2.9 15.0 1.0
CE1 B:HIS95 2.9 12.6 1.0
CG B:HIS95 3.1 14.3 1.0
CG B:HIS145 3.1 13.9 1.0
CB B:CYS136 3.1 13.2 1.0
CE B:MET150 3.2 14.8 1.0
CB B:HIS95 3.5 14.9 1.0
CB B:HIS145 3.6 12.7 1.0
CA B:HIS95 3.9 14.9 1.0
CG B:MET150 3.9 12.5 1.0
NE2 B:HIS145 4.1 14.0 1.0
NE2 B:HIS95 4.1 13.4 1.0
CG B:PRO138 4.2 16.0 1.0
CD2 B:HIS95 4.2 13.5 1.0
CD2 B:HIS145 4.2 15.3 1.0
SD B:MET62 4.3 15.6 1.0
O B:MET94 4.3 16.0 1.0
CB B:MET150 4.4 11.6 1.0
CD B:PRO138 4.6 15.1 1.0
CA B:CYS136 4.6 12.6 1.0
N B:ASN96 4.7 13.9 1.0
CA B:HIS145 4.8 12.7 1.0
C B:HIS95 4.8 14.8 1.0
CB B:MET62 4.9 13.4 1.0
N B:HIS95 4.9 15.5 1.0

Copper binding site 4 out of 6 in 2pp8

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Copper binding site 4 out of 6 in the Formate Bound to Oxidized Wild Type Afnir


Mono view


Stereo pair view

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

b:14.8
occ:1.00
NE2 B:HIS100 2.0 12.5 1.0
NE2 C:HIS306 2.0 11.2 1.0
NE2 B:HIS135 2.0 14.2 1.0
O2 B:FMT401 2.1 25.3 0.5
O1 B:FMT401 2.4 25.6 1.0
C B:FMT401 2.6 25.4 0.5
CE1 B:HIS100 2.9 12.3 1.0
CE1 C:HIS306 2.9 11.7 1.0
CD2 B:HIS135 3.0 13.2 1.0
CE1 B:HIS135 3.0 12.6 1.0
CD2 C:HIS306 3.1 10.7 1.0
CD2 B:HIS100 3.1 12.6 1.0
C B:FMT401 3.2 25.0 0.5
OD1 B:ASP98 3.9 18.4 0.5
ND1 B:HIS100 4.1 11.4 1.0
ND1 C:HIS306 4.1 10.1 1.0
ND1 B:HIS135 4.1 13.1 1.0
CG B:HIS135 4.2 13.2 1.0
CG B:HIS100 4.2 11.5 1.0
CG C:HIS306 4.2 11.1 1.0
NE2 C:HIS255 4.3 17.4 1.0
O B:HOH1880 4.3 27.9 1.0
O2 B:FMT401 4.4 24.3 0.5
CE1 C:HIS255 4.4 18.4 1.0
CG B:ASP98 4.4 16.4 0.5
CD2 C:HIS255 4.6 17.0 1.0
OD2 B:ASP98 4.7 17.6 0.5
ND1 C:HIS255 4.8 17.8 1.0
CD2 C:LEU308 4.9 13.3 1.0
CG1 C:ILE257 5.0 18.5 1.0
CG C:HIS255 5.0 15.9 1.0

Copper binding site 5 out of 6 in 2pp8

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Copper binding site 5 out of 6 in the Formate Bound to Oxidized Wild Type Afnir


Mono view


Stereo pair view

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

b:20.6
occ:1.00
ND1 C:HIS145 2.0 19.4 1.0
ND1 C:HIS95 2.0 19.4 1.0
SG C:CYS136 2.3 18.3 1.0
SD C:MET150 2.4 19.1 1.0
CE1 C:HIS145 2.9 19.6 1.0
CE1 C:HIS95 2.9 19.4 1.0
CG C:HIS145 3.1 17.6 1.0
CG C:HIS95 3.1 19.4 1.0
CB C:CYS136 3.1 16.4 1.0
CE C:MET150 3.3 18.9 1.0
CB C:HIS145 3.5 16.3 1.0
CB C:HIS95 3.5 19.6 1.0
CG C:MET150 3.8 17.0 1.0
CA C:HIS95 3.9 19.6 1.0
NE2 C:HIS145 4.1 18.2 1.0
NE2 C:HIS95 4.1 19.1 1.0
CG C:PRO138 4.2 19.5 1.0
CD2 C:HIS145 4.2 17.6 1.0
CD2 C:HIS95 4.2 19.6 1.0
O C:MET94 4.3 20.9 1.0
CB C:MET150 4.3 15.8 1.0
SD C:MET62 4.4 18.8 1.0
CD C:PRO138 4.6 18.7 1.0
CA C:CYS136 4.6 16.9 1.0
N C:ASN96 4.7 18.9 1.0
CA C:HIS145 4.8 15.8 1.0
CB C:MET62 4.8 18.5 1.0
C C:HIS95 4.9 19.8 1.0
N C:HIS95 4.9 20.5 1.0
C C:MET94 5.0 21.0 1.0

Copper binding site 6 out of 6 in 2pp8

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Copper binding site 6 out of 6 in the Formate Bound to Oxidized Wild Type Afnir


Mono view


Stereo pair view

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

b:17.7
occ:1.00
NE2 C:HIS100 2.0 15.5 1.0
NE2 C:HIS135 2.0 15.7 1.0
NE2 A:HIS306 2.0 13.3 1.0
O2 C:FMT401 2.5 29.4 0.5
O1 C:FMT401 2.5 29.8 1.0
C C:FMT401 2.8 29.6 0.5
CE1 C:HIS100 2.9 16.4 1.0
CE1 A:HIS306 2.9 13.1 1.0
CD2 C:HIS135 3.0 15.5 1.0
CE1 C:HIS135 3.1 14.8 1.0
CD2 A:HIS306 3.1 13.0 1.0
CD2 C:HIS100 3.1 14.9 1.0
C C:FMT401 3.4 29.7 0.5
OD1 C:ASP98 3.9 21.7 0.5
ND1 C:HIS100 4.1 14.7 1.0
ND1 A:HIS306 4.1 12.9 1.0
CG C:HIS135 4.1 14.9 1.0
ND1 C:HIS135 4.2 13.8 1.0
CG A:HIS306 4.2 12.7 1.0
CG C:HIS100 4.2 15.7 1.0
NE2 A:HIS255 4.3 18.4 1.0
CE1 A:HIS255 4.5 17.3 1.0
O2 C:FMT401 4.5 29.7 0.5
CG C:ASP98 4.5 20.4 0.5
O C:HOH1832 4.6 36.8 1.0
CD2 A:HIS255 4.7 17.8 1.0
OD2 C:ASP98 4.7 21.3 0.5
ND1 A:HIS255 4.9 16.3 1.0
CD2 A:LEU308 4.9 12.9 1.0
CG1 A:ILE257 5.0 19.0 1.0
CD1 A:LEU308 5.0 13.8 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: Thu Sep 3 16:47:52 2020
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