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Copper in PDB 3h4h: MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis

Enzymatic activity of MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis

All present enzymatic activity of MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis:
1.7.2.1;

Protein crystallography data

The structure of MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis, PDB code: 3h4h was solved by I.S.Macpherson, I.S.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.301, 102.077, 146.336, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.6

Copper Binding Sites:

The binding sites of Copper atom in the MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis (pdb code 3h4h). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis, PDB code: 3h4h:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3h4h

Go back to Copper Binding Sites List in 3h4h
Copper binding site 1 out of 6 in the MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1501

b:14.2
occ:1.00
 ND1 A:HIS145 2.0 12.3 1.0
ND1 A:HIS95 2.1 13.2 1.0
SG A:CYS136 2.2 13.6 1.0
SD A:MET150 2.5 13.2 1.0
CE1 A:HIS145 2.8 13.4 1.0
CE1 A:HIS95 3.0 14.3 1.0
CG A:HIS145 3.1 12.4 1.0
CB A:CYS136 3.1 11.7 1.0
CG A:HIS95 3.1 12.1 1.0
CE A:MET150 3.3 14.3 1.0
CB A:HIS95 3.5 13.6 1.0
CB A:HIS145 3.5 12.7 1.0
CA A:HIS95 3.8 13.2 1.0
CG A:MET150 3.9 11.3 1.0
NE2 A:HIS145 4.0 13.9 1.0
CD2 A:HIS145 4.1 15.3 1.0
NE2 A:HIS95 4.2 12.4 1.0
CG A:PRO138 4.2 17.3 1.0
CD2 A:HIS95 4.2 13.1 1.0
O A:THR94 4.3 16.5 1.0
CB A:MET150 4.3 10.2 1.0
SD A:MET62 4.3 15.5 1.0
CD A:PRO138 4.6 14.4 1.0
CA A:CYS136 4.6 12.1 1.0
N A:ASN96 4.6 12.3 1.0
CA A:HIS145 4.7 12.1 1.0
CB A:MET62 4.8 14.1 1.0
C A:HIS95 4.8 13.1 1.0
N A:HIS95 4.9 13.9 1.0
C A:THR94 5.0 15.7 1.0

Copper binding site 2 out of 6 in 3h4h

Go back to Copper Binding Sites List in 3h4h
Copper binding site 2 out of 6 in the MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1502

b:13.6
occ:1.00
 O A:HOH1337 1.9 25.6 1.0
NE2 A:HIS135 2.0 12.2 1.0
NE2 B:HIS306 2.0 13.1 1.0
NE2 A:HIS100 2.1 10.1 1.0
CD2 A:HIS135 3.0 13.1 1.0
CE1 A:HIS100 3.0 9.8 1.0
CE1 B:HIS306 3.0 9.6 1.0
CD2 B:HIS306 3.0 11.1 1.0
CE1 A:HIS135 3.1 13.1 1.0
CD2 A:HIS100 3.1 12.7 1.0
O B:HOH1347 3.4 68.6 1.0
OD1 A:ASP98 3.8 20.9 1.0
O A:HOH480 4.0 32.3 1.0
NE2 B:HIS255 4.1 13.9 1.0
CG A:HIS135 4.1 12.8 1.0
ND1 A:HIS100 4.1 12.4 1.0
ND1 B:HIS306 4.1 11.3 1.0
ND1 A:HIS135 4.1 11.7 1.0
CG B:HIS306 4.2 10.8 1.0
CG A:HIS100 4.2 10.9 1.0
CG A:ASP98 4.2 17.4 1.0
CE1 B:HIS255 4.4 14.8 1.0
CD2 B:HIS255 4.5 13.9 1.0
OD2 A:ASP98 4.5 15.1 1.0
O A:HOH511 4.6 53.5 1.0
O B:HOH532 4.8 16.9 1.0
ND1 B:HIS255 4.8 17.0 1.0
CG B:HIS255 4.9 13.1 1.0
CD1 B:LEU308 4.9 15.7 1.0

Copper binding site 3 out of 6 in 3h4h

Go back to Copper Binding Sites List in 3h4h
Copper binding site 3 out of 6 in the MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2501

b:18.2
occ:1.00
 ND1 B:HIS95 2.1 14.8 1.0
ND1 B:HIS145 2.1 19.1 1.0
SG B:CYS136 2.2 17.6 1.0
SD B:MET150 2.5 16.2 1.0
CE1 B:HIS145 3.0 21.4 1.0
CE1 B:HIS95 3.0 18.6 1.0
CG B:HIS95 3.1 17.3 1.0
CG B:HIS145 3.2 19.2 1.0
CB B:CYS136 3.2 16.2 1.0
CE B:MET150 3.4 17.5 1.0
CB B:HIS95 3.5 18.3 1.0
CB B:HIS145 3.6 18.8 1.0
CA B:HIS95 3.9 18.6 1.0
CG B:MET150 4.0 14.9 1.0
NE2 B:HIS145 4.1 18.8 1.0
NE2 B:HIS95 4.1 16.2 1.0
CG B:PRO138 4.2 21.4 1.0
O B:THR94 4.2 20.1 1.0
CD2 B:HIS145 4.2 19.2 1.0
CD2 B:HIS95 4.2 16.6 1.0
SD B:MET62 4.3 18.3 1.0
CB B:MET150 4.4 13.8 1.0
CA B:CYS136 4.6 16.2 1.0
CD B:PRO138 4.6 21.2 1.0
N B:ASN96 4.7 18.0 1.0
CA B:HIS145 4.8 18.1 1.0
CB B:MET62 4.8 16.6 1.0
C B:HIS95 4.8 18.7 1.0
N B:HIS95 4.9 19.4 1.0
C B:THR94 4.9 19.7 1.0

Copper binding site 4 out of 6 in 3h4h

Go back to Copper Binding Sites List in 3h4h
Copper binding site 4 out of 6 in the MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2502

b:17.9
occ:1.00
 O B:HOH1346 2.0 31.1 1.0
NE2 B:HIS135 2.0 15.1 1.0
NE2 B:HIS100 2.1 16.6 1.0
NE2 C:HIS306 2.1 14.3 1.0
CE1 B:HIS100 3.0 13.7 1.0
CD2 B:HIS135 3.0 14.6 1.0
CE1 B:HIS135 3.0 13.4 1.0
CD2 C:HIS306 3.1 16.3 1.0
CE1 C:HIS306 3.1 15.2 1.0
CD2 B:HIS100 3.1 16.9 1.0
OD1 B:ASP98 3.5 25.8 1.0
O B:HOH423 3.8 42.3 1.0
NE2 C:HIS255 4.0 19.9 1.0
ND1 B:HIS100 4.1 13.9 1.0
ND1 B:HIS135 4.1 14.6 1.0
CG B:HIS135 4.2 12.9 1.0
CG B:ASP98 4.2 21.1 1.0
ND1 C:HIS306 4.2 16.3 1.0
CG C:HIS306 4.2 13.6 1.0
CG B:HIS100 4.2 14.4 1.0
CD2 C:HIS255 4.3 20.8 1.0
CE1 C:HIS255 4.4 19.1 1.0
OD2 B:ASP98 4.6 19.0 1.0
CG C:HIS255 4.8 17.9 1.0
ND1 C:HIS255 4.8 19.3 1.0
O B:HOH544 4.8 20.3 1.0
CD1 C:LEU308 5.0 16.6 1.0

Copper binding site 5 out of 6 in 3h4h

Go back to Copper Binding Sites List in 3h4h
Copper binding site 5 out of 6 in the MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu3501

b:23.7
occ:1.00
 ND1 C:HIS145 2.0 21.9 1.0
ND1 C:HIS95 2.1 23.1 1.0
SG C:CYS136 2.2 21.8 1.0
SD C:MET150 2.5 20.1 1.0
CE1 C:HIS145 2.9 24.1 1.0
CE1 C:HIS95 3.0 23.4 1.0
CG C:HIS145 3.1 22.8 1.0
CB C:CYS136 3.1 22.3 1.0
CE C:MET150 3.2 20.3 1.0
CG C:HIS95 3.2 23.8 1.0
CB C:HIS145 3.5 22.0 1.0
CB C:HIS95 3.6 24.4 1.0
CG C:MET150 3.8 20.5 1.0
CA C:HIS95 3.8 24.5 1.0
NE2 C:HIS145 4.0 25.9 1.0
CD2 C:HIS145 4.1 23.9 1.0
NE2 C:HIS95 4.2 22.4 1.0
O C:THR94 4.2 27.0 1.0
CG C:PRO138 4.2 26.9 1.0
CD2 C:HIS95 4.3 24.9 1.0
CB C:MET150 4.3 20.7 1.0
SD C:MET62 4.5 23.1 1.0
CA C:CYS136 4.5 22.4 1.0
N C:ASN96 4.6 24.4 1.0
CD C:PRO138 4.6 25.8 1.0
CA C:HIS145 4.8 22.2 1.0
C C:HIS95 4.8 24.5 1.0
CB C:MET62 4.8 21.6 1.0
N C:HIS95 4.9 25.5 1.0
C C:THR94 4.9 26.3 1.0

Copper binding site 6 out of 6 in 3h4h

Go back to Copper Binding Sites List in 3h4h
Copper binding site 6 out of 6 in the MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of MET94THR/PHE312CYS Variant of Nitrite Reductase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu3502

b:20.5
occ:1.00
 O C:HOH1339 2.0 32.9 1.0
NE2 C:HIS100 2.0 19.2 1.0
NE2 C:HIS135 2.1 19.8 1.0
NE2 A:HIS306 2.1 16.0 1.0
CE1 C:HIS100 2.9 17.2 1.0
CD2 C:HIS135 3.0 18.6 1.0
CE1 A:HIS306 3.0 18.4 1.0
CD2 C:HIS100 3.1 18.3 1.0
CD2 A:HIS306 3.1 18.5 1.0
CE1 C:HIS135 3.1 17.5 1.0
OD1 C:ASP98 3.6 29.7 1.0
ND1 C:HIS100 4.1 19.2 1.0
O C:HOH667 4.1 42.2 1.0
ND1 A:HIS306 4.2 17.8 1.0
CG C:HIS135 4.2 19.2 1.0
CG C:HIS100 4.2 20.2 1.0
NE2 A:HIS255 4.2 21.3 1.0
ND1 C:HIS135 4.2 19.0 1.0
CG A:HIS306 4.3 15.5 1.0
CG C:ASP98 4.3 24.6 1.0
CE1 A:HIS255 4.4 24.6 1.0
CD2 A:HIS255 4.5 22.4 1.0
OD2 C:ASP98 4.7 23.9 1.0
ND1 A:HIS255 4.8 21.8 1.0
O A:HOH379 4.9 25.4 1.0
CG A:HIS255 4.9 19.2 1.0
CD1 A:LEU308 4.9 21.6 1.0
CG1 A:ILE257 5.0 22.3 1.0

Reference:

I.S.Macpherson, F.I.Rosell, M.Scofield, A.G.Mauk, M.E.Murphy. Directed Evolution of Copper Nitrite Reductase to A Chromogenic Reductant. Protein Eng.Des.Sel. V. 23 137 2010.
ISSN: ISSN 1741-0126
PubMed: 20083495
DOI: 10.1093/PROTEIN/GZP084
Page generated: Wed Jul 31 01:00:35 2024

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