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Copper in PDB 3h4f: MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis

Enzymatic activity of MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis

All present enzymatic activity of MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis:
1.7.2.1;

Protein crystallography data

The structure of MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis, PDB code: 3h4f was solved by I.S.Macpherson, F.I.Rosell, M.Scofield, A.G.Mauk, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.52 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.132, 102.223, 146.145, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 22.7

Copper Binding Sites:

The binding sites of Copper atom in the MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis (pdb code 3h4f). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis, PDB code: 3h4f:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3h4f

Go back to Copper Binding Sites List in 3h4f
Copper binding site 1 out of 6 in the MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:16.2
occ:1.00
 ND1 A:HIS145 2.1 13.0 1.0
SG A:CYS136 2.1 12.5 1.0
ND1 A:HIS95 2.2 16.6 1.0
SD A:MET150 2.4 12.4 1.0
CE1 A:HIS145 3.0 12.4 1.0
CG A:HIS145 3.1 12.7 1.0
CB A:CYS136 3.2 11.8 1.0
CE1 A:HIS95 3.2 16.3 1.0
CG A:HIS95 3.2 16.3 1.0
CE A:MET150 3.4 10.2 1.0
CB A:HIS95 3.5 14.8 1.0
CB A:HIS145 3.5 12.7 1.0
CG A:MET150 3.7 10.3 1.0
CA A:HIS95 3.9 15.2 1.0
NE2 A:HIS145 4.1 11.8 1.0
CB A:MET150 4.2 11.3 1.0
CD2 A:HIS145 4.2 12.0 1.0
NE2 A:HIS95 4.3 16.9 1.0
CD2 A:HIS95 4.3 15.5 1.0
CG A:PRO138 4.4 13.8 1.0
O A:MET94 4.4 14.9 1.0
CA A:CYS136 4.6 11.7 1.0
CA A:HIS145 4.7 12.5 1.0
CB A:LEU62 4.7 13.8 1.0
N A:ASN96 4.7 15.8 1.0
CD1 A:LEU62 4.7 12.1 1.0
CD A:PRO138 4.8 13.5 1.0
C A:HIS95 4.9 15.1 1.0
N A:HIS95 5.0 15.3 1.0

Copper binding site 2 out of 6 in 3h4f

Go back to Copper Binding Sites List in 3h4f
Copper binding site 2 out of 6 in the MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:17.9
occ:1.00
 NE2 A:HIS100 2.0 12.0 1.0
NE2 B:HIS306 2.1 11.6 1.0
NE2 A:HIS135 2.2 9.9 1.0
O B:HOH2121 2.2 26.4 1.0
CE1 A:HIS100 3.0 13.4 1.0
CE1 B:HIS306 3.0 11.8 1.0
CE1 A:HIS135 3.1 12.7 1.0
CD2 A:HIS100 3.1 11.3 1.0
CD2 B:HIS306 3.1 12.7 1.0
CD2 A:HIS135 3.2 11.7 1.0
ND1 A:HIS100 4.1 12.4 1.0
ND1 B:HIS306 4.1 13.0 1.0
CG A:HIS100 4.2 12.9 1.0
NE2 B:HIS255 4.2 16.4 1.0
ND1 A:HIS135 4.2 11.6 1.0
CG B:HIS306 4.2 13.0 1.0
CG A:HIS135 4.3 12.4 1.0
CE1 B:HIS255 4.4 15.2 1.0
CD2 B:HIS255 4.6 15.4 1.0
ND1 B:HIS255 4.8 16.1 1.0
CD2 B:LEU308 4.8 13.0 1.0
OD1 A:ASP98 4.9 21.6 1.0
CG1 B:ILE257 4.9 15.9 1.0
CG B:HIS255 4.9 15.9 1.0

Copper binding site 3 out of 6 in 3h4f

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Copper binding site 3 out of 6 in the MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:21.7
occ:1.00
 ND1 B:HIS95 2.1 18.4 1.0
ND1 B:HIS145 2.1 16.2 1.0
SG B:CYS136 2.1 16.4 1.0
SD B:MET150 2.5 16.3 1.0
CE1 B:HIS145 3.0 16.3 1.0
CE1 B:HIS95 3.0 17.8 1.0
CG B:HIS95 3.1 19.2 1.0
CG B:HIS145 3.1 17.1 1.0
CB B:CYS136 3.2 16.3 1.0
CE B:MET150 3.4 16.8 1.0
CB B:HIS95 3.4 20.6 1.0
CB B:HIS145 3.5 17.5 1.0
CG B:MET150 3.7 14.9 1.0
CA B:HIS95 4.0 20.8 1.0
NE2 B:HIS145 4.1 16.7 1.0
NE2 B:HIS95 4.1 17.7 1.0
CD2 B:HIS95 4.2 18.9 1.0
CD2 B:HIS145 4.2 16.6 1.0
CB B:MET150 4.2 15.8 1.0
CG B:PRO138 4.4 20.4 1.0
O B:MET94 4.4 21.7 1.0
CD1 B:LEU62 4.5 11.8 1.0
CA B:CYS136 4.6 17.0 1.0
CB B:LEU62 4.7 16.2 1.0
CA B:HIS145 4.7 17.3 1.0
CD B:PRO138 4.8 19.6 1.0
N B:ASN96 4.8 20.3 1.0
N B:HIS95 5.0 21.4 1.0

Copper binding site 4 out of 6 in 3h4f

Go back to Copper Binding Sites List in 3h4f
Copper binding site 4 out of 6 in the MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:22.2
occ:1.00
 NE2 C:HIS306 2.0 18.1 1.0
NE2 B:HIS100 2.0 13.3 1.0
NE2 B:HIS135 2.2 12.8 1.0
O C:HOH2120 2.3 24.0 1.0
CE1 C:HIS306 3.0 17.6 1.0
CE1 B:HIS100 3.0 14.2 1.0
CD2 C:HIS306 3.1 17.7 1.0
CD2 B:HIS100 3.1 13.8 1.0
CD2 B:HIS135 3.2 12.8 1.0
CE1 B:HIS135 3.2 13.5 1.0
NE2 C:HIS255 4.1 18.7 1.0
ND1 C:HIS306 4.1 18.5 1.0
ND1 B:HIS100 4.1 14.0 1.0
CG C:HIS306 4.2 17.1 1.0
CG B:HIS100 4.2 15.6 1.0
CE1 C:HIS255 4.3 18.8 1.0
ND1 B:HIS135 4.3 14.3 1.0
CG B:HIS135 4.3 14.3 1.0
CD2 C:HIS255 4.5 18.4 1.0
CD2 C:LEU308 4.8 15.4 1.0
ND1 C:HIS255 4.8 18.6 1.0
CG C:HIS255 4.9 17.6 1.0
OD1 B:ASP98 4.9 29.6 1.0
O C:HOH1575 5.0 17.5 1.0
CG1 C:ILE257 5.0 20.0 1.0

Copper binding site 5 out of 6 in 3h4f

Go back to Copper Binding Sites List in 3h4f
Copper binding site 5 out of 6 in the MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:29.9
occ:1.00
 ND1 C:HIS145 2.0 23.6 1.0
SG C:CYS136 2.2 23.8 1.0
ND1 C:HIS95 2.2 27.9 1.0
SD C:MET150 2.5 21.3 1.0
CE1 C:HIS145 2.8 25.3 1.0
CG C:HIS145 3.1 22.9 1.0
CG C:HIS95 3.2 27.5 1.0
CB C:CYS136 3.2 21.8 1.0
CE1 C:HIS95 3.2 27.1 1.0
CE C:MET150 3.4 21.7 1.0
CB C:HIS95 3.5 27.6 1.0
CB C:HIS145 3.5 21.1 1.0
CG C:MET150 3.7 21.1 1.0
CA C:HIS95 3.8 27.7 1.0
NE2 C:HIS145 3.9 25.2 1.0
CD2 C:HIS145 4.1 23.4 1.0
CB C:MET150 4.2 20.7 1.0
O C:MET94 4.2 29.0 1.0
NE2 C:HIS95 4.3 27.3 1.0
CG C:PRO138 4.4 23.6 1.0
CD2 C:HIS95 4.4 27.8 1.0
CD1 C:LEU62 4.5 23.2 1.0
N C:ASN96 4.6 27.0 1.0
CB C:LEU62 4.6 24.8 1.0
CA C:CYS136 4.7 22.1 1.0
CA C:HIS145 4.7 21.0 1.0
CD C:PRO138 4.7 22.8 1.0
C C:HIS95 4.8 27.6 1.0
N C:HIS95 4.8 28.2 1.0
C C:MET94 5.0 29.2 1.0
O C:ASN96 5.0 26.4 1.0

Copper binding site 6 out of 6 in 3h4f

Go back to Copper Binding Sites List in 3h4f
Copper binding site 6 out of 6 in the MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of MET62LEU Variant of Nitrite Reductase From Alcaligenes Faeclis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:24.3
occ:1.00
 NE2 C:HIS135 2.0 23.1 1.0
NE2 C:HIS100 2.1 18.3 1.0
NE2 A:HIS306 2.1 16.9 1.0
O C:HOH2122 2.2 18.8 1.0
O C:HOH1703 2.2 33.4 1.0
CE1 C:HIS135 3.0 21.2 1.0
CE1 C:HIS100 3.0 19.7 1.0
CD2 A:HIS306 3.0 17.1 1.0
CD2 C:HIS135 3.1 22.0 1.0
CE1 A:HIS306 3.1 15.8 1.0
CD2 C:HIS100 3.2 19.6 1.0
ND1 C:HIS135 4.1 20.7 1.0
ND1 C:HIS100 4.2 19.3 1.0
CG C:HIS135 4.2 20.6 1.0
NE2 A:HIS255 4.2 22.4 1.0
CG A:HIS306 4.2 16.2 1.0
ND1 A:HIS306 4.2 16.1 1.0
CG C:HIS100 4.3 21.0 1.0
CE1 A:HIS255 4.5 22.7 1.0
CD2 A:HIS255 4.5 21.5 1.0
CG1 A:ILE257 4.8 20.5 1.0
CD2 A:LEU308 4.8 19.0 1.0
ND1 A:HIS255 4.9 21.0 1.0
CG A:HIS255 4.9 19.6 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 00:59:30 2024

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