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Copper in PDB 2p80: Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis

Enzymatic activity of Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis

All present enzymatic activity of Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis:
1.7.2.1;

Other elements in 2p80:

The structure of Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis also contains other interesting chemical elements:

Gadolinium (Gd) 180 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis (pdb code 2p80). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 7 binding sites of Copper where determined in the Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis, PDB code: 2p80:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7;

Copper binding site 1 out of 7 in 2p80

Go back to Copper Binding Sites List in 2p80
Copper binding site 1 out of 7 in the Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu345

b:9.4
occ:1.00
ND1 A:HIS145 2.1 9.4 1.0
ND1 A:HIS95 2.1 8.6 1.0
SG A:CYS136 2.2 9.4 1.0
SD A:MET150 2.4 8.8 1.0
HB3 A:HIS145 2.8 0.0 1.0
CE1 A:HIS145 3.0 9.4 1.0
HB3 A:HIS95 3.0 0.0 1.0
CE1 A:HIS95 3.0 9.4 1.0
HE1 A:MET150 3.1 0.0 1.0
HB3 A:CYS136 3.1 0.0 1.0
CG A:HIS95 3.1 8.8 1.0
CG A:HIS145 3.1 7.9 1.0
HE1 A:HIS145 3.1 0.0 1.0
CB A:CYS136 3.1 7.6 1.0
HA A:HIS95 3.2 0.0 1.0
HE1 A:HIS95 3.2 0.0 1.0
CE A:MET150 3.3 9.5 1.0
HB2 A:CYS136 3.4 0.0 1.0
CB A:HIS95 3.4 8.8 1.0
CB A:HIS145 3.5 7.7 1.0
HD3 A:PRO138 3.6 0.0 1.0
HE2 A:MET150 3.6 0.0 1.0
HG3 A:PRO138 3.7 0.0 1.0
CG A:MET150 3.8 7.4 1.0
CA A:HIS95 3.8 8.7 1.0
HG2 A:PRO138 3.9 0.0 1.0
HG2 A:MET150 3.9 0.0 1.0
H A:ASN96 3.9 0.0 1.0
HB3 A:MET62 4.1 0.0 1.0
NE2 A:HIS145 4.1 9.2 1.0
CG A:PRO138 4.1 9.7 1.0
NE2 A:HIS95 4.1 9.6 1.0
HB2 A:HIS145 4.2 0.0 1.0
CD2 A:HIS145 4.2 9.7 1.0
HB3 A:MET150 4.2 0.0 1.0
CD2 A:HIS95 4.2 9.2 1.0
HB2 A:MET150 4.2 0.0 1.0
HE3 A:MET150 4.2 0.0 1.0
CD A:PRO138 4.2 8.8 1.0
CB A:MET150 4.3 7.6 1.0
SD A:MET62 4.3 11.1 1.0
HA A:HIS145 4.4 0.0 1.0
HB2 A:HIS95 4.5 0.0 1.0
HD2 A:PRO138 4.5 0.0 1.0
CA A:HIS145 4.5 7.7 1.0
CA A:CYS136 4.5 7.9 1.0
O A:MET94 4.6 9.3 1.0
N A:ASN96 4.6 8.8 1.0
HG3 A:MET150 4.7 0.0 1.0
C A:HIS95 4.8 8.9 1.0
HZ A:PHE64 4.8 0.0 1.0
HB2 A:MET62 4.8 0.0 1.0
C A:CYS136 4.8 8.2 1.0
CB A:MET62 4.9 9.6 1.0
N A:HIS95 4.9 8.7 1.0
HE2 A:HIS145 5.0 0.0 1.0

Copper binding site 2 out of 7 in 2p80

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Copper binding site 2 out of 7 in the Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu346

b:9.2
occ:1.00
NE2 A:HIS100 2.0 8.3 1.0
NE2 B:HIS306 2.1 8.1 1.0
NE2 A:HIS135 2.1 8.8 1.0
CE1 A:HIS100 2.9 8.0 1.0
CE1 B:HIS306 3.0 7.9 1.0
CE1 A:HIS135 3.1 7.0 1.0
CD2 B:HIS306 3.1 7.7 1.0
CD2 A:HIS135 3.1 8.3 1.0
CD2 A:HIS100 3.1 7.6 1.0
HE1 A:HIS100 3.1 0.0 1.0
HE1 B:HIS306 3.2 0.0 1.0
HE1 A:HIS135 3.3 0.0 1.0
HD2 A:HIS135 3.3 0.0 1.0
HD2 B:HIS306 3.3 0.0 1.0
HD2 A:HIS100 3.4 0.0 1.0
CE1 B:HIS255 3.8 13.6 1.0
NE2 B:HIS255 3.9 12.8 1.0
HE1 B:HIS255 3.9 0.0 1.0
HE2 B:HIS255 4.0 0.0 1.0
ND1 A:HIS100 4.1 7.8 1.0
ND1 B:HIS306 4.2 7.5 1.0
CG A:HIS100 4.2 7.2 1.0
ND1 A:HIS135 4.2 7.9 1.0
CG B:HIS306 4.3 7.5 1.0
CG A:HIS135 4.3 8.1 1.0
ND1 B:HIS255 4.3 11.9 1.0
HA2 A:GLY286 4.3 0.0 1.0
CD2 B:HIS255 4.4 12.7 1.0
OD2 A:ASP98 4.5 19.0 1.0
HD22 B:LEU308 4.6 0.0 1.0
CG B:HIS255 4.6 9.3 1.0
HA3 A:GLY286 4.7 0.0 1.0
HD1 B:HIS255 4.7 0.0 1.0
HD23 B:LEU308 4.9 0.0 1.0
HD2 B:HIS255 4.9 0.0 1.0
HG12 B:ILE257 4.9 0.0 1.0
HG12 A:VAL133 5.0 0.0 1.0
HD1 A:HIS100 5.0 0.0 1.0
CA A:GLY286 5.0 7.3 1.0

Copper binding site 3 out of 7 in 2p80

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Copper binding site 3 out of 7 in the Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu345

b:11.1
occ:1.00
ND1 B:HIS145 2.1 10.6 1.0
ND1 B:HIS95 2.1 9.7 1.0
SG B:CYS136 2.2 11.0 1.0
SD B:MET150 2.5 10.2 1.0
HB3 B:HIS145 2.8 0.0 1.0
CE1 B:HIS145 3.0 11.9 1.0
CE1 B:HIS95 3.0 10.2 1.0
HE3 B:MET150 3.0 0.0 1.0
HB3 B:HIS95 3.1 0.0 1.0
HB3 B:CYS136 3.1 0.0 1.0
CG B:HIS95 3.1 10.3 1.0
CG B:HIS145 3.1 10.0 1.0
HE1 B:HIS145 3.1 0.0 1.0
HA B:HIS95 3.1 0.0 1.0
CB B:CYS136 3.2 10.2 1.0
HE1 B:HIS95 3.2 0.0 1.0
CE B:MET150 3.2 11.3 1.0
HB2 B:CYS136 3.5 0.0 1.0
CB B:HIS95 3.5 10.4 1.0
CB B:HIS145 3.5 9.8 1.0
HG3 B:PRO138 3.6 0.0 1.0
HD3 B:PRO138 3.6 0.0 1.0
HE1 B:MET150 3.6 0.0 1.0
HG2 B:PRO138 3.8 0.0 1.0
CA B:HIS95 3.8 10.5 1.0
CG B:MET150 3.9 9.7 1.0
HG2 B:MET150 4.0 0.0 1.0
H B:ASN96 4.0 0.0 1.0
CG B:PRO138 4.0 12.3 1.0
NE2 B:HIS145 4.1 11.8 1.0
NE2 B:HIS95 4.1 10.8 1.0
HB2 B:HIS145 4.1 0.0 1.0
HB3 B:MET62 4.2 0.0 1.0
CD2 B:HIS95 4.2 10.7 1.0
CD2 B:HIS145 4.2 11.3 1.0
CD B:PRO138 4.2 10.2 1.0
HE2 B:MET150 4.2 0.0 1.0
SD B:MET62 4.3 12.4 1.0
HB2 B:MET150 4.3 0.0 1.0
HB3 B:MET150 4.3 0.0 1.0
CB B:MET150 4.4 9.3 1.0
HB2 B:HIS95 4.5 0.0 1.0
HA B:HIS145 4.5 0.0 1.0
HD2 B:PRO138 4.5 0.0 1.0
CA B:CYS136 4.5 9.8 1.0
O B:MET94 4.6 11.9 1.0
CA B:HIS145 4.6 9.5 1.0
N B:ASN96 4.6 10.6 1.0
C B:HIS95 4.7 10.8 1.0
HG3 B:MET150 4.7 0.0 1.0
HZ B:PHE64 4.8 0.0 1.0
C B:CYS136 4.8 9.6 1.0
HB2 B:MET62 4.8 0.0 1.0
N B:HIS95 4.9 10.7 1.0
CB B:MET62 4.9 10.6 1.0
HE2 B:HIS145 5.0 0.0 1.0
HE2 B:HIS95 5.0 0.0 1.0

Copper binding site 4 out of 7 in 2p80

Go back to Copper Binding Sites List in 2p80
Copper binding site 4 out of 7 in the Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu346

b:10.6
occ:1.00
NE2 B:HIS100 2.1 9.0 1.0
NE2 B:HIS135 2.1 9.8 1.0
NE2 C:HIS306 2.1 9.8 1.0
CE1 B:HIS100 3.0 9.7 1.0
CE1 C:HIS306 3.0 9.9 1.0
CD2 B:HIS135 3.1 9.5 1.0
CE1 B:HIS135 3.1 9.6 1.0
CD2 B:HIS100 3.1 8.2 1.0
HE1 B:HIS100 3.1 0.0 1.0
CD2 C:HIS306 3.2 9.3 1.0
HE1 C:HIS306 3.2 0.0 1.0
HD2 B:HIS135 3.3 0.0 1.0
HE1 B:HIS135 3.3 0.0 1.0
HD2 C:HIS306 3.4 0.0 1.0
HD2 B:HIS100 3.4 0.0 1.0
NE2 C:HIS255 3.9 14.3 1.0
HE2 C:HIS255 3.9 0.0 1.0
CE1 C:HIS255 4.1 13.2 1.0
ND1 B:HIS100 4.1 9.0 1.0
ND1 B:HIS135 4.2 9.1 1.0
CG B:HIS100 4.2 8.9 1.0
ND1 C:HIS306 4.2 8.7 1.0
CG B:HIS135 4.2 9.2 1.0
CD2 C:HIS255 4.2 14.3 1.0
CG C:HIS306 4.3 9.7 1.0
HE1 C:HIS255 4.3 0.0 1.0
HA2 B:GLY286 4.3 0.0 1.0
HD23 C:LEU308 4.4 0.0 1.0
OD2 B:ASP98 4.4 20.7 1.0
ND1 C:HIS255 4.6 12.4 1.0
HD2 C:HIS255 4.6 0.0 1.0
CG C:HIS255 4.7 11.0 1.0
HA3 B:GLY286 4.8 0.0 1.0
HG12 C:ILE257 4.9 0.0 1.0
HD1 B:HIS100 5.0 0.0 1.0

Copper binding site 5 out of 7 in 2p80

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Copper binding site 5 out of 7 in the Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu345

b:14.3
occ:1.00
ND1 C:HIS145 2.1 13.7 1.0
ND1 C:HIS95 2.1 14.6 1.0
SG C:CYS136 2.2 13.7 1.0
SD C:MET150 2.5 13.1 1.0
HB3 C:HIS145 2.8 0.0 1.0
CE1 C:HIS145 3.0 14.8 1.0
HB3 C:HIS95 3.0 0.0 1.0
CE1 C:HIS95 3.0 13.5 1.0
HB3 C:CYS136 3.0 0.0 1.0
HE3 C:MET150 3.0 0.0 1.0
CG C:HIS145 3.1 11.6 1.0
CG C:HIS95 3.1 13.8 1.0
CB C:CYS136 3.1 12.5 1.0
HA C:HIS95 3.2 0.0 1.0
HE1 C:HIS145 3.2 0.0 1.0
HE1 C:HIS95 3.2 0.0 1.0
CE C:MET150 3.3 12.8 1.0
CB C:HIS145 3.4 11.2 1.0
CB C:HIS95 3.4 14.1 1.0
HB2 C:CYS136 3.4 0.0 1.0
HD3 C:PRO138 3.5 0.0 1.0
HG3 C:PRO138 3.5 0.0 1.0
HE1 C:MET150 3.6 0.0 1.0
HG2 C:PRO138 3.7 0.0 1.0
CA C:HIS95 3.8 13.7 1.0
CG C:MET150 3.9 12.7 1.0
H C:ASN96 3.9 0.0 1.0
HG2 C:MET150 3.9 0.0 1.0
CG C:PRO138 4.0 14.1 1.0
HB2 C:HIS145 4.1 0.0 1.0
CD C:PRO138 4.1 13.3 1.0
NE2 C:HIS145 4.1 13.7 1.0
NE2 C:HIS95 4.1 14.2 1.0
CD2 C:HIS95 4.2 14.3 1.0
HB3 C:MET62 4.2 0.0 1.0
CD2 C:HIS145 4.2 13.2 1.0
HE2 C:MET150 4.2 0.0 1.0
SD C:MET62 4.3 14.5 1.0
HB2 C:MET150 4.3 0.0 1.0
HB3 C:MET150 4.3 0.0 1.0
HD2 C:PRO138 4.4 0.0 1.0
CB C:MET150 4.4 11.3 1.0
HA C:HIS145 4.4 0.0 1.0
HB2 C:HIS95 4.4 0.0 1.0
CA C:CYS136 4.5 12.1 1.0
CA C:HIS145 4.6 11.3 1.0
N C:ASN96 4.6 13.5 1.0
O C:MET94 4.7 15.1 1.0
HG3 C:MET150 4.7 0.0 1.0
HB2 C:MET62 4.7 0.0 1.0
C C:HIS95 4.8 13.5 1.0
C C:CYS136 4.8 12.2 1.0
HZ C:PHE64 4.9 0.0 1.0
CB C:MET62 4.9 13.4 1.0
N C:HIS95 4.9 13.9 1.0

Copper binding site 6 out of 7 in 2p80

Go back to Copper Binding Sites List in 2p80
Copper binding site 6 out of 7 in the Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu346

b:11.8
occ:1.00
NE2 C:HIS100 2.0 10.3 1.0
NE2 A:HIS306 2.1 10.8 1.0
NE2 C:HIS135 2.1 11.3 1.0
CE1 C:HIS100 2.9 10.4 1.0
CE1 A:HIS306 3.0 9.9 1.0
CD2 C:HIS135 3.1 10.5 1.0
CE1 C:HIS135 3.1 10.3 1.0
HE1 C:HIS100 3.1 0.0 1.0
CD2 C:HIS100 3.1 10.3 1.0
CD2 A:HIS306 3.1 9.9 1.0
HE1 A:HIS306 3.2 0.0 1.0
HD2 C:HIS135 3.3 0.0 1.0
HE1 C:HIS135 3.3 0.0 1.0
HD2 A:HIS306 3.4 0.0 1.0
HD2 C:HIS100 3.4 0.0 1.0
NE2 A:HIS255 3.9 14.8 1.0
HE2 A:HIS255 3.9 0.0 1.0
ND1 C:HIS100 4.1 9.8 1.0
CE1 A:HIS255 4.1 15.3 1.0
CD2 A:HIS255 4.2 14.0 1.0
ND1 A:HIS306 4.2 9.2 1.0
CG C:HIS100 4.2 9.9 1.0
ND1 C:HIS135 4.2 11.1 1.0
CG A:HIS306 4.3 10.2 1.0
CG C:HIS135 4.3 10.7 1.0
HD23 A:LEU308 4.3 0.0 1.0
HA2 C:GLY286 4.3 0.0 1.0
HE1 A:HIS255 4.4 0.0 1.0
HD2 A:HIS255 4.5 0.0 1.0
OD2 C:ASP98 4.5 24.2 1.0
ND1 A:HIS255 4.6 13.7 1.0
HG13 C:VAL133 4.6 0.0 1.0
CG A:HIS255 4.6 11.0 1.0
HA3 C:GLY286 4.7 0.0 1.0
HG12 A:ILE257 4.7 0.0 1.0
HD1 C:HIS100 5.0 0.0 1.0
HG1 A:THR280 5.0 0.0 1.0
CA C:GLY286 5.0 8.9 1.0

Copper binding site 7 out of 7 in 2p80

Go back to Copper Binding Sites List in 2p80
Copper binding site 7 out of 7 in the Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Solution Structure of the Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu124

b:27.4
occ:1.00
ND1 D:HIS40 2.1 20.5 1.0
SG D:CYS78 2.2 21.1 1.0
ND1 D:HIS81 2.3 26.6 1.0
HB2 D:HIS81 2.8 0.0 1.0
HA D:HIS40 2.8 0.0 1.0
SD D:MET86 2.8 20.5 1.0
HB3 D:HIS40 3.0 0.0 1.0
CE1 D:HIS40 3.1 19.4 1.0
CG D:HIS40 3.1 20.3 1.0
CB D:CYS78 3.2 15.4 1.0
HG2 D:PRO80 3.2 0.0 1.0
HB2 D:CYS78 3.2 0.0 1.0
CG D:HIS81 3.3 22.6 1.0
CE1 D:HIS81 3.3 26.4 1.0
HE1 D:HIS40 3.3 0.0 1.0
HB3 D:CYS78 3.3 0.0 1.0
HE1 D:MET86 3.4 0.0 1.0
CB D:HIS40 3.4 18.0 1.0
CE D:MET86 3.5 14.5 1.0
CB D:HIS81 3.5 16.9 1.0
HE1 D:HIS81 3.5 0.0 1.0
HE2 D:MET86 3.5 0.0 1.0
H D:HIS81 3.5 0.0 1.0
CA D:HIS40 3.6 21.9 1.0
O D:GLY39 3.8 29.1 1.0
H D:ASN41 3.9 0.0 1.0
HD2 D:PRO80 4.2 0.0 1.0
NE2 D:HIS40 4.2 21.1 1.0
CD2 D:HIS40 4.2 21.1 1.0
N D:HIS81 4.2 18.9 1.0
HB3 D:HIS81 4.2 0.0 1.0
CG D:MET86 4.2 14.0 1.0
CG D:PRO80 4.3 25.2 1.0
HG2 D:MET86 4.4 0.0 1.0
HB3 D:MET86 4.4 0.0 1.0
HG3 D:MET16 4.4 0.0 1.0
C D:GLY39 4.4 28.0 1.0
CD2 D:HIS81 4.4 21.1 1.0
NE2 D:HIS81 4.4 20.3 1.0
N D:HIS40 4.4 23.2 1.0
HB2 D:HIS40 4.4 0.0 1.0
CA D:HIS81 4.5 15.7 1.0
HB2 D:MET86 4.5 0.0 1.0
HE3 D:MET86 4.5 0.0 1.0
CA D:CYS78 4.6 15.0 1.0
CB D:MET86 4.6 14.5 1.0
N D:ASN41 4.6 19.6 1.0
HB3 D:MET16 4.7 0.0 1.0
C D:HIS40 4.7 22.0 1.0
CD D:PRO80 4.8 23.6 1.0
HG3 D:PRO80 4.8 0.0 1.0
SD D:MET16 4.8 25.9 1.0
HB2 D:PRO80 4.9 0.0 1.0
HA D:CYS78 4.9 0.0 1.0
HB3 D:MET7 4.9 0.0 1.0
HG2 D:MET7 5.0 0.0 1.0

Reference:

M.D.Vlasie, R.Fernandez-Busnadiego, M.Prudencio, M.Ubbink. Low Resolution Solution Structure of the 152 kDa Complex Between Nitrite Reductase and Pseudoazurin From A. Faecalis By Paramagnetic uc(Nmr). To Be Published.
Page generated: Sun Dec 13 11:06:35 2020

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