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Copper in PDB 2zon: Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C

Enzymatic activity of Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C

All present enzymatic activity of Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C:
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C, PDB code: 2zon was solved by M.Nojiri, H.Koteishi, K.Yamaguchi, S.Suzuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.345, 103.942, 163.144, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.5

Other elements in 2zon:

The structure of Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C also contains other interesting chemical elements:

Iron (Fe) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C (pdb code 2zon). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C, PDB code: 2zon:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2zon

Go back to Copper Binding Sites List in 2zon
Copper binding site 1 out of 6 in the Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu400

b:17.8
occ:1.00
ND1 A:HIS89 2.1 14.9 1.0
ND1 A:HIS139 2.1 14.3 1.0
SG A:CYS130 2.2 14.9 1.0
SD A:MET144 2.6 17.5 1.0
CE1 A:HIS139 3.0 14.8 1.0
CE1 A:HIS89 3.0 17.1 1.0
CG A:HIS89 3.1 14.2 1.0
CG A:HIS139 3.1 13.9 1.0
CB A:CYS130 3.1 14.4 1.0
CE A:MET144 3.3 17.6 1.0
CB A:HIS89 3.5 14.7 1.0
CB A:HIS139 3.5 13.4 1.0
CA A:HIS89 3.9 15.0 1.0
CG A:PRO132 4.0 14.3 1.0
CG A:MET144 4.1 15.7 1.0
NE2 A:HIS139 4.2 16.0 1.0
NE2 A:HIS89 4.2 16.3 1.0
O A:PRO88 4.2 16.0 1.0
CD2 A:HIS139 4.2 14.8 1.0
CD2 A:HIS89 4.2 15.3 1.0
SD A:MET56 4.3 17.7 1.0
CD A:PRO132 4.4 14.9 1.0
CA A:CYS130 4.6 13.3 1.0
CB A:MET144 4.6 14.0 1.0
CA A:HIS139 4.7 13.0 1.0
N A:ASN90 4.7 13.5 1.0
N A:HIS89 4.9 15.3 1.0
C A:HIS89 4.9 14.5 1.0
C A:PRO88 4.9 15.8 1.0

Copper binding site 2 out of 6 in 2zon

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Copper binding site 2 out of 6 in the Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:15.2
occ:1.00
NE2 B:HIS300 2.0 13.4 1.0
NE2 A:HIS129 2.0 14.4 1.0
NE2 A:HIS94 2.1 9.9 1.0
O A:HOH622 2.1 29.3 1.0
CD2 A:HIS129 2.9 12.9 1.0
CE1 A:HIS94 2.9 10.7 1.0
CE1 B:HIS300 3.0 10.1 1.0
CD2 B:HIS300 3.0 10.6 1.0
CE1 A:HIS129 3.1 14.2 1.0
CD2 A:HIS94 3.2 12.4 1.0
OD2 A:ASP92 3.8 23.2 1.0
NE2 B:HIS249 3.9 20.4 1.0
ND1 B:HIS300 4.1 10.3 1.0
ND1 A:HIS94 4.1 10.9 1.0
CG A:HIS129 4.1 13.3 1.0
CG B:HIS300 4.1 11.0 1.0
ND1 A:HIS129 4.2 13.6 1.0
CG A:HIS94 4.3 11.0 1.0
CE1 B:HIS249 4.3 18.3 1.0
CD2 B:HIS249 4.3 16.3 1.0
O A:HOH695 4.4 37.5 1.0
CG A:ASP92 4.4 19.4 1.0
OD1 A:ASP92 4.7 20.4 1.0
ND1 B:HIS249 4.9 15.9 1.0
CG B:HIS249 5.0 12.4 1.0

Copper binding site 3 out of 6 in 2zon

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Copper binding site 3 out of 6 in the Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu400

b:17.5
occ:1.00
ND1 B:HIS139 2.1 15.7 1.0
ND1 B:HIS89 2.1 12.9 1.0
SG B:CYS130 2.2 13.8 1.0
SD B:MET144 2.6 16.6 1.0
CE1 B:HIS139 3.0 16.2 1.0
CE1 B:HIS89 3.0 15.7 1.0
CG B:HIS139 3.1 14.5 1.0
CB B:CYS130 3.1 14.1 1.0
CG B:HIS89 3.1 13.2 1.0
CE B:MET144 3.4 16.0 1.0
CB B:HIS139 3.5 12.7 1.0
CB B:HIS89 3.5 13.7 1.0
CA B:HIS89 3.8 13.8 1.0
CG B:PRO132 3.9 15.3 1.0
O B:PRO88 4.1 14.7 1.0
NE2 B:HIS139 4.1 15.8 1.0
CG B:MET144 4.1 14.4 1.0
NE2 B:HIS89 4.2 12.9 1.0
CD2 B:HIS139 4.2 14.7 1.0
CD2 B:HIS89 4.3 13.3 1.0
CD B:PRO132 4.3 14.4 1.0
CA B:CYS130 4.5 12.4 1.0
SD B:MET56 4.6 17.0 1.0
CB B:MET144 4.6 12.3 1.0
N B:ASN90 4.7 12.7 1.0
CA B:HIS139 4.7 12.7 1.0
N B:HIS89 4.8 14.4 1.0
C B:HIS89 4.8 13.4 1.0
C B:PRO88 4.9 15.1 1.0

Copper binding site 4 out of 6 in 2zon

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Copper binding site 4 out of 6 in the Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:14.8
occ:1.00
NE2 B:HIS129 2.0 13.7 1.0
NE2 B:HIS94 2.0 11.3 1.0
NE2 C:HIS300 2.1 11.8 1.0
O B:HOH528 2.1 25.3 1.0
CE1 B:HIS94 2.9 10.8 1.0
CD2 B:HIS129 2.9 13.2 1.0
CE1 C:HIS300 3.0 10.5 1.0
CD2 C:HIS300 3.1 10.8 1.0
CE1 B:HIS129 3.1 13.1 1.0
CD2 B:HIS94 3.2 11.1 1.0
OD2 B:ASP92 3.7 21.4 1.0
NE2 C:HIS249 3.9 17.1 1.0
ND1 B:HIS94 4.1 9.9 1.0
CG B:HIS129 4.1 12.7 1.0
ND1 C:HIS300 4.1 11.0 1.0
ND1 B:HIS129 4.2 13.5 1.0
CG C:HIS300 4.2 8.5 1.0
CG B:HIS94 4.2 10.0 1.0
CE1 C:HIS249 4.3 15.7 1.0
CD2 C:HIS249 4.4 15.3 1.0
CG B:ASP92 4.4 17.5 1.0
OD1 B:ASP92 4.7 18.4 1.0
ND1 C:HIS249 4.9 14.5 1.0
CG C:HIS249 5.0 12.3 1.0
O B:HOH744 5.0 51.2 1.0

Copper binding site 5 out of 6 in 2zon

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Copper binding site 5 out of 6 in the Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu400

b:21.0
occ:1.00
ND1 C:HIS139 2.1 18.2 1.0
SG C:CYS130 2.2 17.3 1.0
ND1 C:HIS89 2.2 16.5 1.0
SD C:MET144 2.6 19.1 1.0
CE1 C:HIS139 3.0 18.2 1.0
CE1 C:HIS89 3.1 18.2 1.0
CB C:CYS130 3.2 16.5 1.0
CG C:HIS139 3.2 16.6 1.0
CG C:HIS89 3.2 16.1 1.0
CE C:MET144 3.4 18.4 1.0
CB C:HIS89 3.5 17.1 1.0
CB C:HIS139 3.6 15.6 1.0
CA C:HIS89 3.8 17.7 1.0
CG C:PRO132 3.9 19.9 1.0
O C:PRO88 4.1 19.2 1.0
CG C:MET144 4.2 16.2 1.0
NE2 C:HIS139 4.2 19.9 1.0
NE2 C:HIS89 4.3 15.4 1.0
CD2 C:HIS139 4.3 19.6 1.0
CD2 C:HIS89 4.3 16.5 1.0
CD C:PRO132 4.3 18.9 1.0
SD C:MET56 4.5 22.5 1.0
CA C:CYS130 4.6 15.7 1.0
CB C:MET144 4.6 14.9 1.0
N C:ASN90 4.7 17.2 1.0
CA C:HIS139 4.8 15.4 1.0
N C:HIS89 4.8 18.5 1.0
C C:HIS89 4.9 18.1 1.0
C C:PRO88 4.9 19.6 1.0

Copper binding site 6 out of 6 in 2zon

Go back to Copper Binding Sites List in 2zon
Copper binding site 6 out of 6 in the Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu401

b:16.1
occ:1.00
NE2 C:HIS94 2.0 13.9 1.0
NE2 A:HIS300 2.0 11.0 1.0
NE2 C:HIS129 2.1 15.5 1.0
O C:HOH819 2.1 28.3 1.0
CE1 C:HIS94 2.9 13.6 1.0
CD2 C:HIS129 2.9 13.6 1.0
CE1 A:HIS300 3.0 11.8 1.0
CD2 A:HIS300 3.1 12.5 1.0
CD2 C:HIS94 3.1 13.7 1.0
CE1 C:HIS129 3.1 16.0 1.0
OD2 C:ASP92 3.7 24.4 1.0
NE2 A:HIS249 4.1 19.4 1.0
ND1 C:HIS94 4.1 12.4 1.0
ND1 A:HIS300 4.1 11.8 1.0
CG C:HIS129 4.1 13.7 1.0
CG A:HIS300 4.2 11.0 1.0
ND1 C:HIS129 4.2 15.6 1.0
CG C:HIS94 4.2 12.9 1.0
CE1 A:HIS249 4.3 17.5 1.0
CG C:ASP92 4.4 20.1 1.0
O C:HOH1003 4.4 38.3 1.0
CD2 A:HIS249 4.5 19.1 1.0
OD1 C:ASP92 4.7 19.8 1.0
ND1 A:HIS249 4.9 15.8 1.0

Reference:

M.Nojiri, H.Koteishi, T.Nakagami, K.Kobayashi, T.Inoue, K.Yamaguchi, S.Suzuki. Structural Basis of Inter-Protein Electron Transfer For Nitrite Reduction in Denitrification Nature V. 462 117 2009.
ISSN: ISSN 0028-0836
PubMed: 19890332
DOI: 10.1038/NATURE08507
Page generated: Wed Oct 28 14:22:58 2020
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