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Copper in PDB 5b1j: Crystal Structure of the Electron-Transfer Complex of Copper Nitrite Reductase with A Cupredoxin

Enzymatic activity of Crystal Structure of the Electron-Transfer Complex of Copper Nitrite Reductase with A Cupredoxin

All present enzymatic activity of Crystal Structure of the Electron-Transfer Complex of Copper Nitrite Reductase with A Cupredoxin:
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of the Electron-Transfer Complex of Copper Nitrite Reductase with A Cupredoxin, PDB code: 5b1j was solved by M.Nojiri, H.Koteishi, R.Yoneda, D.Hira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.10 / 3.00
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 153.226, 153.226, 153.226, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 23.3

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of the Electron-Transfer Complex of Copper Nitrite Reductase with A Cupredoxin (pdb code 5b1j). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 5 binding sites of Copper where determined in the Crystal Structure of the Electron-Transfer Complex of Copper Nitrite Reductase with A Cupredoxin, PDB code: 5b1j:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in 5b1j

Go back to Copper Binding Sites List in 5b1j
Copper binding site 1 out of 5 in the Crystal Structure of the Electron-Transfer Complex of Copper Nitrite Reductase with A Cupredoxin


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 the Electron-Transfer Complex of Copper Nitrite Reductase with A Cupredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu500

b:46.5
occ:1.00
 ND1 A:HIS139 2.0 45.8 1.0
ND1 A:HIS89 2.2 45.7 1.0
SG A:CYS130 2.2 39.7 1.0
SD A:MET144 2.6 42.6 1.0
CE1 A:HIS139 2.9 47.4 1.0
CG A:HIS139 3.0 47.1 1.0
CE1 A:HIS89 3.0 47.1 1.0
CB A:CYS130 3.1 39.2 1.0
CE A:MET144 3.2 42.7 1.0
CG A:HIS89 3.3 46.0 1.0
CB A:HIS139 3.4 44.5 1.0
CB A:HIS89 3.7 47.6 1.0
CA A:HIS89 3.9 47.8 1.0
NE2 A:HIS139 4.0 48.9 1.0
O A:PRO88 4.1 49.0 1.0
CD2 A:HIS139 4.1 48.8 1.0
CG A:PRO132 4.1 41.1 1.0
CG A:MET144 4.2 38.7 1.0
CD A:PRO132 4.2 39.5 1.0
NE2 A:HIS89 4.2 48.8 1.0
CD2 A:HIS89 4.4 49.2 1.0
SD A:MET56 4.5 51.8 1.0
CA A:CYS130 4.5 40.5 1.0
CB A:MET144 4.6 37.5 1.0
CA A:HIS139 4.7 44.4 1.0
N A:ASN90 4.7 45.3 1.0
C A:PRO88 4.8 49.5 1.0
N A:HIS89 4.8 49.6 1.0
C A:CYS130 4.9 41.8 1.0
C A:HIS89 4.9 46.8 1.0

Copper binding site 2 out of 5 in 5b1j

Go back to Copper Binding Sites List in 5b1j
Copper binding site 2 out of 5 in the Crystal Structure of the Electron-Transfer Complex of Copper Nitrite Reductase with A Cupredoxin


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 the Electron-Transfer Complex of Copper Nitrite Reductase with A Cupredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:47.8
occ:1.00
 NE2 A:HIS94 2.1 44.9 1.0
NE2 A:HIS129 2.2 45.3 1.0
CE1 A:HIS94 3.0 44.6 1.0
CD2 A:HIS94 3.1 48.0 1.0
CD2 A:HIS129 3.2 44.6 1.0
CE1 A:HIS129 3.3 45.3 1.0
OD2 A:ASP92 3.6 55.1 1.0
ND1 A:HIS94 4.1 45.4 1.0
CG A:HIS94 4.2 46.5 1.0
CG A:ASP92 4.3 48.8 1.0
CG A:HIS129 4.3 43.3 1.0
ND1 A:HIS129 4.4 42.2 1.0
OD1 A:ASP92 4.6 48.5 1.0

Copper binding site 3 out of 5 in 5b1j

Go back to Copper Binding Sites List in 5b1j
Copper binding site 3 out of 5 in the Crystal Structure of the Electron-Transfer Complex of Copper Nitrite Reductase with A Cupredoxin


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 the Electron-Transfer Complex of Copper Nitrite Reductase with A Cupredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu500

b:49.3
occ:1.00
 ND1 B:HIS139 2.0 42.2 1.0
SG B:CYS130 2.2 41.9 1.0
ND1 B:HIS89 2.2 43.0 1.0
SD B:MET144 2.6 48.5 1.0
CE1 B:HIS139 3.0 47.3 1.0
CE B:MET144 3.0 44.6 1.0
CG B:HIS139 3.1 43.0 1.0
CG B:HIS89 3.1 44.1 1.0
CB B:CYS130 3.1 42.3 1.0
CE1 B:HIS89 3.2 42.0 1.0
CB B:HIS89 3.3 44.8 1.0
CB B:HIS139 3.4 41.5 1.0
CA B:HIS89 3.6 44.8 1.0
CG B:PRO132 3.7 55.2 1.0
O B:PRO88 3.8 48.9 1.0
CD B:PRO132 4.1 52.2 1.0
NE2 B:HIS139 4.1 48.9 1.0
CD2 B:HIS139 4.2 45.4 1.0
CD2 B:HIS89 4.3 42.9 1.0
NE2 B:HIS89 4.3 39.5 1.0
CG B:MET144 4.3 46.3 1.0
SD B:MET56 4.5 49.5 1.0
CA B:CYS130 4.5 42.5 1.0
N B:HIS89 4.6 46.1 1.0
C B:PRO88 4.6 47.3 1.0
CB B:MET144 4.7 46.0 1.0
CA B:HIS139 4.7 38.9 1.0
C B:HIS89 4.7 43.8 1.0
N B:ASN90 4.7 41.1 1.0
CB B:PRO132 4.8 51.4 1.0

Copper binding site 4 out of 5 in 5b1j

Go back to Copper Binding Sites List in 5b1j
Copper binding site 4 out of 5 in the Crystal Structure of the Electron-Transfer Complex of Copper Nitrite Reductase with A Cupredoxin


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 the Electron-Transfer Complex of Copper Nitrite Reductase with A Cupredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:48.6
occ:1.00
 NE2 B:HIS94 2.0 49.1 1.0
NE2 B:HIS129 2.2 39.5 1.0
CE1 B:HIS94 2.9 49.9 1.0
CD2 B:HIS94 3.1 50.8 1.0
OD2 B:ASP92 3.1 50.5 1.0
CD2 B:HIS129 3.2 40.6 1.0
CE1 B:HIS129 3.2 39.6 1.0
CG B:ASP92 3.9 50.6 1.0
ND1 B:HIS94 4.0 51.9 1.0
CG B:HIS94 4.2 51.0 1.0
ND1 B:HIS129 4.3 41.4 1.0
CG B:HIS129 4.4 42.6 1.0
OD1 B:ASP92 4.4 51.4 1.0
CB B:ASP92 4.9 48.7 1.0

Copper binding site 5 out of 5 in 5b1j

Go back to Copper Binding Sites List in 5b1j
Copper binding site 5 out of 5 in the Crystal Structure of the Electron-Transfer Complex of Copper Nitrite Reductase with A Cupredoxin


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 the Electron-Transfer Complex of Copper Nitrite Reductase with A Cupredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu401

b:54.6
occ:1.00
 SG C:CYS79 2.1 52.5 1.0
ND1 C:HIS82 2.2 56.9 1.0
ND1 C:HIS41 2.4 52.4 1.0
SD C:MET87 2.5 51.8 1.0
CG C:HIS41 3.0 52.2 1.0
CG C:HIS82 3.0 54.0 1.0
CB C:HIS41 3.1 59.4 1.0
CE1 C:HIS82 3.1 55.9 1.0
CB C:HIS82 3.3 47.7 1.0
CB C:CYS79 3.4 55.7 1.0
CE1 C:HIS41 3.5 56.3 1.0
CE C:MET87 3.5 55.1 1.0
CA C:HIS41 3.5 63.0 1.0
CG C:MET87 3.9 46.6 1.0
CD2 C:HIS82 4.1 56.2 1.0
NE2 C:HIS82 4.2 57.4 1.0
O C:SER40 4.2 66.2 1.0
CD2 C:HIS41 4.2 52.7 1.0
CG C:PRO81 4.3 55.9 1.0
CB C:MET87 4.4 45.2 1.0
N C:HIS82 4.4 48.8 1.0
N C:HIS41 4.4 66.7 1.0
NE2 C:HIS41 4.4 54.7 1.0
CA C:HIS82 4.5 48.0 1.0
N C:ASN42 4.6 53.9 1.0
C C:SER40 4.6 70.2 1.0
C C:HIS41 4.6 61.0 1.0
CA C:CYS79 4.7 56.8 1.0
O C:CYS79 4.8 69.1 1.0
CB C:MET17 4.9 50.1 1.0
C C:CYS79 5.0 61.5 1.0

Reference:

M.Nojiri, M.Nojiri, H.Koteishi, R.Yoneda, D.Hira. N/A N/A.
DOI: 10.1039/9781782623762-00091
Page generated: Wed Jul 31 03:52:08 2024

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